tag:blogger.com,1999:blog-75406870284647747482024-03-13T14:14:02.424-07:00Water in BiologyA forum for discussing the behaviour of water in the living cellPhilip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.comBlogger119125tag:blogger.com,1999:blog-7540687028464774748.post-55898351488276856742023-10-02T06:07:00.014-07:002023-10-03T08:47:42.116-07:00Disordered proteins: the next frontier in therapeutics?<p>
</p><p class="MsoNormal"><span style="font-family: "Cambria",serif;">Howard Stone at
Princeton, Ozgur Sahin at Columbia, and their colleagues have written a
wonderfully imaginative review of what they call “hydration solids” (<i>Nature</i>
<b>619</b>, 500; 2023 - <a href="https://www.nature.com/articles/s41586-023-06144-y" target="_blank">here</a>). By
this I don’t mean to imply anything fantastical about it – I simply like this
way of framing the notion that hydration water can play an important structural
and mechanical role in some hygroscopic biological materials. The idea here is
that the mechanical properties are governed by the hydration forces operative
within a fluid-filled porous elastic medium. The notion is motivated and
explored by studying the mechanical behaviour of bacterial spores, but the same
principles might apply to wood, pollen grains, keratinous materials and silk. “Such
‘hydration solids’, which can exchange their essential constituent water with
the environment and have it flow through the material, are potentially abundant
in the environment”, they write.</span></p><p class="MsoNormal"><span style="font-family: "Cambria",serif;"> </span></p>
<p class="MsoNormal"><span style="font-family: "Cambria",serif;">There is a
fascinating paper in <i>PRL</i> from Chunyi Zhang (Mike Klein’s group) at
Temple University in Philadelphia that investigates why the dielectric
permittivity of salt water can actually decrease as more salt is added (C. Zhang <i>et
al.</i>, <i>Phys. Rev. Lett. </i><b>131</b>, 076801; 2023 - <a href="https://doi.org/10.1103/PhysRevLett.131.076801" target="_blank">here</a>). Using a
deep neural network trained on the results of density functional theory, the
authors show that this is not some kind of saturation effect but arises because
of the way the ionic hydration shells disrupt the hydrogen-bonded network of
the water and thereby suppress the collective response to electric fields. <br /></span></p>
<p class="MsoNormal"><span style="font-family: "Cambria",serif;"> </span></p><p class="MsoNormal"><span style="font-family: "Cambria",serif;">It has been
recognized at least since the early 1970s (and explored by the late, great Jack
Dunitz) that changes in enthalpy and in entropy of associations between
biomolecules (such as receptor-ligand pairings), due for example to small
changes in molecular structure, seem often to compensate for one another so as
to entail little change in the Gibbs free energy of binding. Why this is so has
been much debated. An intuitive explanation is that a more favourable enthalpic
contribution to binding creates a corresponding decrease in conformational
freedom and thus a loss in entropy. But consideration of that balance must also
take into account changes in hydration due to reorganization of the local
hydrogen-bonded network. The Whitesides group (Breiten <i>et al</i>., <i>JACS</i><span style="mso-spacerun: yes;"> </span><b>135</b>, 15579; 2013) has argued that
water reorganization is in fact the key source of enthalpy-entropy
compensation. That idea is examined, and ultimately supported, in a study by
Shensheng Chen and Zhen-Gang Wang at Caltech (<i>J. Phys. Chem. B </i><b>127</b>,
6825; 2023 - <a href="https://doi.org/10.1021/acs.jpcb.3c03799" target="_blank">here</a>),
using MD simulations of model charged polymers. They find that the hydrophobic
interactions resulting from reorganization of hydration water show temperature
dependencies that can account for the close correlation between the delta</span><span style="font-family: "Cambria",serif;">H and Tdelta</span><span style="font-family: "Cambria",serif;">S
terms. The effects of electrostatic interactions and polymer conformational
changes are, in comparison, minor. Water is, it seems, in control.</span></p>
<p><span style="font-family: "Cambria",serif;">Liquid-liquid phase separation
(LLPS) has become a vibrant topic in cell biology now that it’s clear cells
make use of it in a variety of ways and circumstances for partitioning and
sequestering biomolecules for purposes ranging from gene regulation to RNA
splicing to stress responses. The globular droplets – condensates – formed in
this process have a higher density than the surrounding cell fluid, but it’s
still not really understood what characteristics of biomolecules promote this
new phase. That understanding could be useful for being able to control the
phase separation process for possible therapeutic purposes – or indeed for
designing peptides to prevent pathogenic aggregation. The condensates are not
biomolecular complexes in any real sense – the binding forces between the
components seem to be rather weak and indiscriminate, and condensates typically
contain proteins with some degree of disorder (intrinsically disordered proteins,
IDPs), which tend to be promiscuous in their interactions. Debasis Saha and
Biman Jana of the Indian Association for the Cultivation of Science in Kolkata
have used MD simulations to investigate the factors that govern the
interactions of model peptides, leading to dimerization, to try to get some
handle on what is going on (<i>J. Phys. Chem. B </i><b>127</b>, 6656; 2023 - <a href="https://doi.org/10.1021/acs.jpcb.3c03087" target="_blank">here</a>).
They consider the effect of charged residues such as arginine, as well as
differing amounts of hydrophobicity in the chains, in altering the free energy
surface for dimerization. For both positively and negatively charged peptides,
the solvation water seems to play an important role, and is the dominant
influence in the latter case. The upshot is that, if dimerization adequately
reflects the condensate formation process, negatively charged peptides seem
more likely to stay in the dilute phase.</span></p>
<p><span style="font-family: "Cambria",serif;">Benjamin Schuler at Chicago and
colleagues look at a similar issue: the interaction between the highly positively
charged histone linker H1 and the highly negatively charged prothymosin<b> </b>α
(ProTα) which acts as a “chaperone” that can help H1 disassociate from the
histone (A. Chowdhury <i>et al.</i>, <i>PNAS </i><b>120</b>, e2304036120; 2023
- <a href="https://doi.org/10.1073/pnas.2304036120" target="_blank">here</a>).
Both are IDPs. They find that in this case there is a large entropic
contribution to the binding coming from the release of counterions – a consideration
that they expect to be most generally applicable to bio-polyelectrolyte
interactions. <span style="mso-spacerun: yes;"> </span></span></p>
<p><span style="font-family: "Cambria",serif;">Meanwhile, in a paper in bioRxiv [<a href="https://doi.org/10.1101/2023.09.05.556343" target="_blank">here</a>], Saumyak
Mukherjeee and Lars Schäfer at Bochum have looked at the thermodynamic driving
forces that govern the formation of condensates from proteins with
intrinsically disordered domains. Aggregation into the dense phase will involve
changes in enthalpy and entropy due both to direct protein interactions and to
changes in solvation. The authors conclude from MD simulations that in this
case the most important factors are protein interaction enthalpy and the
entropic effects of water release from the protein hydration shell into the
bulk. </span></p>
<p><span style="font-family: "Cambria",serif;"></span></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYB24l5t89Egen4upxQzHYP5K9KastjoyczlUneOwayk5bZK5ew-k_1rYzWCUrP_9YG6lJOA3W9AInZ1mtSabkOISbGXi_x6Qc37pMpsKeEnRCSJEIJMwPgvIAibTT-8kvfRoVBGN1MYgmtm1Lnh8Rcwm184VIrwfHMGW39BBy30rY45jPh_szoEjrvUo/s1744/LLPS.jpg" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1744" data-original-width="1706" height="320" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYB24l5t89Egen4upxQzHYP5K9KastjoyczlUneOwayk5bZK5ew-k_1rYzWCUrP_9YG6lJOA3W9AInZ1mtSabkOISbGXi_x6Qc37pMpsKeEnRCSJEIJMwPgvIAibTT-8kvfRoVBGN1MYgmtm1Lnh8Rcwm184VIrwfHMGW39BBy30rY45jPh_szoEjrvUo/s320/LLPS.jpg" width="313" /></a></div><span style="font-family: times;"><span style="font-size: medium;">It seems likely that unravelling these
factors governing IDP associations of various sorts will ultimately be valuable
as we seek to make pharmaceutical interventions in molecular interactions of
this kind that seem connected to disease (such as Alzheimer’s). Christine Lim
at Cambridge and colleagues have developed a bioinformatics platform for
identifying proteins involved in LLPS that seem to be potential therapeutic targets
(C. M. Lim <i>et al.</i>, <i>PNAS </i><b>120</b>, e2300215120; 2023 - <a href="https://www.pnas.org/doi/10.1073/pnas.2300215120" target="_blank">here</a>).
They test it by looking at the in vitro phase behaviour of three targets that
their scheme identifies. I don’t think it is too much to suggest that this
points towards something of a new paradigm for therapeutics, in which the goal
is not to develop some inhibitor that might compete with a protein’s normal ligand
but rather to engineer collective and less selective interactions at a larger
scale. </span></span><p></p>
<p><span style="font-family: "Cambria",serif;">I’m intrigued by a paper in press
in <i>J. General Physiology</i> (</span><span style="font-family: "Cambria",serif;">preprint <a href="https://www.biorxiv.org/content/10.1101/2023.01.02.522450v1" target="_blank">here</a>)
by Alan Kay at the University of Iowa and Gerald Manning at Rutgers, arguing
that what drives osmosis is still not fully understood and that the mechanism
proposed by Peter Debye in 1923 is in fact the right one, despite being now
largely forgotten. It is one thing to explain osmotic flow thermodynamically in
terms of differences in chemical potential (the textbook account), but another
to explain what actually drives the directional transport of water molecules.
Manning and Kay say that diffusion alone is not able to account for the osmotic
flux, which arises instead because of differential repulsive forces between the
solute molecules and the two interfaces of the semipermeable membrane. This
produces the equivalent of a hydrostatic pressure difference that drives the
flux. I’m certainly not qualified to assess whether this revision of the
textbook explanation is valid, but the history of the Debye model given in the
paper is surely interesting in its own right.<span style="mso-spacerun: yes;">
</span></span></p>
<p class="MsoNormal"><span style="font-family: "Cambria",serif;">There is,
admittedly, not much biology going on in the deep mantle of the Earth with
temperatures of 1,000-2,000 K and pressures of up to 22 GPa. All the same, such
conditions pose quite a test of molecular-dynamics water potential functions,
which Roberto Car at Princeton, Giulia Galli at Chicago, and colleagues have
put through their paces (C. Zhang <i>et al</i>., J. <i>Phys. Chem B </i><b>127</b>,
7011; 2023 - <a href="https://doi.org/10.1021/acs/jpcb.3c02972" target="_blank">here</a>). They set out to
calculate the thermal conductivity of water in these conditions, using a
potential found by fitting to density-functional theory using a deep-learning
algorithm. The conductivity varies only slightly with temperature, decreasing
from its ambient value, but is much more strongly (and positively) correlated
with density. The heat transport of water at high P and T could have important
implications for processes in the interiors of gas-giant planets.</span></p>
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{page:WordSection1;}</style></p>Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com0tag:blogger.com,1999:blog-7540687028464774748.post-48935393520593890782023-07-24T10:06:00.000-07:002023-07-24T10:06:29.615-07:00It's back!<p>
</p><p class="MsoNormal">Back by popular demand” always seemed a self-congratulatory
phrase, but in this case it really is the case that I’m reviving this blog
because so many people have said they found it helpful. I’m touched by that,
and also grateful to be given the motivation to continue pursuing this
endlessly fascinating topic. So here we go.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">One of the things that led me to let the blog languish was
that there were so many other areas in which I have been striving to deepen my
knowledge over the past several years. Happily, at least one of these remains
relevant to the topic at hand: I have been delving deeper into the thickets of
molecular and cell biology for my <a href="https://press.uchicago.edu/ucp/books/book/chicago/H/bo207403562.html" target="_blank">latest book</a>, <i>How Life Works</i>, which is
published in the autumn/fall of 2023.
Among many other things, this looks at issues such as the roles of disordered
proteins and of biomolecular condensates, in which issues of solvation are
clearly important.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">As if to underscore that, I am kicking off this post with a
fascinating <a href="https://doi.org/10.1038/s41586-023-06329-5" target="_blank">paper</a> in <i>Nature</i> by Benjamin Schuler at Zurich and colleagues
[N. Galvanetto <i>et al.</i>, <i>Nature </i>10.1038/s41586-023-06329-5; 2023],
which looks at biomolecular dynamics within such a dense condensate. I probably
don’t need now to say much about the importance of condensates in cell biology;
as Schuler and colleagues say, these dense but loose associations of proteins
and nucleic acids “play a key role in cellular processes operating at different
scales, such as ribosome assembly, RNA splicing, stress response, mitosis and
chromatin organization, and they are involved in a range of diseases” (and
also, I’d add, in gene regulation). Their significance was confirmed by the
fact that Tony Hyman and Cliff Brangwynne, who did much of the early work to
bring them to wider attention, were awarded last year’s <a href="https://breakthroughprize.org/News/73" target="_blank">Breakthrough Prize</a>
in the life sciences. As Schuler <i>et al</i>. say, intrinsically disordered proteins
seem often to play a key part in the formation of condensates, thanks to their
rather promiscuous binding capacity.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The dense fluid of these phase-separated blobs can have a
greatly enhanced local concentration of constituents relative to the bulk
cytoplasm, and indeed this is a central feature of their function: they help to
concentrate particular biomolecular species to enable repeated, low-affinity
encounters of the kind that seem important for e.g. gene regulation or
splicing. That density, however, results in a water viscosity that can be
several orders of magnitude greater than it is in the bulk. Schuler and
colleagues use single-molecule spectroscopy and MD simulations to examine the
consequences of this for the dynamics of proteins. They study in vitro proxies
for in vivo condensates, consisting of droplets (coacervates – I’m interested to
see the return of that word from the days of the “prebiotic” speculations of
Sidney Fox!) made from two highly and oppositely charged IDPs, both of which
are known to influence chromatin condensation and transcriptional regulation.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">The result is that, despite a 300-fold increase in water
viscosity in the droplets and the formation of a dense network of
indiscriminately associated proteins, leading to drastically slowed
translational motion, the local conformational dynamics of the chains that influence
residue-residue contacts remain fast, happening on pico- to nanosecond
timescales. The conclusions are nicely summarized in this image:</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal"></p><div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiI7_ZVNmY3QLSKX1Co08oU-60KAdvdDx8hAlIkIQadHsjwBfzxaZ0qA0E2gMgzEUtUKdj2dpR_FlobqVaWLCCw8Lwx9ZfL-b-xZdtcPD5kFR6alkys8x0gwmewZ_sLlCKgm-tTA0Xt3gmx5bsUyYwHfcQAf47nEqjLK1NekkkLIGbPz5KAMq4VtWSXlk4/s1464/Schuler.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1464" data-original-width="1284" height="360" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiI7_ZVNmY3QLSKX1Co08oU-60KAdvdDx8hAlIkIQadHsjwBfzxaZ0qA0E2gMgzEUtUKdj2dpR_FlobqVaWLCCw8Lwx9ZfL-b-xZdtcPD5kFR6alkys8x0gwmewZ_sLlCKgm-tTA0Xt3gmx5bsUyYwHfcQAf47nEqjLK1NekkkLIGbPz5KAMq4VtWSXlk4/w316-h360/Schuler.jpg" width="316" /></a></div><br /> <p></p><p class="MsoNormal">As the authors say: “The behaviour we observe is an example
of the subtle balance of</p>
<p class="MsoNormal">intermolecular interactions in biomolecular phase
separation. On the one hand, the interactions must be strong enough for the
formation of stable condensates; on the other hand, they need to be
sufficiently weak to enable translational diffusion and liquid-like dynamics
within the dense phase and molecular exchange across the phase boundary—
processes that are essential for function, such as biochemical reactions
occurring in condensates.” I have to say that this doesn’t entirely surprise
me, as it seems to reflect in a more extreme way what seems to happen in cells
more generally: the cytoplasm can look somewhat gel-like at mesoscales, and
translational diffusion can be anomalous, while at the molecular scale dynamics
are not so different from those in dilute solution. Of course, the usual caveats
about in vitro studies – which have been stressed in particular for studies of
condensates (see e.g <a href="https://www.chemistryworld.com/features/how-does-a-cell-know-what-kind-of-cell-it-should-be/4012667.article" target="_blank">here</a>)
– apply too. But this is a really nice study, which to my mind illustrates the
possibility of a separation of dynamical timescales that makes life possible:
the benefits of forming condensates do not need to come at the expense of
compromising the local dynamics needed for biomolecular function.</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Needless to say, I have from time to time seen some
wonderful papers touching on water in biology come and go in the time between
my last blog and now, and I fear these are lost now to being documented here.
But there are a few recent ones that I still have to hand. There has been a
particularly vigorous debate in the past year or two on the issue of the
putative liquid-liquid phase transition in pure water. The evidence for this
<a href="https://www.chemistryworld.com/news/evidence-mounts-that-water-has-two-liquid-forms/3008766.article" target="_blank">continues to accumulate</a>, and looks now to be rather strong
– although that clinching proof remains elusive. <a href="https://www.science.org/doi/10.1126/science.aao7049" target="_blank">This paper</a> [<i>Science</i> <b>359</b>,
1127; 2018] by Sander
Woutersen in Amsterdam – including the late and much missed Austen Angell –
reported a direct sighting of such a transition in an aqueous solution of
hydrazinium trifluoroacetate, which could be deeply supercooled to 140 K. And <a href="https://www.pnas.org/doi/full/10.1073/pnas.2113411119" target="_blank">work</a>
by Yoshiharu Suzuki in Tsukuba adds to that suggestive evidence with a study
[<i>PNAS </i><b>119</b>, e2113411119; 2022]
of supercooled aqueous trehalose, which reports a direct signature of a
first-order liquid-liquid transition. You can see some responses to the work
<a href="https://www.chemistryworld.com/news/direct-evidence-emerges-for-the-existence-of-two-forms-of-liquid-water/4015144.article" target="_blank">here</a>.
Meanwhile, Nguyen Vinh and colleagues at Virginia Tech have <a href="arixv 2305.19560; 2023 http://www.arxiv.org/abs/2305.19560" target="_blank">performed</a> terahertz measurements of
water over a wide temperature range, down to the deeply supercooled state, which
they say can be interpreted it terms of two liquid forms with different
transition temperatures. <span style="mso-spacerun: yes;"> </span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I am (not so?) secretly delighted that my PhD supervisor Bob
Evans at Bristol decided some time ago to delve into water phase behaviour,
having warned me (wisely!) to steer clear of any liquid so anomalous. <a href="https://pubs.aip.org/aip/jcp/article/158/3/034508/2871194/Understanding-the-physics-of-hydrophobic-solvation" target="_blank">Here</a> [<i>J.
Chem. Phys. </i><b>158</b>, 034508; 2023]
Bob, Mary Coe and Nigel Wilding suggest that the well known density depletion
and enhanced fluctuations evident in water near hydrophobic surfaces be
interpreted as the remnant of a critical surface (drying, or as some call it,
dewetting) phase transition. In other words – and this seems to me quite significant
– there is in a sense nothing unusual about water in this respect, and no need
to invoke any specialness about its liquid-state structure. Rather, this is
well-understood statistical physics at work. I notice that this was the topic
of Mary’s 2021 PhD thesis: <span style="font-family: helvetica;">“Hydrophobicity
across length scales: The role of surface criticality” – which I’d love to see.</span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I can’t touch on that topic without remembering that for my
last post in January 2018, I seem not yet to have caught up with the news of
the death in April 2017 of David Chandler, a giant in the field of liquid-state
theory, as well as statistical mechanics more broadly. David’s work with John
Weeks and Ka Lum on the <a href="https://pubs.acs.org/doi/10.1021/jp984327m" target="_blank">hydrophobic interaction</a> [<i>JPCB </i><b>103</b>, 4570;
1999]
has of course been one of the most influential contributions to this topic
since it was published in 1999. David’s work has certainly been a huge
influence on my thinking in this field – and indeed that influence went right
back to my work with Bob in the mid-1980s. David was always generous but
rigorous, and phenomenally insightful, and his absence is deeply felt. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Francesco Paesani of UCSD has let me know about the new
water potential he and his colleagues <a href="https://www.nature.com/articles/s41467-023-38855-1" target="_blank">have developed</a> from first-principles
quantum simulations, which is able to capture the phase diagram very
realistically [Bore & Paesani, <i>Nat. Commun</i>. <b>14</b>, 3349; 2023]
– see also the <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.3c00326" target="_blank">improvements</a> in Zhu <i>et al</i>., <i>J. Chem. Theory Comput. </i><b>19</b>,
3551-3566; 2023]. Francesco
has already been applying it to a variety of real-world problems, including the
<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.3c00271" target="_blank">hydration of a simple model of the protein backbone</a> (N-methylacetamide) [Zhou <i>et
al</i>., <i>J. Chem. Theory Comput. </i><b>19</b>, 4308; 2023]. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I just noticed <a href="https://pubs.acs.org/doi/10.1021/acscentsci.3c00803" target="_blank">this interesting article</a> [A. Katsnelson, <i>ACS
Cent. Sci. </i>10.1021/acscentsci.3c00803; 2023]
on “artificial saliva” and synthetic mucins. I knew nothing about such work,
which sound like rich ground for exploring hydration issues. </p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">I can’t end this first post without mentioning the ongoing
story of “life (or not) in the clouds of Venus”. This intriguing idea was <a href="https://www.nature.com/articles/s41550-020-1174-4" target="_blank">first put forward</a> by Sara Seager and her colleagues following the apparent
identification [J. S. Greaves <i>et al.</i>, <i>Nat. Astron. </i><b>5</b>, 655;
2021] of phosphine – for
which no abiotic natural source is known – in the Venusian atmosphere. Much of
the immediate debate (aside from that about how secure the signature of
phosphine really was, a discussion that is still ongoing) centred on the
extreme acidity of the cloud droplets. But I was more concerned about how low
the water activity in the droplets must be – we know that no life on Earth has
been seen for water activities below 0.585, a fact that I am sure is related to
the minimal hydration requirements for functional biomolecules. When I
mentioned this to microbiologist John Hallsworth at Queens in Belfast, he
convened a team of experts who <a href="https://www.nature.com/articles/s41550-021-01391-3" target="_blank">made calculations</a> to estimate the water activity
in the Venusian clouds and a variety of other planetary environments, revealing
that on Venus this is indeed orders of magnitude too low to permit
terrestrial-type life given what we currently know about it [J. E. Hallsworth <i>et
al.</i>, <i>Nat. Astron. </i><b>5</b>, 665; 2021].
Sara and her coworkers have <a href="https://www.liebertpub.com/doi/10.1089/ast.2022.0113" target="_blank">now suggested</a> [W. Bains <i>et al.</i>, <i>Astrobiol.
</i>10.1089/ast.2022.0113; 2023]
possible ways around this problem, which in the end amount to having to posit
life unlike that on Earth – a possibility we recognized in our paper. To my
mind, this could usefully sharpen the discussion about what “habitable” can and
should mean in astrobiology, as I explore <a href="https://www.chemistryworld.com/opinion/can-life-exist-outside-of-the-habitable-zone/4017685.article" target="_blank">here</a>.
I welcome anything that prompts deeper, quantitative thinking about the
conditions needed to support something we might reasonably call life in
extraterrestrial environments. But I would argue that such discussions need to
go beyond “well, X can also act as a hydrogen-bonding solvent”, and should take
into consideration just how subtle water’s roles are in terrestrial
biochemistry, and <a href="https://link.springer.com/chapter/10.1007/978-3-642-31730-9_6" target="_blank">how much the “specialness” of water</a> might matter in this
regard. Given
the richness of emerging knowledge about extraterrestrial environments, and the
prospects of much more to come through planned missions (e.g. to Enceladus and
Titan) and JWST observations, I’d love to see this issue engaged with head-on
by e.g. ESA or NASA. <span style="mso-spacerun: yes;"> </span></p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">Well, there we are: I’m open for business again. So do feel
free to send things my way for inclusion; I’d be delighted to hear about them.<span style="mso-spacerun: yes;"> </span></p>
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{page:WordSection1;}</style></p>Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com0tag:blogger.com,1999:blog-7540687028464774748.post-6169285757284543032018-01-24T09:14:00.000-08:002018-01-24T09:14:54.787-08:00Hydration as a design element in biomaterialsGiven what is known about water’s active role in the structure, dynamics and function of biomolecules, can it be used as a design element in synthetic molecular and nanoscale structures derived from them, which might have more amenable levels of complexity? Sam Stupp at Northwestern and colleagues ask this question in relation to the amphiphilic peptide-based nano-architectures they have been developing. They have used Overhauser dynamic nuclear polarization relaxometry to characterize the hydration of such a peptide nanofibre [J. H. Ortony <i>et al., JACS</i> <b>139</b>, 8915; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.7b02969">here</a>]. They find a wide range of water dyamics, from rapid translational diffusion within the hydrophobic interior to near-immobilization of water on the hydrophilic surface. Water further from the core and close to the inner peptide domain is slowed relative to the bulk, and more so for fibres in the gelled than in the solution state. The same applies to water close to the (charged) nanofibre surface, which may be slowed to a degree comparable to that of water confined within protein cavities. MD simulations echo these findings. Sam and colleagues suggest that the surface water might play an active role in gelation and interactions with biomolecules, and in consequence that “water dynamics not only play an important role in the function of nanostructured biomaterials, but… may also be tunable in soft matter at molecular length scales to optimize performance for a variety of biomedical applications.”
<br />
<br />
In a similar spirit, Geraldine Richmond at Oregon and coworkers use vibrational sum frequency spectroscopy to look at water orientational ordering close to the surface of nanoemulsion aggregates: micelles and reverse micelles [J. K. Hensel <i>et al., PNAS</i> <b>114</b>, 13351; 2017 – paper <a href="www.pnas.org/cgi/doi/10.1073/pnas.1700099114">here</a>]. Water seems to be electrostatically ordered by the surfactant head groups and their counterions at the interface.
<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOkCIx4sabWqIOc08ggHXnTma_E9_fmu7J54PMDky6x0GRsi8c78TWchLXxp9PmT7-q8_B0A3HQez5o-U9Jz0hMiFbEfkP2sZ6khMDChIj458aLHHtcZbG6SlyL8k_Pv2WNKdAElphCEU/s1600/richmond.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhOkCIx4sabWqIOc08ggHXnTma_E9_fmu7J54PMDky6x0GRsi8c78TWchLXxp9PmT7-q8_B0A3HQez5o-U9Jz0hMiFbEfkP2sZ6khMDChIj458aLHHtcZbG6SlyL8k_Pv2WNKdAElphCEU/s320/richmond.jpg" width="320" height="150" data-original-width="520" data-original-height="244" /></a>
<br />
<i>Proposed orientation of water at surfactant (AOT)-counterion surfaces, both for the curved surfaces of micelles and the planar surfaces of lamellae.</i>
<br />
<br />
How exactly does one quantify water order or disorder? Various measures have been suggested; Fabio Sterpone of the Université Paris Diderot and colleagues suggest that it might be sought in the connectivity of the hydrogen-bond network (O. Rahaman <i>et al., JPCB</i> <b>121</b>, 6792; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.7b03888">here</a>). They have looked at this measure in simulations of the protein (here lysozyme) dynamical transition at around 240 K. There is a fairly abrupt change in the connectivity at the transition, in that the degree of percolation is constant below about 220-240 K but decreases with temperature above it. A closer analysis shows that at 240 K the hydration water network begins to sample a larger number of configuration states, corresponding to an abrupt increase in configurational entropy. Fabio and colleagues interpret these findings in terms of the hydration water acting as an ‘entropic reservoir’ that, above the dynamical transition, enables the protein to undergo configurational changes.
<br />
<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjl_qinznoPiaTr3Sczp5wmi0wVInd6J9YI588AyDpRDttydM-MZKs8PDu7cqiRC95ZWhNk75DtCOeM9nQHSdkJl9hTHTsl6csk3XX5ValofDi91C9-mh9p28rEcueYBjAXgtxDmRdXalQ/s1600/Sterpone-percolation.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjl_qinznoPiaTr3Sczp5wmi0wVInd6J9YI588AyDpRDttydM-MZKs8PDu7cqiRC95ZWhNk75DtCOeM9nQHSdkJl9hTHTsl6csk3XX5ValofDi91C9-mh9p28rEcueYBjAXgtxDmRdXalQ/s320/Sterpone-percolation.jpg" width="320" height="285" data-original-width="527" data-original-height="469" /></a>
<br />
<i>Probability distribution of hydration-water percolation propensity for lysozyme as a function of temperature.</i>
<br />
<br />
Not strictly water in biology, but Daniel Munoz-Santiburcio and Dominik Marx in Bochum describe ab initio simulations of proton transport in alkaline water films confined between the layers of the mineral mackinawite [<i>Nat. Commun.</i> <b>7</b>, 12625; 2016 – paper <a href="https://www.nature.com/articles/ncomms12625">here</a>]. They find that orientation and coordination of hydroxide can alter the hydrogen-bond network in ways that make transport of protons and mobility of negative-charge defects sensitive to the width of the confining space: different structures in the layered water films support qualitatively different transport mechanisms. Daniel and Dominik conclude that “it should be possible to rationally design different nanostructures that will allow for different charge transport rates of confined alkaline aqueous solutions.” Meanwhile, in another paper they show that water within mackinawite layers has a boosted tendency to self-dissociate (<i>Phys. Rev. Lett.</i> <b>119</b>, 056002; 2017 – paper <a href="https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.056002">here</a>).
<br />
<br />
And in a third paper they consider the effect of water confinement (between mineral layers) on a whole set of chemical reactions, particularly those involved in peptide formation – which may serve as a model of prebiotic chemistry at nanoconfined mineral surfaces (<i>Chem. Sci.</i> <b>8</b>, 3444; 2017 – paper <a href="http://pubs.rsc.org/en/content/articlelanding/2017/sc/c6sc04989c">here</a>). Under these conditions both the energetics and the mechanisms of the reactions can be significantly altered relative to the bulk.
<br />
<br />
X-ray free electron lasers are already transforming structural biology with their ability to provide diffraction data on very small samples in some cases down to the single-molecule scale, at high time resolution for studying dynamical processes. Jessica Thomaston and coworkers have used the Japanese Spring-8 XFEL source to obtain a new structure of the influenza M2 proton channel under ambient conditions (J. L. Thomaston <i>et al., PNAS</i> <b>114</b>, 13357; 2017 – paper <a href="http://www.pnas.org/content/114/51/13357.abstract">here</a>). They find that an ordered network of hydrogen-bonded water molecules spans the pore at pH5.5, providing a proton-conduction pathway and stabilizing the protonated His37 residue present in the intermediate open state of the channel. These ordered waters decrease in number as pH increases and the open state becomes less stable.
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<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuB8o35nBXcGVbrdsx0GHb5xgdVjI9mMxqN9bR5Yu3uCo6Zzd9c8fV5Ti5m4AHuzuDPUzFXv8G11Wh0LJQodRwYY_YaKxUeKbjPhLHEVkThmCuMSdcpEHk8sWeY7JD338YPyhvqSzZFlk/s1600/M2_channel.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjuB8o35nBXcGVbrdsx0GHb5xgdVjI9mMxqN9bR5Yu3uCo6Zzd9c8fV5Ti5m4AHuzuDPUzFXv8G11Wh0LJQodRwYY_YaKxUeKbjPhLHEVkThmCuMSdcpEHk8sWeY7JD338YPyhvqSzZFlk/s320/M2_channel.jpg" width="320" height="180" data-original-width="1098" data-original-height="616" /></a>
<br />
<i>The room-temperature XFEL structures of the M2 channel at different pH. Red spheres show waters with full occupancy, light and dark blue with half-occupancy.</i>
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<br />
The idea has been around for some time that water might play an important role in protein (mis)folding into amyloid fibrils associated with neurodegenerative diseases. Mei Hong at MIT and colleagues have now used solid-state NMR to characterize the reservoirs of water within and around fibrils of the Alzheimer’s β-amyloid peptide Aβ-40 (T. Wang <i>et al., JACS</i> <b>139</b>, 6242; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.7b02089">here</a>). They find five distinct pools, ranging from surrounding bulk-like matrix water to mobile interfibrillar water channels and relatively immobile peptide-bound reservoirs. Exchange of water happens between the two dynamic pools on very long (second) timescales. The balance between the various pools is shifted in some mutant fibrils.
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<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgB9Uj38OEgrtbvEysaMp-bKk-t1WA6QEOdms9gx7IKdZUi5eeEQ8wG2Ftfs9CUhl8rxWXF6ZSY9Fcuvh1y9N6ifaY3UjNg1zppDQtWIvHd-2O_1w-zOFYAfyKLmeY7Nq-IdD4tfnnNzd0/s1600/amyloid+water.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgB9Uj38OEgrtbvEysaMp-bKk-t1WA6QEOdms9gx7IKdZUi5eeEQ8wG2Ftfs9CUhl8rxWXF6ZSY9Fcuvh1y9N6ifaY3UjNg1zppDQtWIvHd-2O_1w-zOFYAfyKLmeY7Nq-IdD4tfnnNzd0/s320/amyloid+water.jpg" width="320" height="128" data-original-width="920" data-original-height="368" /></a>
<br />
<i>The five water pools in wild-type Aβ-40 amyloid fibrils.</i>
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<br />
Much attention has been given to the roles of hydration water in the binding of ligands by proteins, but less to the idea that solvation is also important for unbinding. Paolo Carloni at Jülich and colleagues have simulated the unbinding kinetics of an anti-inflammatory agent (a urea derivative) that binds to p38 MAP kinase (R. Casanovas <i>et al., JACS</i> <b>139</b>, 4780; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jacs.6b12950">here</a>). They find that a rotation of the urea group during unbinding creates a more –solvent-exposed state in which the hydrophobic interactions between the t-butyl substituent of the ligand and a hydrophobic part of the cavity are weakened. Water molecules that enter into the cavity play an essential role in this step, forming hydrogen bonds to the urea group and mediating those with residues in the cavity.
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<br />
An important role for water-mediated contacts is identified in the DNA binding of transcription factors of the ETS family by Gregory Poon and colleagues at Georgia State University (S. Xhani <i>et al., JPCB</i> <b>121</b>, 2748; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.7b00325">here</a>). One in particular, denoted PU.1, shows a strong osmotic sensitivity in its binding, which the researchers attribute to the water-mediated binding between a tyrosine residue and DNA. Mutation of this residue removes this sensitivity. In the homologue Ets-1, which lacks this sensitivity, it seems that the same Tyr residue, while apparently engaging in the same water-mediated contact in the bound state, actually plays a different role in binding, by influencing the local dynamics of the free protein. I guess this underscores once more how hard it is to identify general rules of thumb for how hydration structures affect biomolecular function and molecular recognition.
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<br />
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKB7FauNY2TMnPhe18toIWWwA9CsxBJkX65So2Wc00xSLpwZ-r95iJZBtGuzbZCApbtufcJASjLGn62SxANn1DQz_CYFVa9FhvWy126F07DLOSZdZTSKklqdGlqimKOrVEhNJA8FCkm2Q/s1600/PU.1.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiKB7FauNY2TMnPhe18toIWWwA9CsxBJkX65So2Wc00xSLpwZ-r95iJZBtGuzbZCApbtufcJASjLGn62SxANn1DQz_CYFVa9FhvWy126F07DLOSZdZTSKklqdGlqimKOrVEhNJA8FCkm2Q/s320/PU.1.jpg" width="319" height="320" data-original-width="514" data-original-height="516" /></a>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiasvMPhSNeSmbaklUVdybXV2qjsx6F9Z8ipJ4DwX9wOr-a71KS9aveRJ79i6gSTQT9SUdKAvO6LicYcXvtWbdTsbN0kaop_rrwgmKh6s5i0I0BlzlLap92HKdMqyk0O0y6as1cPCesHOc/s1600/Ets-1.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiasvMPhSNeSmbaklUVdybXV2qjsx6F9Z8ipJ4DwX9wOr-a71KS9aveRJ79i6gSTQT9SUdKAvO6LicYcXvtWbdTsbN0kaop_rrwgmKh6s5i0I0BlzlLap92HKdMqyk0O0y6as1cPCesHOc/s320/Ets-1.jpg" width="319" height="320" data-original-width="515" data-original-height="516" /></a>
<br />
<i>The same and not the same: these two water-mediated contacts between a Tyr residue and DNA in the homologous transcription factors PU.1 (top) and Ets-1 (bottom) actually play different roles in the molecular-recognition process. </i>
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<br />
Cytochtome c oxidase (CcO) pumps protons across membranes using the energy of dioxygen reduction. The mechanism seems to involve a change in hydration – a switch between ‘wet’ and ‘dry’ configurations – in an internal cavity that is connected to the proton’s exit channel. Qiang Cui and colleagues at the University of Wisconsin have studied that process using MD simulations (C. Y. Son <i>et al., PNAS</i> <b>114</b>, E8830; 2017 – paper <a href="http://www.pnas.org/content/114/42/E8830.abstract">here</a>). They show how the protonation state of one residue acts as a switch between the dry and wet states, and that in the wet state the pKa of a Glu residue is lowered to facilitate proton transfer. Here, then, is a functional role for the dry-wet switching of the cavity.
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<br />
What about the proton channel itself in CcO? It’s not in fact yet clear what route it takes – three possible channels (labelled D, K and H) have been proposed. Vivek Sharma at the University of Helsinki and colleagues use simulations to show that the H channel alone doesn’t seem able to do the job, unless a buried histidine residue is protonated (which seems unlikely); otherwise there’s a gap that the transient water networks in the channel can’t span (V. Sharma <i>et al., PNAS</i> <b>114</b>, E10339; 2017 – paper <a href="http://www.pnas.org/content/114/48/E10339.abstract">here</a>).
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<br />
Here’s a rather old paper that I only noticed recently. Molecular recognition in proteins is still often discussed in biochemistry textbooks in terms of the induced-fit model. But there’s more to it. An alternative (if not necessarily mutually exclusive) picture has been developing recently in which binding occurs preferentially for particular, perhaps weakly populated conformations in an ensemble of protein states, stabilizing that conformation. Oliver Lange at the MPI Göttingen and colleagues used NMR to characterize the conformational states of ubiquitin in solution, and their results offer support for this notion of conformational selection (O. F. Lange <i>et al., Science</i> <b>320</b>, 1471; 2008 – paper <a href="http://science.sciencemag.org/content/320/5882/1471">here</a>). This work strengthens the idea that protein dynamics – which of course are highly influenced by hydration and by solvent fluctuations – have a prominent role in their functionality, an issue I discussed briefly in a recent column in Chemistry World (here https://www.chemistryworld.com/opinion/snapshots-of-lifes-dancers/3008393.article). The Lange <i>et al.</i> work was nicely summarized in a Perspective article by David Boehr and Peter Wright at Scripps (<i>Science</i> <b>320</b>, 1429; 2008 – paper <a href="http://science.sciencemag.org/content/320/5882/1429">here</a>).
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<br />
In an intriguing simulation study, Sridip Parui and Biman Jana at the Indian Association for the Cultivation of Science in Kolkata have looked at the hydrophobic interactions between two hydrocarbon molecules, and also two rod-like model hydrophobes, at low temperatures (240 K) (<i>JPCB</i> <b>121</b>, 7016; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.7b02676">here</a>). They find that there is a second solvent-separated minimum for both systems, roughly 1 nm apart. This corresponds to weaker hydrophobic interactions between the solutes, due to stronger water-water interactions. The authors suggest that such a state could play a role in cold denaturation of proteins.
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<br />
The effect of osmolytes on the denaturation of a model protein (stem bromelain) is considered in detail by Pannuru Venkatesu of the University of Delhi and coworkers (A. Rani <i>et al., JPBC</i> <b>121</b>, 6456; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.7b01776">here</a>). They use a whole battery of experimental techniques (fluorescence, UV-Vis and circular dichroism spectroscopy and dynamic light scattering), along with MD simulations, to study the stabilizing effect of a series of osmolytes (proline, betaine, arginine, sarcosine) against thermal denaturation. In all cases the effects seem to be caused by direct interactions. Betaine, sarcosine and arginine all interact with the protein via hydrogen-bonding. Proline, meanwhile, which confers the greatest stabilizing effect, binds in the protein’s active site.
<br />
<br />
Michael Feig at Michigan State and others have published a nice review article on biomeolecular crowding (M. Geig <i>et al., JPCB</i> <b>121</b>, 8009; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.7b03570">here</a>). This considers the effects of crowding on molecular diffusion, conformation and dynamics, but also on the solvent, which – as the authors say – can have altered structure, dynamics and dielectric response in typical crowded geometries.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjJEzvRQ3oByvt9ID3oEQ4I_0eOTTkFmqZTINznnfd4FG_ZPW0JjhCnHJzvHo3WoiEx95U3ciKg8ttxhAirLADj46cA5i2zCsewMGjDkjhyphenhyphen6t4VZTzf4SpWqHXRdhBYG20o3E6cixELrs/s1600/crowding.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjjJEzvRQ3oByvt9ID3oEQ4I_0eOTTkFmqZTINznnfd4FG_ZPW0JjhCnHJzvHo3WoiEx95U3ciKg8ttxhAirLADj46cA5i2zCsewMGjDkjhyphenhyphen6t4VZTzf4SpWqHXRdhBYG20o3E6cixELrs/s320/crowding.jpg" width="320" height="178" data-original-width="505" data-original-height="281" /></a>
<br />
<i>A typical crowded environment in the cell.</i>
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<br />
Coralie Pasquier at the University of Lund and coworkers have studied the effect of electrolytes with multivalent (trivalent yttrium) ions on protein-protein interactions, using MD and MC simulations (C. Pasquier <i>et al., JPCB</i> <b>121</b>, 3000; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.7b01051">here</a>). The Y ions bind to the surface of the proteins (human serum albumin), but the consequences are complex. In a coarse-grained model, increasing Y3+ concentration could increase protein repulsion at low ionic strength but increase it at high ionic strength. The first situation is due to double-layer effects, the second is a Coulombic repulsion due to high charging of the protein surface. These interactions are water-mediated, and screened out by addition of NaCl, resulting in protein attraction. At intermediate concentrations of YCl3 there is also a net attraction between the proteins, due to ion-ion correlations.
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<br />
Takeshi Yamada of CROSS in Naka, Japan, and coworkers have used quasi-elastic neutron scattering to look at the dynamics of water sandwiched between phospholipid bilayers (T. Yamada <i>et al., JPCB</i> <b>121</b>, 8322; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.7b01276">here</a>). They see three distinct populations of water molecules: free and almost bulk-like, loosely bound and tightly bound to the phospholipid head groups.
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Concentrated ionic solutions aren’t so commonly encountered in biology, but they are important in some technologies, such as rechargeable aqueous batteries. Water is known to have slowed rotation in such solutions, and Wei Zhuang of the Fujian Institute of Research on the Structure of Matter and coworkers suggest why (Q. Zhang <i>et al., PNAS</i> <b>114</b>, 1123; 2017 – paper <a href="http://www.pnas.org/content/114/38/10023.abstract">here</a>). Their simulations suggest that the key contribution comes from a coupling of the slow, collective component of rotation with ion clusters, rather than from faster single-molecule motions. They say that there are similarities with water rotations near large biomolecules.
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Do we finally have an accurate, predictive, tractable ab initio model of water? Mohan Chen at Temple University and collaborators think so (M. Chen <i>et al., PNAS</i> <b>114</b>, 10846; 2017 – paper <a href="http://www.pnas.org/content/114/41/10846.abstract">here</a>). They call their model the strongly constrained and appropriately normed (SCAN) density functional, and say that it captures many of the structural, dynamic and electronic properties of liquid water as well as the density difference with ice Ih.
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Talking of such things, Tomotaka Oroguchi and Masayoshi Nakasako of Keio University say that to accurately simulate the directionality of hydrogen bonds from donor atoms in hydrophilic amino acid residues, one needs to include in the force fields off-atom charge sites that mimic the lone-pair electrons (<i>Sci. Rep.</i> <b>7</b>, 15859; 2017 – paper <a href="https://www.nature.com/articles/s41598-017-16203-w">here</a>).
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com56tag:blogger.com,1999:blog-7540687028464774748.post-41694105780512139122017-06-19T03:53:00.000-07:002017-06-19T03:53:34.745-07:00Chiral water in DNA's hydration shellIn a clever study of DNA hydration using SFG spectroscopy, Poul Petersen and his coworkers have found that the chiral spine of hydration in the minor groove, inferred from oxygen locations for hydrated crystalline DNA by Dickerson and collaborators in the 1980s, exists also in aqueous solution under ambient conditions, and entails orientational ordering of the hydrogen bonds in the single-file water chain that fits into this narrow groove (M. L. McDermott <i>et al., ACS Centr. Sci.</i> 10.1021/acscentsci.7b00100; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facscentsci.7b00100">here</a>). I wrote a news story for <i>Chemistry World</i> on this work (<a href="https://www.chemistryworld.com/news/dna-helix-has-chiral-water-spine/3007545.article">here</a>).
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I applaud the ambition of Modesto Orozco of the Barcelona Institute of Science and Technology and colleagues in writing a paper called “The multiple roles of waters in protein solvation” (A. Hospital <i>et al., JPCB</i> <b>121</b>, 3636; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b09676">here</a>). There’s a title guaranteed to say to me “Read this now!” And the ambition continues in the extent of the systems they investigate with MD: a range of proteins, at a range of temperatures, some denatured, some with crowding agents, some with high concentrations of urea. They say that the results illustrate “the dramatic plasticity of water, and its chameleonic ability to stabilize proteins under a variety of conditions”, which seems a fair way to summarize the matter. I’m not sure I see any surprises here, and the denaturant effects of urea are discussed with something of a “water structure” flavour, but it’s a kind of snapshot of the sorts of things hydration water gets up to.
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A more specific study of protein hydration dynamics is described by Dongping Zhong and colleagues at Ohio State University, who use tryptophan as the reporter group to characterize the dynamics at 17 sites on the surface of the β-barrel protein rat liver fatty acid binding protein (J. Yang <i>et al</i>., <i>JACS</i> <b>139</b>, 4399; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.6b12463">here</a>). They observe three quite distinct dynamical timescales. The water in the outer hydration layer is bulk-like, relaxing quickly (hundreds of fs). For the inner layer, reorientational motion happens on a few-ps timescale, while larger-scale network restructuring takes many tens of ps. The last of these seem to drive protein fluctuations on comparable timescales.
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The dynamics of the protein hydration layer are examined by Biman Bagchi and colleagues of the Indian Institute of Science in Bangalore by calculating those around residues (Trp, Tyr, His) previously used as natural probes in spectroscopic studies (S. Mondal <i>et al</i>., arxiv preprint <a href="https://arxiv.org/abs/1701.04861">1701.04861</a>). They find a range of different timescales, including accelerated as well as retarded rotations. Since NMR measurements give average values, these findings might explain the apparently discrepancy between such studies and those (such as Zewail’s) that focus on specific residues. The protein side-chain dynamics seem particularly to influence the slow solvation component.
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The role of hydration in the protein dynamical transition around 230 K has been widely debated. Prithwish Nandi and Niall English at University College Dublin find in MD simulations of lysozyme that the protein and hydration water dynamics seem to be correlated up to about 285 K, at which point the protein-water hydrogen-bond network becomes too disrupted to sustain the coupling (<i>JPCB</i> <b>120</b>, 12031; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b06683">here</a>).
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However, the whole notion of coupling between the protein and hydration dynamics in the vicinity of the ~200-220 K dynamical transition is challenged by Antonio Benedetto of University College Dublin on the basis of elastic neutron-scattering from lysozyme (arxiv preprint <a href="https://arxiv.org/abs/1705.03128">1705.03128</a>). Specifically, the water begins to relax at 179 K, while the protein doesn’t do so until 195 K. It seems puzzling, and no explanation is advanced here for the discrepancy with a considerable body of earlier results.
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I missed previously this nice paper from H. F. M. C. Martiniano and Nuno Galamba in Lisbon on the structure and dynamics of water around a hydrophobic amino acid (<i>PCCP</i> <b>18</b>, 27639; 2016 – paper <a href="http://pubs.rsc.org/en/Content/ArticleLanding/2016/CP/c6cp04532d#!divAbstract">here</a>). It reports MD simulations of the hydration of valine, and distinguishes between two populations of water molecules in the hydration shell: those that have have four and less than four neighbours. The latter, they say, have faster librational dynamics than bulk water and faster orientational dynamics than four-coordinated “tetrahedral” water. Meanwhile, four-coordinate water in the hydration shell are “more tetrahedral” than bulk water at all temperatures. It would seem, then, that this work argues the case for “tetrahedrality” as a useful concept for characterizing water structure, while advising caution about how it is used and interpreted for the bulk.
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Guanidinium is a complicated osmolyte. It can act as both a protein denaturant and stabilizer, depending on the counteranion. Jan Heyda at the Institut für Weiche Materie und Funktionale Materialien in Berlin and colleagues have setout to understand why, using MD simulations and FTIR (J. Heyda <i>et al</i>., <i>JACS</i> <b>139</b>, 863; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.6b11082">here</a>). Their test peptide, an elastin-like polypeptide, was stabilized in the collapsed state by Gnd sulphate by an excluded volume effect (Gnd being depleted at the peptide/water interface). GndSCN was stabilizing at low concentrations thanks to Gnd+’s ability to crosslink the polymer chains, but at higher concentration it became a denaturant. GndCl, meanwhile, was a denaturant at all concentrations, since in this case partitioning of the chloride to the polymer surface enables recruitment of Gnd+ to the surface too, where it stabilizes the unfolded state. A very graphic example of how the details of direct interactions between polymer, anion, cation (and potentially water) all matter in figuring out what is going on.
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Essentially the same team – which includes Paul Cremer, Joachim Dzubiella and Pavel Jungwirth – have put together a review of such ion-specific effects that, it seems to me, will be the go-to resource for this field for some time to come (H. I. Okur <i>et al., JPCB</i> <b>121</b>, 1997; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b10797">here</a>). I need say no more; if you want to understand how the thinking on Hofmeister has developed over the past several years, this is where to come.
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Does water play the role of reactant in O-O bond formation in photosystem II? That idea has been suggested, water acting as a nucleophile that attacks a terminal oxo group. But Per Siegbahn of Stockholm University uses DFT calculations to determine the free-energy barriers for the six most plausible modes of attack and finds that these barriers are all too high (<i>PNAS</i> <b>114</b>, 4966; 2017 – paper <a href="http://www.pnas.org/content/114/19/4966.abstract">here</a>) – a notion put forward previously but here refined using improved structural data and computational methods.
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I didn’t even know that lipid bilayers, like proteins, show a dynamical transition around 200 K or so. But it seems they do. V. N. Syryamina and S. A. Dzuba of the Russian Academy of Sciences in Novosibirsk have studied thus for two types of phosphocholine bilayers in water using a technique (also new to me) called electron spin echo envelope modulation spectroscopy to follow hydrogen (deuterium) motions (<i>JPCB</i> <b>121</b>, 1026; 2017 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b10133">here</a>). They find that the dynamical transition in the bilayer interior at 188 K is accompanied by the onset of water motion in the first hydration layer, and that another transition around 100 K is accompanied by restricted reorientational motions of water. What I can’t tell from these results is whether there is any sign of slaving of water to lipid dynamics or vice versa.
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I’m not going to pretend to understand the Bayseian model used by Nathan Baker of PNNL in Washington and colleagues to estimte small-molecule solvation free energies (L. J. Gosink <i>et al., JPCB</i> <b>121</b>, 3458; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b09198">here</a>). But it’s basically a method for aggregating many other calculational procedures, and seems to work better than any such techniques in isolation.
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Mihail Barbiou of the European Institute of Membranes in Montpellier and colleagues have used artificial water channels in liposomes, made from stacked imidazoles, to investigate water transport along water wires, analogous to those that thread through aquaporins (E. Licsandru <i>et al., JACS</i> <b>138</b>, 5403; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.6b01811">here</a>). The channels can conduct around a million water molecules per second, a rate two orders of magnitude greater than AQPs, and also conduct protons (but not other ions) efficiently. The chirality of the channels seems to be important for producing strong dipolar orientation in the water wire. Let me also draw attention to Mihail’s nice review of artificial water channels, which includes this example, in <i>Chem. Commun.</i> <b>52</b>, 5657 (2016) (paper <a href="http://pubs.rsc.org/en/content/articlelanding/2016/cc/c6cc01724j#!divAbstract">here</a>).
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRLqtBgIjpiXoOU8gfqZCF8jQ-SxZUBa_dlsZ7D3HrOiHEQq5rQn82EF-PTAHhPrs6mMHutyRvpDFuIafG43KXwxkHoIQiJh0FjcepBnY3k-SYRYCPMSq5GJx9NWxlll0sBlggxRxkgAM/s1600/imidazole_channel.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjRLqtBgIjpiXoOU8gfqZCF8jQ-SxZUBa_dlsZ7D3HrOiHEQq5rQn82EF-PTAHhPrs6mMHutyRvpDFuIafG43KXwxkHoIQiJh0FjcepBnY3k-SYRYCPMSq5GJx9NWxlll0sBlggxRxkgAM/s320/imidazole_channel.jpg" width="320" height="197" data-original-width="481" data-original-height="296" /></a>
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<i>The water channel in stacked imidazoles.</i>
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More on water confined in pores: in MD simulations, Xiao Cheng Zeng at the University of Nebraska and colleagues see low- and high-density liquid states of water within single-walled carbon nanotubes of 1.25 nm diameter at ambient temperature (K. Nomura <i>et al., PNAS</i> <b>114</b>, 4066; 2017 – paper <a href="http://www.pnas.org/content/114/16/4066.abstract">here</a>). The two phases are, however, separated by a hexagonal “tubular ice” phase (which has already been observed experimentally).
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How does water freeze at liquid-vapour interfaces? Specifically, does the interface itself nucleate or suppress freezing? That’s a question relevant to a host of real-world phenomena such as ice nucleation in clouds and other atmospheric processes, but it’s been hard to study experimentally, but Amir Haji-Akbari and Pablo Debenedetti in Princeton study it computationally in a free-standing 4-nm-thick water nanofilm (<i>PNAS</i> <b>114</b>, 3316; 2017 – paper <a href="http://www.pnas.org/content/114/13/3316.abstract">here</a>). Although the rate of ice nucleation in this confined geometry is seven orders of magnitude greater than that in the bulk, nucleation doesn’t start in the surface layers but rather in the (non-bulk-like) interior of the film, where the conditions favour the formation of “double-diamond” water cages that serve as the seeds for the nucleation and growth of cubic ice.
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And here’s a truly surprising thing, discovered by Pablo and Amir in another paper working with Elia Altabet: making hydrophobic plates confining water to a space just over 1 nm wide more flexible by just an order of magnitude decrease in the modulus increases the evaporation rate by nine orders of magnitude, and decreases the condensation rate from the vapour by no less than 24 orders of magnitude, changing the timescale of the process from nanoseconds to tens of millions of years (Y. E. Altabet <i>et al., PNAS</i> <b>114</b>, E2548; 2017 – paper <a href="http://www.pnas.org/content/114/13/E2548.abstract">here</a>). This, at any rate, is what is implied by simulations for plates 3 nm square. Evaporation proceeds via the formation of bubbles at the surfaces that then grow and coalesce to form a gap-spanning cavity. For stiff plates this coalescence is rare, and so is the subsequent growth of the cavity above the critical size for nucleation of the vapour phase. For softer, more flexible plates these configurations occur much more frequently. Such a sensitivity of a drying transition to subtle changes in the mechanical properties may well have implications for processes involving hydration changes at or close to membrane proteins, and could presumably have ramifications for materials design of surfaces on which protein adhesion needs to be controlled.
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Optimization of lead compounds for drug discovery is a complicated business, and when this is done by empirical combinatorial screening, the results can sometimes be counterintuitive, with nonpolar groups in the ligand juxtaposed to polar groups in the target for example. Ariel Fernandez at the Argentine Institute of Mathematics and Ridgway Scott of the University of Chicago review a method for understanding some of those apparent conundrums that involves a consideration of the relevant hydration structures, and in particular the role of what Ariel calls dehydrons (water-exposed backbone hydrogen bonds, which lead to frustration in the hydrogen-bonding arrangements of adjacent water molecules) (<i>Trends Biotechnol.</i> <b>35</b>, 490; 2016 – paper <a href="http://www.cell.com/trends/biotechnology/fulltext/S0167-7799(16)30220-7">here</a>). Their approach uses the WaterMap software to identify “hot” water molecules that might profitably be displaced by a ligand to increase the binding energy and drug specificity.
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The hydrogen-bond network of pure water is of course riddled with defects which underpin fluctuations of the network. Because of topological constraints these tend to occur in correlated pairs. Ali Hassanali at the ASICTP in Trieste and colleagues have studied these correlations using ab initio modelling (P. Gasparotto <i>et al., J. Chem. Theor. Comput.</i> <b>12</b>, 1953; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jctc.5b01138">here</a>). They say that the defect pairs have some similarities to those in solid states of water, and are rather insensitive to the details of the water potentials used.
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One of water’s well known “anomalies” is the decrease in viscosity with increasing applied pressure, which seems to be a consequence of a collapse of the hydrogen bonding network. This effect is larger at low temperatures, but whether that trend continues into the supercooled region hasn’t been studied previously. Now Frédéric Caupin and colleagues at the University of Lyon have investigated this effect down to 244 K and for pressures of up to 300 MPa, and find that indeed the viscosity reduction can be dramatic – by as much as 42% (L. P. Singh <i>et al., PNAS</i> <b>114</b>, 4312; 2017 – paper <a href="http://www.pnas.org/content/114/17/4312.abstract">here</a>). They argue that the results can be understood by invoking a two-state model under these conditions: a mixture of a high-density “fragile” liquid and a low-density “strong” liquid.
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Finally, I have taken what I hope is a somewhat fresh look at the many roles of water in molecular biology in an article for <i>PNAS</i>, for a special issue on water (2017 – paper <a href="http://www.pnas.org/content/early/2017/06/06/1703781114.full">here</a>), which I hope extends the general message of my 2008 <i>Chem Rev</i> article (paper <a href="http://pubs.acs.org/doi/abs/10.1021/cr068037a">here</a>) using some more recent examples.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com16tag:blogger.com,1999:blog-7540687028464774748.post-1533066050607317842017-01-17T07:31:00.000-08:002017-01-17T07:31:01.083-08:00Hydration water in drug designElectrostatic interactions with lipid heads groups retard water molecules near the surface of a membrane. But how are those dynamics affected by a membrane protein? Lars Schäfer at the Ruhr University of Bochum and colleagues attempt to answer that question using (ODNP-enhanced) NMR and simulations to deduce water motions (O. Fisette <i>et al., JACS</i> <b>138</b>, 11526; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.6b07005">here</a>). They conclude that the water-protein interactions have a weaker retarding effect, and dominate only at distances of more than 10 Å above the membrane surface. Moreover, the protein (here annexin B12) and membrane effects are additive. This creates a gradient in water entropy with distance from the surface, with potential consequences for recognition and binding events involving membrane proteins.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrjcjUG402DEixZJ89Cij5y_o63gK7C76L41PfUXUVAHauGYcmTkH9YZCA7jQJW-6Y3NVdYKR6HjrIpQV5qtWdpGpDaBIOGxO3dZoIT23HFbSnNXntGw3JhjN9OvylmRG7zQIYa6KRbxw/s1600/annexin+B12.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjrjcjUG402DEixZJ89Cij5y_o63gK7C76L41PfUXUVAHauGYcmTkH9YZCA7jQJW-6Y3NVdYKR6HjrIpQV5qtWdpGpDaBIOGxO3dZoIT23HFbSnNXntGw3JhjN9OvylmRG7zQIYa6KRbxw/s320/annexin+B12.jpg" width="320" height="230" /></a>
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<i>The hydration environment of membrane protein annexin B12 in a lipid membrane.</i>
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A technique called oriented-sample solid-state NMR can supply information about the water-accessibility of individual residues of membrane proteins in situ, say Gianluigi Veglia and colleagues at the University of Minnesota (A. Dicke <i>et al., JPCB</i> <b>120</b>, 10959; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b08282">here</a>). They’ve used the method to gather this information for the archetypal small transmembrane protein sarcolipin in synthetic bilayers, and find that, as one might expect, there is a relatively smooth gradient of water accessibility with increasing depth within the membrane.
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Does the denaturing effect of osmolytes such as urea and guanidinium chloride depend on concentration? Experiments using FRET and SAXS have produced conflicting results, and Robert Best at the NIH and colleagues try to resolve the matter using simulations (W. Zheng <i>et al., JACS</i> <b>138</b>, 11702; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.6b05443">here</a>). Their test case is the intrinsically disordered protein ACTR, for which they calculate the chain swelling and radius of gyration as a function of denaturant concentration. The protein does indeed swell to a degree proportional to concentration, but the researchers show that nevertheless the structural changes are consistent with SAXS results that appear to show no change in radius of gyration. The denaturant effects operate by a direct mechanism of weak association with the protein.
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What is there is a mixture of denaturants such as urea and stabilizing osmolytes such as TMAO? It seems that TMAO can counteract urea’s effects, but how exactly is the hydrophobic interaction affected in that environment? Indrajit Tah and Jagannath Mondal at the Tata Institute in Hyderabad look into that question via simulations of a model hydrophobic polymer and polystyrene (<i>JPCB</i> <b>120</b>, 10969; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b08378">here</a>). In contrast to what is observed with proteins, for the hydrophobic polymer TMAO actually reinforces the destabilizing effect of urea. This seems to be due to the different direct interactions with the polymer chain: for proteins, TMAO is excluded from the surface while urea remains bound, whereas for the hydrophobic polymer both osmolytes may individually bind to the surface. In this latter case, exclusion of TMAO by urea in the mixed solution depletes the opportunities of TMAO to stabilize the collapsed state.
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Guangzhao Zhang and colleagues at the South China University of Technology in Guangzhou look at the same denaturant-inhibiting effect of betaine, this time with lysozyme as the model protein (J. Chen <i>et al., JPCB</i> <b>120</b>, 12327; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b10172">here</a>). Using proton NMR, they conclude that in this case betaine interacts directly with urea to form dimers, removing the urea from the protein surface where otherwise it interacts directly to stabilize the denatured state.
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Ion-specific “Hofmeister” effects on protein stability and aggregation are still not fully understood at the molecular level. Simon Ebbinghaus at the Ruhr University of Bochum and colleagues seek insights through thermodynamic (DSC) measurements on bovine ribonuclease A (M. Senske <i>et al., PCCP</i> <b>18</b>, 29698; 2016 – paper <a href="http://pubs.rsc.org/en/content/articlehtml/2016/CP/C6CP05080H">here</a>). By measuring ion effects over the whole temperature- and concentration-dependent landscape of protein stability, they find a very complicated picture, due to a complex interplay of contributions. At low concentrations, electrostatic (non-ion-specific) effects dominate, but at higher concentrations there is ion specificity. It’s hard (for me, anyway) to summarize the findings, but I believe it if fair to say that the authors are seeking a unified molecular picture that helps to explain not only ion effects but also those of non-electrolyte cosolutes on protein stability, in terms of a balance between entropic and enthalpic contributions to the excess free energy.
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A belated addition from the Bochum group: Yao Xu and Martina Havenith have provided a nice summary of recent work using THz spectroscopy to look at ps-scale collective hydrogen-bond dynamics in the hydration shells of proteins, and the role that they play in molecular-recognition processes (<i>JCP</i> <b>143</b>, 10.1063/1.4934504; 2015 – paper <a href="http://aip.scitation.org/doi/10.1063/1.4934504">here</a>).
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A further use of THz spectroscopy to investigate hydration is reported by Y Ogawa and colleagues ay Kyoto University (K. Shiraga <i>et al., Appl. Phys. Lett.</i> <b>106</b>, 253701; 2016 – paper <a href="http://aip.scitation.org/doi/10.1063/1.4922918">here</a>). Their aim is simply to get some bulk estimate of how much of the water in a cell (they use HeLa cells) has retarded dynamics – a question explored here in the context of the now more or less obsolete notion of “biological water” in cells. Their answer: about a quarter of the total water content has reorientational dynamics slower than the bulk, presumably because of its involvement in biomolecular hydration. This is more than the 10-15% reported previously in prokaryotes and human red blood cells. But of course the absolute numbers must depend on where one places the thresholds in a dynamical continuum.
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The voltage-dependent proton transport channel Hv1 is implicated in diseases ranging from cancer to some forms of brain damage. This makes it a potential drug target, and some inhibitors seem to expel bound water from the pore when they bind. Because this water forms intermittent hydrogen-bonded clusters and water wires, it seems likely that there’s a hydration-related entropic contribution to the binding free energy. With this in mind, Mike Klein at Temple University and colleagues have used modeling and simulations to look at water fluctuations in the pore, so as to identify potential binding sites (E. Gianti <i>et al., PNAS</i> <b>113</b>, E8359 2016 – paper <a href="http://www.pnas.org/content/113/52/E8359.abstract">here</a>). Their analysis reveals two such sites: one the binding site known already, another at the outlet of the proton pathway, both of them associated with maximal fluctuation, apparently on the brink of a drying transition, and in locations where replacement by a hydrophobic ligand is optimal. The researchers say that the second, new site should therefore also be considered as a locus of drug design.
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The same group has also considered the mechanism of proton transport (S C. van Keulen <i>et al., JPCB</i> 10.1021/acs.jpcb.6b08339; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b08339">here</a>). It’s been suggested previously that this occurs via Grotthuss hopping along a water wire. But the results of these quantum/molecular mechanics simulations suggest that instead the proton hops between three acidic residues via mediating water molecules.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyTK5_-KBosfxb24Qm2A-ynCY5nSz6JlMaTlLFukPuWrx36X9hvvi1Wwy5dOue49E8QUznMzDVpJXdN8leBeBFmZqR1QHI4X0dzoMgkE34uv5KEDTn7Dz6NlHPnGmhZiVS4Zpm75OXAH4/s1600/Hv1+proton+transport.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjyTK5_-KBosfxb24Qm2A-ynCY5nSz6JlMaTlLFukPuWrx36X9hvvi1Wwy5dOue49E8QUznMzDVpJXdN8leBeBFmZqR1QHI4X0dzoMgkE34uv5KEDTn7Dz6NlHPnGmhZiVS4Zpm75OXAH4/s320/Hv1+proton+transport.jpg" width="320" height="227" /></a>
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<i>How a proton (circled in purple) makes its way down the channel of Hv1: via a series of water-mediated hops between acidic residues. </i>
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More proton transport: on the basis of FTIR experiments, Udita Brahmachari and Bridgette Barry at Georgia Tech say that a crucial stage of the oxygen-forming S-cycle of photosynthesis involves the insertion of a proton into a hydrogen-bonded water network (<i>JPCB</i> <b>120</b>, 11464; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b10164">here</a>). Thus bound water here acts as a catalytic proton acceptor and donor.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtPPT7k9aDszEWioTGnM_zl5QM3Bc97QSs6YcP0PSQsahypsnNI0cMIRsb-lBCqcGeUCkifcGY6VVNaQrppm0zepIRz9BiTspXFHdqWHlcxVpXwXV-OS5jlSshZzaWs4OxSQIS7yErvU0/s1600/oxygen_evolution.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtPPT7k9aDszEWioTGnM_zl5QM3Bc97QSs6YcP0PSQsahypsnNI0cMIRsb-lBCqcGeUCkifcGY6VVNaQrppm0zepIRz9BiTspXFHdqWHlcxVpXwXV-OS5jlSshZzaWs4OxSQIS7yErvU0/s320/oxygen_evolution.jpg" width="320" height="145" /></a>
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<i>The catalytic water network in the S3-S0 stage of the photosynthetic cycle.</i>
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Jonathan Nickells at Oak Ridge and coworkers have characterized the general hydration environment of green fluorescent protein using neutron scattering spectroscopy to probe the dynamics (S. Perticaroli <i>et al., JACS</i> 10.1021/jacs.6b08845; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.6b08845">here</a>). These dynamics are slowed over just two hydration shells: by a factor of 4-10 in the first shell and 2-5 in the second.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBIlA_inpQ1527FsxVwsvpA1BmMoRLF_hVvlF-XRJ51qdvJFttDDy2D79NnNrwVE8M36rAhBnJNHTmwwTzjkqVSVsK38ksaUTXgpZuP_eDFsNIOfrpI75e1q8ZJ6v7SMreaZoXwv8KV10/s1600/GFP.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjBIlA_inpQ1527FsxVwsvpA1BmMoRLF_hVvlF-XRJ51qdvJFttDDy2D79NnNrwVE8M36rAhBnJNHTmwwTzjkqVSVsK38ksaUTXgpZuP_eDFsNIOfrpI75e1q8ZJ6v7SMreaZoXwv8KV10/s320/GFP.jpg" width="314" height="320" /></a>
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<i>The hydration of GFP.</i>
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In comparison, Keiichiro Shiraga and colleagues at Kyoto see dynamical perturbations out to three or four hydration layers (a distance of around 8.5 Å) around albumin, based on THz spectroscopy (K. Shiraga <i>et al., Biophys. J.</i> <b>111</b>, 2629; 2016 – paper <a href="http://www.cell.com/biophysj/abstract/S0006-3495(16)31039-6">here</a>). They say that the hydrogen-bond network in the hydration layers seems to be less defective than that in the bulk, even though there seems to be greater distortion of the network away from tetrahedral.
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Meanwhile, Monique Tourell and Konstantin Momot at the Queensland University of Technology have zeroed in on the single-water-molecule bridges that link parts of the peptide chains in collagen (<i>JPCB</i> <b>120</b>, 12432; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b08499">here</a>). Some experimental studies have apparently implied that the waters are “ice-like” in their dynamics, although I’m not clear quite what this is meant to imply. In any event, these MD simulations suggest otherwise: the waters exhibit strongly anisotropic rotation in which a single molecule might flip back and forth many times while remaining resident at the bridging site for more than 100 picoseconds.
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When a particle is solvated at the air-water surface, fluctuations of the interface such as capillary waves may contribute to the solvation free energy – the solute might dampen the fluctuations, for example. Kaustubh Rane and Nico van der Vegt set out to quantify this using Monte Carlo simulations (<i>JPCB</i> <b>120</b>, 9697; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b05237">here</a>). They find that the contribution of fluctuations is not negligible in general, and that the dampening effect is a generic one that doesn’t depend on the chemical nature of solute or solvent. However, the strength of the interactions between ions and water will determine the magnitude of the effect of fluctuations, so that one can expect ion-specific propensities towards proximity to the water surface.
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Ariel Fernández, now at the Argentine Mathematics Intitute, has been for some time exploring the role of hydrogen-bond frustration in protein-protein and protein-ligand interactions. The idea here is that such frustration contributes to interfacial tension via its effects on “non-Debye” polarization. Now he has studied how “minimal frustration” might guide these molecular assembly processes and be exploited in drug design, potentially enabling a high degree of binding selectivity (<i>FEBS Lett.</i> <b>590</b>, 3481; 2016 – paper <a href="http://onlinelibrary.wiley.com/doi/10.1002/1873-3468.12418/abstract">here</a>).
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There’s more on the use of hydration information for drug design from Gerhard Klebe of the University of Marburg and colleagues (S. G. Krimmer <i>et al., J. Med. Chem.</i> <b>59</b>, 10530; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jmedchem.6b00998">here</a>). They say that optimizing the water layers covering ligands bound to their target – here hydrophobic inhibitors of thermolysin – can boost the enthalpic contribution to binding free energy. MD simulations enabled the prediction of high binding affinity for a series of ligands, one of which then proved to have 50 times better binding affinity than the known (and patented) parent ligand. This is a really nice piece of work, showing that it’s not just trapped or displaced water molecules that are important in drug design but also the final bound-ligand hydration profile.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYGblhevz8sqy9yCMkIMwu9UTxdvErDSly4OHDhq2cJwzaWN2aW_FShWDsvCEREBARmRmpzoh1MUFXPw2yH51nf0YcYB0JuGJ9XoXyKnNXqLgnAvJJo00DRz9cvkLQl1DM_v1IZUOq4UY/s1600/thermolysin_ligand.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYGblhevz8sqy9yCMkIMwu9UTxdvErDSly4OHDhq2cJwzaWN2aW_FShWDsvCEREBARmRmpzoh1MUFXPw2yH51nf0YcYB0JuGJ9XoXyKnNXqLgnAvJJo00DRz9cvkLQl1DM_v1IZUOq4UY/s320/thermolysin_ligand.jpg" width="318" height="320" /></a>
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<i>The hydration structure of the best drug candidate for binding in the hydrophobic pocket of thermolysin.</i>
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Nested fullerenes, or “carbon onions”, cluster in water. Adam Makarucha have used MD simulations to look at the size- and shape-dependence of the effect (A. J. Kakarucha <i>et al., JPCB</i> <b>120</b>, 11018; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b07471">here</a>). As one might expect for a hydrophobic surface, there is layering of water at the surface of these particles, and the disruption of the hydrogen-bond network increases with increasing particle size because of the increased shape anisotropy: the tendency for the larger fullerene shells to become faceted with vertices (where the pentagonal rings sit).
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To what extent are the bulk properties of pure water altered by confinement? Debates about confinement-induced changes in “water structure” have sometimes tended to overlook generic effects such as layering of a liquid close to a wall. Roland Netz and colleagues at the Free University of Berlin bring some clarity to the problem by using MS simulations to look at changes in the dielectric properties of water due to confinement-induced correlations in the polarization of neighbouring water molecules (A. Schlaich <i>et al., Phys. Rev. Lett.</i> <b>117</b>, 048001; 2016 – paper <a href="http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.117.048001">here</a>). They find that these effects – specifically an anticorrelation for neighbouing molecules – result in a significantly decreased dielectric response perpendicular (but not so much parallel) to a pair of walls (here consisting of closely packed decanol monolayers) separated by up to a nanometre or so. This behaviour has obvious consequences for, say, water’s ability to screen electrostatic interactions between closely spaced surfaces (of proteins or lipid membranes, say). [There’s also an APS Physics comment piece on this <a href="http://physics.aps.org/synopsis-for/10.1103/PhysRevLett.117.048001">here</a>]
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The existence of a quasiliquid layer on the surface of ice below 273 K is now fairly well attested. Mischa Bonn and Ellen Backus of the MPI for Polymer Research at Mainz and their colleagues have studied this layer using SFG and simulations (M. A. Sánchez <i>et al., PNAS</i> <b>114</b>, 227; 2016 – paper <a href="http://www.pnas.org/content/114/2/227.abstract">here</a>). They find evidence of a stepwise transition from a single to a double bilayer of water molecules around 257 K. They say that there is evidence for the single bilayer being quasiliquid all the way down to 235 K.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com28tag:blogger.com,1999:blog-7540687028464774748.post-7797038949623595832016-10-28T01:03:00.002-07:002016-10-28T01:03:17.690-07:00Are hydrophobic protein surfaces like big or small hydrophobes?It seems to me that a paper on protein denaturation by Michele Vendruscolo at Cambridge, Stefano Gianni at the University of Rome La Sapienza, and their colleagues will repay careful study (C. Camilloni <i>et al., Sci. Rep.</i> <b>6</b>, 28285; 2016 – paper <a href="http://www.nature.com/articles/srep28285">here</a>). The researchers use MD simulations to model observed NMR shifts during hot and cold denaturation, and thereby to gain insight into transition-state structures, changes in hydration and thermodynamic parameters. This enables them to characterize in some detail the differences between hot and cold denaturation: the former has more secondary structure, being more influenced by hydrophobic interactions. In effect this points to the existence of two alternative folding mechanisms from denatured states. What’s more, water molecules at the protein surface have the same number of hydrogen bonds on average as those in the bulk. This is what theory predicts for small hydrophobes (<1 nm or so), whereas for larger extended hydrophobic surfaces some hydrogen bonding is thought to be inevitably lost. In other words, it seems that the hydrophobicity of proteins must, on account of their complex surface topography and chemical heterogeneity, be considered to be more akin to that of small rather than large hydrophobes.
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A detailed look at how protein surface topography and chemistry affects local water organization is described by Tom Kurtzman of Lehman College and coworkers (K. Haider <i>et al., JPCB</i> <b>120</b>, 8743; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b01094">here</a>). They look at the ligand-binding clefts of six structurally diverse proteins and identify circumstances where the constraints on local water structure compromise the enthalpy. These include deep and narrow cavities and ones with weak water-solute interactions, but also sometimes sites with charged residues in which there can be frustration of adjacent water-water interactions. Clearly this kind of information should be useful for designing ligands that bind competitively to a site, but it remains unclear whether one can yet identify generic design features or whether each case must be considered on its own terms. The broader question is perhaps whether the hydration characteristics must be considered to have been selectively fine-tuned or simply a necessary compromise occasioned by conflicting demands on the binding site. That’s to say, are the hydration environments each individually ‘functional’ or at least partly an epiphenomenon?
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One of the clearest cases I can remember seeing for the coupling of hydration structure with protein motions and function is supplied by Tomotaka Oroguchi and Masayoshi Nakasako at Keio University (<i>Sci. Rep.</i> <b>6</b>, 26302; 2016 – paper <a href="http://www.nature.com/articles/srep26302">here</a>). They have looked at the hexameric multi-domain protein glutamate dehydrogenase (GDH) using MD simulations and AFM. The opening and closing of a hydrophobic pocket HS1 are accompanied by wetting and drying of the pocket, while binding and unbinding of water molecules in a hydrophilic crevice HS2 accompany changes in its length. These two changes in hydration are coupled, creating a kind of hydration-driven mechanism for large-scale conformational change in GDH.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoRYioEkWR56Y884dAuQKh-GGZ2t3T6xVNAg5qFj1Mx0UjImXM8nY9tgHdME3UJPgCkfPj7df8gSgoIWinl6Wp-CSERWP265CTP_PJ65E6ECjI5KSH10MHeqeIqvEAqeX2PfUqxNn5DKM/s1600/HS1+hydration+changes.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhoRYioEkWR56Y884dAuQKh-GGZ2t3T6xVNAg5qFj1Mx0UjImXM8nY9tgHdME3UJPgCkfPj7df8gSgoIWinl6Wp-CSERWP265CTP_PJ65E6ECjI5KSH10MHeqeIqvEAqeX2PfUqxNn5DKM/s320/HS1+hydration+changes.jpg" width="320" height="276" /></a>
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<i>Drying and wetting of the hydrophobic pocket HS1 accompanying the opening and closing of the cleft.</i>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIUDTUTXrHXoUP8zjz42FFq4fP58FO-MtsPf1bydKiG5tHgQuKsc4RkYAz8-ZuNNNYYkhPRCtyxhccX1cBUfT7yT4yDmSmsxkzZDq1H-LIXgR-HPHr5gRomyTGqcQ3vAz4Sz96whUs5WQ/s1600/GDH+conformational+change.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIUDTUTXrHXoUP8zjz42FFq4fP58FO-MtsPf1bydKiG5tHgQuKsc4RkYAz8-ZuNNNYYkhPRCtyxhccX1cBUfT7yT4yDmSmsxkzZDq1H-LIXgR-HPHr5gRomyTGqcQ3vAz4Sz96whUs5WQ/s320/GDH+conformational+change.jpg" width="320" height="261" /></a>
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<i>Conformational changes in the GDH protein due to coupled hydration changes at the sites HS1 and HS2.</i>
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The coupling of hydration change to large-scale protein dynamics is also the subject of an experimental study by Keisuke Tominaga and colleagues at Kobe University using dielectric spectroscopy at THz frequencies (N. Yamamoto <i>et al., JPCB</i> <b>120</b>, 4743; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b01491">here</a>). They look at lysozyme in the solid state under different hydration conditions, and see two relaxational modes. They attribute the faster of them, with a ~20 ps relaxation time, to coupled water-protein motion: the mode is primarily due to hydration water dynamics, but the hydration water “drags” with it the hydrophilic groups at the protein surface. The slower (~100 ps) mode might be due to motions of the amino-acid side-chains induced by hydration. Looking at the temperature dependence of the spectra, the authors also see a signature of the familiar dynamical transition around 200 K.
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The same issue is explored by Dongping Zhong and colleages at Ohio State University using femtosecond spectroscopy of tryptophan relaxation (Y. Qin <i>et al., PNAS</i> <b>113</b>, 8424; 2016 – paper <a href="http://www.pnas.org/content/113/30/8424.abstract">here</a>). They too see coupling between hydration water and protein side-chain dynamics which slows down the water reorientational relaxation at the interface relative to the bulk. (They study DNA polymerase IV.) Mutational studies and MD simulations imply that causation here goes in the direction of the protein side-chain fluctuations being slaved to the cooperative dynamics of the hydration water.
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A closer look at the dynamics of hydration water is provided by Peter Bolhuis of the University of Amsterdam and colleagues, who compare MD simulations with femtosecond IR spectroscopy of the hydration of bovine α-lactalbumin, both in its native and a misfolded state (Z. F. Brotzakis <i>et al., JPCB</i> <b>120</b>, 4756; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b02592">here</a>). The water relaxation times here are typically of the order of tenths of to several picoseconds; ‘slow’ waters have relaxation times > 7 ps, some as much as 20 ps. These waters tend to be located in concavities on the protein surface and make fewer hydrogen bonds with surrounding waters than do molecules in the bulk. Moreover, waters near hydrophobic groups tend to be slower on average than those near hydrophilic groups. But although misfolding exposes more of the hydrophobic surface, it also means that these hydrophobic regions are less concave, and so the water dynamics is somewhat faster on average and there are fewer of the “ultraslow” sites.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6kA7cHIjSIGipNmmJMmXTgrtHureSb3Ak7Of4Njxay5w6xiFv58lFeysb8Qqf79gq9lYKz3DD5U1UEZq_9yLd6LHcj2o09s2DTiJ4x28rfm1wEFLAcO7_ERL5nvfq_nXlpfxCQQaJzus/s1600/lactalbumin+dynamics.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6kA7cHIjSIGipNmmJMmXTgrtHureSb3Ak7Of4Njxay5w6xiFv58lFeysb8Qqf79gq9lYKz3DD5U1UEZq_9yLd6LHcj2o09s2DTiJ4x28rfm1wEFLAcO7_ERL5nvfq_nXlpfxCQQaJzus/s320/lactalbumin+dynamics.jpg" width="320" height="175" /></a>
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<i>Water reorientational decay times seen in simulations of native (left) and misfolded (right) bovine α-lactalbumin.</i>
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A somewhat comparable exercise is conducted for B-DNA by James Hynes and Damien Laage at the ENS Paris and colleagues (E. Duboué-Dijon <i>et al., JACS</i> <b>138</b>, 7610; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jacs.6b02715">here</a>). And there are some commonalities: while the hydration water is generally rather slower to reorient than in the bulk, the waters confined in the narrow minor groove are much more significantly retarded (relaxation times 30-85 ps). Moreover, there is considerable heterogeneity, and some of this comes from coupling of the macromolecular fluctuations with the water dynamics, especially in the minor groove. In other words, there does not seem in this case to be slaving of biomolecular dynamics to those of the solvent, but more or less the reverse.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3weATj-axyj5xe1dTirbEgBtPX6NLjgvyXaLDh9eyg5HlANLpeYQkfVHkxxdjNCYrm-j9UVRATs4qW_xM9o-VsSJOn2QniLC00dQQpL_vO_f1_xNmah0J0ZAvrKpGllm80Y3RRR11WtE/s1600/DNA-dynamics.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh3weATj-axyj5xe1dTirbEgBtPX6NLjgvyXaLDh9eyg5HlANLpeYQkfVHkxxdjNCYrm-j9UVRATs4qW_xM9o-VsSJOn2QniLC00dQQpL_vO_f1_xNmah0J0ZAvrKpGllm80Y3RRR11WtE/s320/DNA-dynamics.jpg" width="320" height="224" /></a>
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<i>Water reorientational times on the minor and major grooves of the B-DNA dodecamer (CGCCAATTCGCG)2</i>
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Lorna Dougan at Leeds and colleagues have found evidence of a low-density form of water at low temperatures (285-238K), which might be related to the putative phase transition separating low- and high-density liquids in the metastable regime (J. J. Towey <i>et al., JPCB</i> <b>120</b>, 4439; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b01185">here</a>). They keep the water liquid by mixing it with the cryoprotectant glycerol. Neutron scattering and simulation show that at low temperatures the mixture segregates at the nanoscale, and the water nanophase has greater tetrahedral ordering than the bulk.
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Predicting protein structure from sequence data often draws on information on homologous structures or fragments from the Protein Data Base. But such homologies cannot always be spotted, or might not be present in the database, or might not be reliable. Peter Wolynes and colleagues at Rice have developed a scheme for predicting structures <i>ab initio</i>, without bioinformatics input, using what they call the atomistic, associative memory, water mediated structure and energy model (AAWSEM) (M. Chen <i>et al., JPCB</i> <b>120</b>, 8557; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b02451">here</a>). This uses coarse-grained simulations at the whole-protein level while drawing on atomistic simulation of fragments – and crucially, incorporates water-mediated interactions in the folding process. It’s a smart approach to the folding problem that draws on the biological reality – the fact that protein folding is funneled to make it evolutionarily robust to small variations in sequence – rather than brute-force number-crunching.
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Water mediation is thought to be important too for the aggregation of amyloid fibrils. Samrat Mukhopadhyay and colleagues at the Indian Institute of Science Education and Research in Mohali have used time-resolved fluorescence measurements on the human prion protein (PrP) to investigate how (V. Dalal <i>et al., ChemPhysChem</i> <b>17</b>, 2804; 2016 – paper <a href="http://dx.doi.org/10.1002/cphc.201600440">here</a>). They find that water hydrating the amyloid-competent oligomers has mobility retarded by three orders of magnitude relative to the bulk, perhaps because of entrapment in the collapsed polypeptide chains. They say that this water might create a hydrogen-bonded network that stabilizes the partly unfolded, molten oligomer conformation and acts as a scaffolding for the assembly of oligomers into fibrils.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEid8AZs7laLWTYpJs2UnDNc_lsTgTXc36eFn-vpTM36292ldFOxC0NoA2I-WANXyVuGDX6zjwLQCTzD8ty9EEaDrjEdTufni_cjGAtUQs9GHEF0goO0_WEG-O37VI272N01BsKRkMUCN0E/s1600/amyloid.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEid8AZs7laLWTYpJs2UnDNc_lsTgTXc36eFn-vpTM36292ldFOxC0NoA2I-WANXyVuGDX6zjwLQCTzD8ty9EEaDrjEdTufni_cjGAtUQs9GHEF0goO0_WEG-O37VI272N01BsKRkMUCN0E/s320/amyloid.jpg" width="320" height="173" /></a>
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<i>Proposed role of ordered water molecules in the misfolding and amyloid formation of PrP – and in protein misfolding diseases more generally.</i>
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Antiviral drugs against influenza B could work by blocking the proton-conducting channel BM2, but no such have yet been devised. Mei Hong at MIT and colleagues have used NMR to investigate the mechanism of proton transport in BM2 and the role of hydration, and to elucidate the differences with AM2 from influenza A (J. K. Williams <i>et al., JACS</i> <b>138</b>, 8143; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jacs.6b03142">here</a>). The His19 residue in BM2 remains unprotonated to lower pH than the corresponding His 37 in AM2, but increasing channel hydration in acidic conditions seems to enhance proton transport to His 19 from water molecules.
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Why trehalose acts as a cryoprotectant of protein structure still isn’t fully understood. Jan Swenson and coworkers at Chalmers University of Technology in Göteborg try to develop a comprehensive picture by looking at how trehalose affects the protein glass transition, denaturation temperature, and solution viscosity (C. Olsson <i>et al., JPCB</i> <b>120</b>, 4723; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b02517">here</a>). They study the myoglobin-trehalose-water system using DSC and viscometry. In short, their results seem to exclude the picture in which trehalose displaces water in the solvation shell; on the contrary, they suggest that the protein retains one or two layers of water within a stabilizing water-trehalose matrix. This would be consistent with an apparent lack of coupling between the trehalose-water matrix dynamics and the stability of the native protein.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXmtxuLy9Qy7GkNitp-H9sKNlvNWSOjMLF7QPapg4xY9DOnXS-X1t9a4c0PRWM_Uu5CkDpchGaYHqGGd-gAeF0GWBk29M2nd4K89EM50Cxo7X4jtV73EXyA9Qpu7GVWPrWjtpEGBpz1ac/s1600/trehalose.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgXmtxuLy9Qy7GkNitp-H9sKNlvNWSOjMLF7QPapg4xY9DOnXS-X1t9a4c0PRWM_Uu5CkDpchGaYHqGGd-gAeF0GWBk29M2nd4K89EM50Cxo7X4jtV73EXyA9Qpu7GVWPrWjtpEGBpz1ac/s320/trehalose.jpg" width="320" height="198" /></a>
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<i>Schematic of the interactions between water, trehalose and protein.</i>
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That picture of a lack of direct interaction between trehalose and proteins – the disaccharide is in fact preferentially excluded from the protein hydration layer – is also the general context for an experimental study by Christina Othon of Wesleyan University in Connecticut and colleagues of trehalose bioprotection (N. Shukla <i>et al., JPCB</i> <b>120</b>, 9477; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b07751">here</a>). Using ultrafast fluorescence spectroscopy for two fluorescent probes, they see a slowdown of water reorganizational dynamics at relatively low trehalose concentrations (0.1-0.25 M, well below the vitrification threshold). At these concentrations, there is around 7 water layers between osmolyte molecules. These results therefore support an indirect mechanism for cryoprotection. Sucrose has much the same effect, but less markedly, the researchers say.
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The interaction between two hydrophobic particles in water is generally attractive: this is simply the (water-mediated) hydrophobic effect. But Alenka Luzar and coworkers at Virginia Commonwealth University show that this interaction can become repulsive (B. S. Jabes <i>et al., JPC Lett</i> <b>7</b>, 3158; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpclett.6b01442">here</a>). Such repulsion has been seen before in simulations of fullerenes and carbon nanotubes in water, and has sometimes been attributed to specific structural changes in the water. But Alenka and her colleagues show that it can be explained purely as a geometric effect of the thermodynamic cost of formation of a liquid-vacuum interface bridging the hydrophobic particles (in these calculations, pure and propyl-terminated graphitic nanoparticles) when drying occurs in the intervening space. This process can be modeled with a straightforward, bulk-like Young-type calculation of the surface free energies.
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Nanoconfinement effects on water structure and properties are investigated by Vrushali Hande and Suman Chakrabarty of the National Chemical Laboratory in Pune through simulations of water inside reverse micelles and water-in-oil nanodroplets (<i>Phys. Chem. Chem. Phys.</i> <b>18</b>, 21767; 2016 – paper <a href="http://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp04378j">here</a>). For the reverse micelles the interface is (negatively) charged, and the deviations from bulk-like behaviour are longer-ranged for orientational order than they are for translational ordering. These effects are far less pronounced for nanodroplets in oil, where the interface is hydrophobic, indicating that electrostatic influences on the hydrogen bonding are more pronounced than spatial confinement per se.
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Also on nanoconfinement: quite why water has an enhanced mobility in carbon nanotubes remains a matter of some debate. Using IR spectroscopy, Pascale Roy at the Synchrotron Soleil in Gif-sur-Yvette and colleagues suggest that it may be due to unusually “loose” hydrogen-bond networks among water molecules inside the nanotubes (S. D. Bernadina <i>et al., JACS</i> <b>138</b>, 10437; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jacs.6b02635">here</a>). They look at nanotubes with diameters of 0.7-2.1 nm, in which the water varies from single-file chains to multilayers, and find a spectroscopic signature of “loosely bonded water” in all cases – in the latter seeming to correspond to waters in the outer layers with dangling OH bonds pointing towards the nanotube walls.
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The distance dependence of the hydrophobic force between two hydrophobic walls is investigated in MD simulations by Biman Bagchi and colleagues at the Indian Institute of Science in Bangalore (preprint <a href="https://arxiv.org/abs/1608.04107">arxiv.1608.04107</a>). They find a bi-exponential force law, with correlation lengths of 2 nm and 0.5 nm, and a crossover close to 1.5 nm. This behaviour is mimicked by the tetrahedral order parameter, but I’m not entirely clear what the authors’ mechanistic explanation is.
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Of course, the issue with many studies of this kind is that your results might only be as good as your model. Angelos Michaelidies and colleagues at UCL offer an overview of the extent to which density-functional theory supplies a good description of water, from small clusters to the bulk (M. J. Gillan <i>et al., JCP</i> <b>144</b>, 130901; 2016 – paper <a href="http://scitation.aip.org/content/aip/journal/jcp/144/13/10.1063/1.4944633">here</a>). In particular they consider how well different functional forms of exchange-correlation terms perform, and what role many-body terms play. Looks like essential reading for anyone using DFT to model aqueous systems.
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Many-body effects are also central to a study by Shelby Straight and Francesco Paesani at UCSD of influences of water’s dipole moment on the hydrogen-bond network of pure water (<i>JPCB</i> <b>120</b>, 8539; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b02366">here</a>). They use simulations to predict the infrared spectra of HOD in H2O, and in particular the shape of the OD stretch. They find that the calculated spectral diffusion of this vibrational frequency depends rather strongly on exactly how one truncates a many-body expansion of the water dipole.
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How effectively can hydration be described with a coarse-grained model? Bill Jorgensen and colleagues consider the performance of one attempt to balance accuracy and speed that mixes all-atom and coarse-grained descriptions – the so-called AAX-CGS model, in which all-atom solutes are solvated with coarse-grained water (X. C. Yan <i>et al., JPCB</i> <b>120</b>, 8102; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b00399">here</a>). The approach works well for hydrophobic and halogenated alkane solutes, less so for those that are more polar or engage in hydrogen bonding (amines, alcohols). But the efficiency of the calculations beats that of all-atom simulations by about an order of magnitude or more.
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Why are ion hydration free energies asymmetric with respect to ion charge? Rick Remsing and John Weeks investigate that question using an analytical model for calculating hydration free energies that involves gradually “turning on” the ion-solvent Coulomb interaction (<i>JPCB</i> <b>120</b>, 6238; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.6b02238">here</a>). This enables them to see why the Born solvation model fails to capture the asymmetry: in short, it works well enough for slowly varying Gaussian charge distributions but not for the abrupt, delta-function-like distributions in ion cores. Only in the latter case is the asymmetry in response to ion charge recovered.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com37tag:blogger.com,1999:blog-7540687028464774748.post-58853556525069838402016-05-27T00:26:00.002-07:002016-05-27T00:26:22.087-07:00Dewetting and its originsSeveral thermophilic proteins are known to have internal water-filled cavities, and some are known to denature when these cavities are emptied. Could this internal water be the secret to their thermal stability? Fabio Sterpone in Paris and his colleagues have investigated that question by using MD simulations to calculate the hydration free energy of buried water for several homologous mesophilic and thermophilic proteins (D. Chakraborty <i>et al., JPCB</i> <b>119</b>, 12760; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b05791">here</a>). Their findings support that main contention: the buried water contributes favourably and significantly to the stability of the thermophilic proteins. This could therefore offer a strategy for designing proteins robust against high temperatures.
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Protein folding is studied with proton NMR by Francesco Mallamace, Gene Stanley and their collaborators (F. Mallamace <i>et al., PNAS</i> <b>113</b>, 3159; 2016 – paper <a href="http://www.pnas.org/content/113/12/3159.abstract">here</a>). In particular, they aim to elucidate the role of water in the folding process, taking lysozyme as the paradigmatic example. They examine the evolution of hydrophilic (amide NH) and hydrophobic (methyl and methine CH) groups as folding proceeds, both for a reversible unfolded intermediate state and the irreversible denatured state. Hydrogen bonding between amide groups and internal water seems to play a crucial role: water acts as a kind of “glue” between buried amide and carbonyl groups, while the increased mobility of hydrophobic groups as they form clusters in the folded state compensates for the loss of configurational entropy that this entails.
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Studying the binding and unbinding kinetics of cavity-ligand interactions could offer valuable insights into the efficacy of drugs and drug candidates. But it’s tough to do using MD simulations, because the timescales are often too long. Bruce Berne at Columbia and his colleagues have developed a “metadynamics” scheme that allows MD to probe timescales of not just many seconds but an hour or so (P. Tiwary <i>et al., PNAS</i> <b>112</b>, 12015; 2015 – paper <a href="http://www.pnas.org/content/112/39/12015.abstract">here</a>). They examine a prototypical ligand–cavity system: a fullerene in a simple hydrophobic pocket, with explicit water. They find that binding involves an abrupt dewetting transition when the fullerene is constrained to move only along the central axis of symmetry of the system, but that dewetting is continuous, and binding is 20-fold shorter-lived (around 200s), when this steric constraint is removed.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2MWJ6ZrWCh__gc_84Gf6wRAxouMzsOyh29Cs-DnNbV57Vj9MDE-LSytqA0rIC8ezD46y1_fwsrJqyrldoBRDe2yt-pHlWl2dbmspRKzFnGmjoq3OL4wokX1JqaaeoE-t7PTT_chaL334/s1600/Berne_cavity.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2MWJ6ZrWCh__gc_84Gf6wRAxouMzsOyh29Cs-DnNbV57Vj9MDE-LSytqA0rIC8ezD46y1_fwsrJqyrldoBRDe2yt-pHlWl2dbmspRKzFnGmjoq3OL4wokX1JqaaeoE-t7PTT_chaL334/s320/Berne_cavity.jpg" /></a>
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<i>Hydration of a fullerene in a simple binding cavity.</i>
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Abrupt dewetting has been observed between two planar hydrophobic surfaces at small separations, where it is simply capillary evaporation by another name. But Matej Kanduc and Roland Netz at the Free University of Berlin find that it can also occur between a hydrophobic and mildly hydrophilic surface, if they are both polar but electrically neutral (<i>PNAS</i> <b>112</b>, 12338; 2015 – paper <a href="http://www.pnas.org/content/112/40/12338.abstract">here</a>). This leads to dry adhesion of the dissimilar surfaces. Kanduc and Netz construct the full phase diagram for any pair of surfaces, showing that dry adhesion can happen even for appreciable hydrophilicity of one surface (say, contact angle of 45 degrees) if the other is markedly hydrophobic (contact angle around 120 degrees).
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7O6QAyFQYZ0R3cHDFGNQerTdfR4m3a7Ut1DW3wofKjTLmYoVr7VqIq3nVup_XHh-krhHJPwHEVhCEKkRcl60BvKN2Pe1Ylgglla4AWJI4amU9RB6vWUg7lkXNhAXEEN_mxEcsyvhrLO4/s1600/netz_phase_diagram.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg7O6QAyFQYZ0R3cHDFGNQerTdfR4m3a7Ut1DW3wofKjTLmYoVr7VqIq3nVup_XHh-krhHJPwHEVhCEKkRcl60BvKN2Pe1Ylgglla4AWJI4amU9RB6vWUg7lkXNhAXEEN_mxEcsyvhrLO4/s320/netz_phase_diagram.jpg" /></a>
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<i>The phase diagram of attractive/dewetting regimes for two planar surface of different contact angle.</i>
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Masataka Nagaoka at Nagoya University and colleagues look at another dewetting process, which takes place in the binding pocket of thrombin when it binds a ligand (I. Kurisaki <i>et al., JPCB</i> <b>119</b>, 15807; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b09581">here</a>). The process is quite complicated. These MD simulations indicate that, following the establishment of a hydrogen-bonding interaction between the substrate and an Asp group in the pocket, the water is gradually removed from the pocket, going not into the bulk phase but into a water channel within the protein – which thus turns out to have a functional role.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1o757t7F06qUBYIyMuhM5GLo6TFYC78mJo0cSI1Qz5CyzZgqg4hkYpvbCJBSFJWu0P_QfZmSX3HA_Ji88O1HAu9nkwOocGv6UMjOb2BHqwbmRNsre4ERrmVGmBJ1-lIfbCDRqsGPJ4WQ/s1600/thrombin.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj1o757t7F06qUBYIyMuhM5GLo6TFYC78mJo0cSI1Qz5CyzZgqg4hkYpvbCJBSFJWu0P_QfZmSX3HA_Ji88O1HAu9nkwOocGv6UMjOb2BHqwbmRNsre4ERrmVGmBJ1-lIfbCDRqsGPJ4WQ/s320/thrombin.jpg" /></a>
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<i>The water channel of thrombin.</i>
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The importance of density fluctuations at the interface in nanoscale (as opposed to atomic-scale) hydrophobic interactions driven by drying transitions has been asserted for some time now by David Chandler and his colleagues. Phillip Geissler and Suriyanarayanan Vaikuntanathan recently developed this idea by showing that the Lum-Chandler-Weeks drying-induced hydrophobic attraction needs to pay close attention to capillary waves (Phys. Rev. Lett. 112, 020603; 2014). Now they and their coworkers have put this theory to the test in a coarse-grained lattice model (S. Vaikuntanathan <i>et al., PNAS</i> <b>113</b>, E2224; 2016 – paper <a href="http://www.pnas.org/content/113/16/E2224.abstract">here</a>). Despite the relative simplicity of the model, it seems to capture very efficiently the nanoscale density fluctuations and their relevance for hydrophobic hydration in the case of a hydrophobic solute particle at the air-water interface and a pair of nanoscale hydrophobic plates. In both cases the “minimalistic” model agrees very well with detailed atomistic simulations, suggesting that it succeeds in modeling the basic physics of these situations. What seems striking here, I think, is how this long-problematic issue of hydrophobic hydration seems to be turning back towards the “old-style” basic physics of wetting and inhomogeneous fluids (compare, for example, R. Evans & M. C. Stewart, <i>J. Phys. Condens. Matt.</i> <b>27</b>, 194111; 2015; R. Evans & N. B. Wilding, <i>PRL</i> <b>115</b>, 016103; 2015).
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Another coarse-grained description of hydration is offered by Bill Jorgensen at Yale and colleagues (X. C. Yan <i>et al., JPCB</i> jpcb.6b00399; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.6b00399">here</a>). They use techniques I’m frankly not familiar with to couple a coarse-grained approach with all-atom solute models, and find that the resulting multiscale simulations compare acceptably with the all-atom case while achieving a 7-30-fold reduction in computational cost.
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And on the same track, Kenichiro Koga at Okayama and colleagues report a mean-field approximation for inhomogeneous liquids to study hydrophobic hydration, specifically the solvation of methane at the air-water interface (K. Abe <i>et al., JPCB</i> <b>120</b>, 2012; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b10169">here</a>). The approach here is to consider two steps in the solvation process: creation of the cavity for a hydrophobic solute, and insertion of the solute itself.
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Ions modify hydrophobic interactions in an ion-specific manner, familiar as Hofmeister effects. But to what extent do these influences depend on the arrangements and mobility of the ions? Izabela Szlufarska at the University of Wisconsin and colleagues examine that question using MD simulations of hydrophobic interactions between a nonpolar surface and nonpolar or amphiphilic nanorods mimicking β-peptides (K. Huang <i>et al., JPCB</i> <b>119</b>, 13152; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b05220">here</a>). They compare the cases of free ions in solution, and ionic groups tethered to the rods both randomly and in organized spatial arrangements (such as a row down one side). Free ions generally strengthen hydrophobic interactions according to the conventional ion-specific series, in a manner that is correlated with (and assumed to be due to) fluctuations in water density close to the surface. But these interactions can be switched on or off by different arrangements of the immobilized ions, and the ion-specific effects now don’t follow the usual Hofmeister ranking. The authors analyse the findings in a dynamical picture, concluding that “Our analysis of the structure and dynamics of water near the hydrophobic nanorod shows that dynamics is a better indicator of the specific ion effect than the static water structure.” Is this perhaps an emerging consensus for such situations?
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZ0WbgJUiYLkAfgMdTt6C7iyq0VAhwlE3HqZH4CF-cTYK3RPT_VFSBc9Q2uer0bkJitsXlg18RbZKkouJ_uEOAsdUqJb6t9lxIAbJrFq3-PDCkL_FyZZ5ieZSSS239bkgGB4gh0bJSsB8/s1600/nanorods.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhZ0WbgJUiYLkAfgMdTt6C7iyq0VAhwlE3HqZH4CF-cTYK3RPT_VFSBc9Q2uer0bkJitsXlg18RbZKkouJ_uEOAsdUqJb6t9lxIAbJrFq3-PDCkL_FyZZ5ieZSSS239bkgGB4gh0bJSsB8/s320/nanorods.jpg" /></a>
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<i>The nanorods studied by Huang et al.: cyan groups are nonpolar, yellow are immobilized ions.</i>
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Hydration water around intrinsically disordered proteins is more mobile than that around globular proteins, according to simulations by Pooja Rani and Parbati Biswas at the University of Delhi (<i>JPCB</i> <b>119</b>, 13262; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b07248">here</a>). They find that both the translational and rotational diffusion are relatively greater for IDPs. In an earlier study, they found that the residence times of hydration waters for IDPs are relatively long (<i>JPCB</i> <b>119</b>, 10858; 2015) – but that work doesn’t contradict this, they argue, because the enhanced mobility doesn’t actually help the water molecules leave the hydration layer.
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Water wires are essential for transporting protons through the pores of the chloride/proton exchanger ClC-ec1, a member of the CLC superfamily of proteins that exchange protons for halides and other anions across cell membranes. That process is elucidated in detail in simulations by Emad Tajkhorshid at UIUC and colleagues (T. Jiang <i>et al., JACS</i> <b>138</b>, 3066; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b12062">here</a>). They examine how the water wires formed in the presence of chloride bound in the central anion binding site differ from those in the presence of fluoride, nitrate and thiocyanate, giving the channel its anion specificity. For fluoride and nitrate there are only “pseudo water wires” separated by the intervening anion, which can’t sustain proton transport; for thiocyanate there are none at all.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhClG4OWdJBtp6868gY3sAhrRqVpOc6sIOTLQ0oWA2W0WlMOWAgcpVn2zkhvk6rCn25Y7A7p1gHZkzEYiOMf9SGT5_amJpKTl0Pfetyv5PTHpOfP-nstUCdsuBEs-Rl8KxBlzd4a6iIYzk/s1600/CLC_water_wires.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhClG4OWdJBtp6868gY3sAhrRqVpOc6sIOTLQ0oWA2W0WlMOWAgcpVn2zkhvk6rCn25Y7A7p1gHZkzEYiOMf9SGT5_amJpKTl0Pfetyv5PTHpOfP-nstUCdsuBEs-Rl8KxBlzd4a6iIYzk/s320/CLC_water_wires.jpg" /></a>
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<i>Water wires and their disruption/absence for various anions in the channel of the chloride/proton exchanger ClC-ec1.</i>
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Is the air-water interface acidic or basic? In other words, do hydrated excess protons or hydroxide ions have an affinity for the water surface? Simulations and experiments have sometimes seemed to give conflicting results, making this a point of controversy. Greg Voth, now at the University of Chicago, and his coworkers reported several years ago that simulations showed protons having an affinity for the interface. They now confirm this finding using state-of-the-art reactive molecular dynamics (Y.-L. S. Tse <i>et al., JACS</i> <b>137</b>, 12610; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b07232">here</a>). The (weak) preference of the hydrated proton of the water surface, they say, is enthalpically favoured and reduces the loss of hydrogen-bonding there. The hydroxide ion, meanwhile, is repelled from the interface, also for enthalpic reasons.
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Small peptides don’t sample all of the conformational space theoretically available to them. Brigita Urbanc and colleagues at Drexel University in Philadelphia wonder if hydration structure has something to do with this (D. Meral <i>et al., JPCB</i> <b>119</b>, 13237; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b06281">here</a>). Using MD simulations, they show that the so-called polyproline II-like (pPII) and β-strand conformations that are prominent for GXG peptides (with X a “guest” residue) have different hydration structures, the former being enthalpically stabilized and the latter entropically. In general the nature of backbone hydration in the pPII conformations is clathrate-like, and differs for different X depending on the residue’s ability to template this structure.
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It’s looking ever more as though water has an important, even pivotal role in the assembly of the β-amyloid aggregates implicated in neurodegenerative diseases. Nadine Schwierz at UC Berkeley and coworkers report that it drives the growth of these fibrils (N. Schwierz <i>et al., JACS</i> <b>138</b>, 527; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b08717">here</a>). Their simulations suggest that solvent entropy is the main driving force, and that assembly involves collective water motions. As two β strands lock together, motion of the intervening water is significantly retarded, and there is an entropic gain when this water is removed to create a dry binding interface.
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The hydrophobic interaction is still challenging to understand intuitively. That’s emphasized by a report by Lawrence Pratt at Tulane University and colleagues showing that, for argon-argon interactions in water, the “hydrophobic bond” is actually weakened by including solute attractive interactions (M. I. Chaudhari <i>et al., JPCB</i> <b>120</b>, 1864; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b09552">here</a>). They treat the situation using local mean field theory, and I think (but am not sure) that ultimately the reason for this result is that in effect the solute attractive interactions benefit solvation more than they do aggregation.
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Might water networks in a protein binding site be amenable to a thermodynamic treatment that considers them a kind of loose, composite ligand? That seems to be in essence what Gregory Ross at the University of Southampton and colleagues are attempting to enable (G. A. Ross <i>et al., JACS</i> <b>137</b>, 14930; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b07940">here</a>). They have modified the grand canonical MC simulation technique to allow efficient calculation of the binding energy of an entire hydrogen-bonded water network, as well as to estimate the individual water-molecule affinities and the degree of cooperativity between them. They propose that the method might allow the incorporation of water networks into rational drug design.
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How to handle long-ranged forces has, as John Weeks at Maryland and colleagues put it in a paper in PNAS (R. C. Remsing <i>et al., PNAS</i> <b>113</b>, 2819; 2016 – paper <a href="http://www.pnas.org/content/113/11/2819.abstract">here</a>), “plagued theory and simulation alike”. They offer a solution: a way to incorporate long-ranged interactions that uses only short-ranged potentials. They demonstrate it for the case of hydration of ionic and hydrophobic species. It relies on local molecular field theory, in which the interactions are accommodated by finding a simpler, single-particle “mimic system” that can furnish an effective field that takes care of averaged “far-field” interactions in the full system under study.
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Different types of antifreeze proteins have different mechanisms of action, according to Ilja Voets at the Eindhoven University of Technology and colleagues (L. L. C. Olijve <i>et al., PNAS</i> <b>113</b>, 3740; 2016 – paper <a href="http://www.pnas.org/content/113/14/3740.abstract">here</a>). They have measured both the thermal hysteresis and the ice recrystallization inhibition activity for a range of AFPs, and find no correlation between the two. Both of these properties have been considered to be features of antifreeze activity, which the researchers attribute to binding to different ice planes. They conclude that antifreeze activity is many-factored, and that applications and rational design of AFPs “requires a tailored optimization to the specific purpose.”
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More debate on the putative liquid-liquid transition in metastable water: Gyan Johari and José Teixeira argue that the thermodynamic arguments linking this transition to that between low- and high-density amorphous ice don’t stand up (<i>JPCB</i> <b>119</b>, 14210; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b06458">here</a>). They conclude that “The available data show that HDA is not a glass, and the presumed HDL and LDL are not normal liquids. If that is accepted, the HDL−LDL fluctuations view, the two-liquid model, and the virtual liquid−liquid phase transition would all be consequences of a false premise.” I look forward to the next round…
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Two quite different forms of metastable (quasi-)liquid water are reported by Gen Sazaki and colleagues at Hokkaido University. They have previously reported such phases on the surface of ice (Sazaki <i>et al., PNAS</i> <b>109</b>, 1052; 2012); one of the liquid phases wets the ice, the other doesn’t. Using advanced optical microscopy, they now show that these surface phases are kinetically, not thermodynamically, stable, and that they form not by the surface melting of ice but by the deposition of supersaturated water vapour on the ice surface (H. Asakawa <i>et al., PNAS</i> pnas.1521607113; 2016 – paper <a href="http://www.pnas.org/content/113/7/1749.abstract">here</a>).
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Julio Fernández continues his studies of “frustrated” water at the protein interface (dehydrons, which are topologically deprived of hydrogen-bonding opportunities) with a study of the acid-base chemistry of such water, using quantum-chemical calculations (<i>FEBS Lett.</i> <b>590</b>, 215; 2016 – paper <a href="http://onlinelibrary.wiley.com/doi/10.1002/1873-3468.12047/abstract">here</a>). He reports that water surrounding deydrons is proton-accepting, and enables a mechanism for directed Grotthuss transport of protons
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Tryptophan fluorescence has been widely used to study protein dynamics and hydration. Feng Gai and colleagues at the University of Pennsylvania report that a tryptophan analogue, 5-cyanotryptophan can be used in the same way but with greater sensitivity (B. N. Markiewicz <i>et al., JPCB</i> <b>120</b>, 936; 2016 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b12233">here</a>). They show that, among other things, the new probe molecule allows them to distinguish two differently hydrated environments in a folded protein (Trp-cage).
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Whether or not the result reported by Ruth Livingstone and colleagues at the MPI Mainz is relevant to water in biology isn’t clear, but it’s an interesting finding all the same. They use vibrational spectroscopy to look at water interacting with a monolayer of the detergent sodium dodecyl sulfate at the water surface, and see two distinct types of water present (R. Livingstone <i>et al., JACS</i> <b>137</b>, 14912; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b07845">here</a>). Close to the anionic head groups the waters have localized O-H stretches, but further below the monolayer there is a delocalized O-H mode. These two modes are coupled and can exchange energy. The question is obviously whether the same applies for lipid assemblies <i>in vivo</i>.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com18tag:blogger.com,1999:blog-7540687028464774748.post-60054528056859215222016-03-01T01:35:00.000-08:002016-03-01T01:35:44.308-08:00Why DNA hydration is different from that of proteinsWell, it seems that post-Christmas catching up now takes until March… Hopefully normal service hereafter.
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Why trehalose confers protection against urea-induced denaturation of proteins is investigated by Subrata Paul and Sandip Paul of the Indian Institute of Technology in Guwahati using MD simulations for a protein analogue (N-methyl acetamide, NMA) (<i>JPCB</i> <b>119</b>, 9820; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b01576">here</a>). They find that direct interactions are the key. NMA hydration water is displaced by hydrogen-bonded urea, but the addition of trehalose only modestly decreases the urea density close to the amide. Rather, trehalose molecules largely replace water molecules in the hydration shell (so that trehalose and urea bind to NMA simultaneously). For proteins this would reduce the ability of water to solvate exposed backbone in the denatured state.
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Another structure-stabilizing osmolyte, trimethylamine N-oxide (TMAO), is studied by Yuki Nagata of the MPI for Polymer Research in Mainz and colleagues (<i>JPCB</i> <b>119</b>, 10597; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b02579">here</a>). Their <i>ab initio</i> simulations look at the effect of TMAO on water reorientational dynamics, and show that these are retarded significantly close to the TMAO’s oxygen atom due to its hydrogen bonding with water – a result not seen using a simpler force-field model that represents the oxygen as a single point charge. Since TMAO is generally excluded from protein surfaces, its stabilizing influence seems in this case to be an indirect effect, for which the authors say this interaction with water seems likely to be important. These conclusions are supported by the work of Gerhard Schwaab and colleagues at Bochum, who have used THz/FIR and Raman spectroscopy to look at the solvation dynamics of TMAO (L. Knake <i>et al</i>., <i>JPCB</i> <b>119</b>, 13842; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b04152">here</a>). They too find strong hydrogen bonding between TMAO and water, which supports an indirect mechanism for its biological effects.
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How proteins denature in pure water as a result of low temperature or high/low pressure is still not entirely clear – in particular, are the mechanisms of these two processes essentially the same or distinct? That questions is addressed by Valentino Bianco and Giancarlo Franzese at the University of Barcelona using MC simulations of a coarse-grained protein model (represented as a self-avoiding hydrophobic or mixed hydrophobic/hydrophilic chain) with explicit water solvent (<i>Phys. Rev. Lett.</i> <b>115</b>, 108101; 2015 – paper <a href="http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.115.108101">here</a>). They argue that both denaturation processes involve a balance of free energies between hydration and bulk water. For cold denaturation, this balance favours the unfolded protein conformation for energetic reasons relating to the increasing stabilizing effect of water-water hydrogen bonds in the hydration shell. High-pressure denaturation, meanwhile, is driven by changes in local water density near the unfolded protein, giving a dominant PV contribution to the free-energy change of denaturation. And low-pressure denaturation is enthalpically driven, again by changes in the number of water-water hydrogen bonds in the hydration shell. In sum, the authors say, “For [all] these mechanisms is essential to take into account how the protein-water interactions affect the stability of the water-water HB and the water density in the hydration shell.”
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A strategy for attacking antibiotic resistant bacterial pathogens that has been afforded increasing attention recently involves disabling not the mechanisms by which they synthesize key cellular components but those that contribute to virulence. One such target is a dehydratase enzyme DHQ1, present in several typical “superbugs”. Concepción González-Bello at the University of Santiago de Compostella and coworkers describe an inhibitor containing an ammonium group that binds to DHQ1 without relying on the reactive epoxide functionality of previous such drug candidates (C. González-Bello <i>et al., JACS</i> <b>137</b>, 9333; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b04080">here</a>). It binds to and covalently modifies the enzyme’s active site thanks to hydrogen-bonding to a single water molecule, while a second conserved water molecule participates in the reaction that leads to covalent modification.
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Another water-assisted enzymatic mechanism is described by Ana-Nicoleta Bondar of the Free University of Berlin and colleagues. Using MD simulations, they look at the proton-transfer protein PsbO, a subunit of photosystem II, and find low-mobility water molecules close to its surface that form part of a water-carboxylate network that could facilitate proton transport (S. Lorch <i>et al., JPCB</i> <b>119</b>, 12172; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b06594">here</a>). Some of these waters might, they say, also assist the docking of PsbO into the PSII complex.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEheFkjOlY-lMQmkhyphenhyphenxChwvbh5XSqjIkV-z7oE6njlBgreOWZWKNVzdRC7iiHW14VUlr_5EvY3zau_-JDDDDdDgUpk3QkvEB3Q4ePtJrEJ_jTcEVsGxqtKrtq3gam-zubPr2PUdT7-6SCUg/s1600/water-carboxylate+network.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEheFkjOlY-lMQmkhyphenhyphenxChwvbh5XSqjIkV-z7oE6njlBgreOWZWKNVzdRC7iiHW14VUlr_5EvY3zau_-JDDDDdDgUpk3QkvEB3Q4ePtJrEJ_jTcEVsGxqtKrtq3gam-zubPr2PUdT7-6SCUg/s320/water-carboxylate+network.jpg" /></a>
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<i>The water-carboxylate network on the surface of the proton-transfer protein PsbO.</i>
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In contrast to the often slow dynamics of “functional water” at protein surfaces, Songi Han at UCSB and colleagues report anomalously fast water diffusion near DNA surfaces (J. M. Franck <i>et al., JACS</i> <b>137</b>, 12013; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b05813">here</a>). They use Oberhauser effect dynamic nuclear polarization (ODNP) to look at water translation dynamics along the backbone, which entails adding spin centres along a DNA backbone to act as “reporters”. Anomalously fast here means bulk-like, in contrast to the retarded diffusion of most of the hydration water, suggesting that the DNA-water interactions are only weak for a significant proportion of the hydration shell. Such water is relatively easily displaced when proteins bind to the DNA. Thus, in comparison to proteins, DNA would be capable of storing less free energy that can be released entropically in binding interactions – and, the authors argue, makes DNA duplexes less specific in their interactions (outside, of course, of the specificity supplied by the sequence itself). So “the high mobility of the solvation water around DNA may have been tailored to its role in biological function.”
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I had the pleasure of meeting Xiao Cheng Zeng of the University of Nebraska in Shanghai in November, and hearing about his interesting work on monolayer and bilayer ices. He and coworkers have recently explored the mechanism by which a preference for potassium over sodium ion transport arises in synthetic hydrophobic organic nanopores, namely the stacked macrocycles reported by Zhou <i>et al</i>. in <i>Nat. Commun.</i> <b>3</b>, 1-8 (2012), and compare them with carbon nanotubes (H. Li <i>et al., PNAS</i> <b>112</b>, 108512; 2015 – paper <a href="http://www.pnas.org/content/112/35/10851.abstract">here</a>). At face value the preferential K+ transport is surprising, given that K+ has the larger hydration sphere. But the researchers explain this selectivity (which is also seen in some biological ion channels) in terms of the greater robustness and structure of the Na+ hydration shell. Moreover, the roughness of the interior surface of the organic nanopores lowers the diffusivity of both ions – but more so sodium – relative to smooth-sided carbon nanotubes, with the result that the CNTs offer the highest rate of selective K+ transportation.
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Jianzhong Wu at the University of California at Riverside use a combination of thermodynamic measurements (Henry’s constants) and MD simulations to examine how the degree of hydrogen bonding among water molecules changes in hydrophobic hydration shells (J. Kim <i>et al., JPCB</i> <b>119</b>, 12108; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Facs.jpcb.5b05281">here</a>). They find that the extent of H-bonding is slightly reduced, and that this is a significant factor in the positive hydrophobic hydration heat capacity. Certainly nothing ice- or clathrate-like here.
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How do we assess the hydrophobicity of heterogeneous surfaces, composed of a mixture of hydrophobic and hydrophilic patches? Well, it’s complicated. Damián Scherlis at the University of Buenos Aires and colleagues find in simulations with coarse-grained mW water that there is a rather complex variation of water-droplet contact angle on such surfaces with the amount, distribution and arrangement of hydrophilic (hydrogen-bonding) domains on a hydrophobic surface (M. H. Factorovich <i>et al., JACS</i> <b>137</b>, 10618; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjacs.5b05242">here</a>). In this case, there may be a nonlinear variation of contact angle with composition, the angle being largest for a particular fraction of hydrophobic species (about 0.6 when randomly mixed). In other words, this mixture can have a larger contact angle than the purely hydrophobic surface. What’s more, this variation depends on the size of the domains: the nonlinearity tends to vanish for hydrophilic domains bigger than about 2 nm, when the behaviour returns to being reasonably well described by the Cassie model. The same conclusions are supported by looking at the desorption pressure of water in nanopores of these compositions. This appears to offer considerable scope for tuning the wettability of surfaces.
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And I have just discovered that a paper to which I contributed in a very small way, on the notion of chaotropicity as a way of understanding the limiting tolerances of biofuel-producing microorganisms, was published at the end of last year (J. A. Cray <i>et al., Curr. Opin. Biotechnol.</i> <b>33</b>, 228; 2015 – paper <a href="http://www.sciencedirect.com/science/article/pii/S0958166915000294">here</a>). My coauthors are to be credited with everything of real substance in this interesting and potentially useful article.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com47tag:blogger.com,1999:blog-7540687028464774748.post-10941844657164266892015-10-07T06:51:00.000-07:002015-10-07T06:51:48.500-07:00What do you mean, water structure?Ah, water structure. What do we mean by it? How do we measure it? Elise Duboué-Dijon and Damien Laage revisit this old question with a close look at how various popular order parameters fare in describing the hydration shell of a hydrophobic solute in MD simulations (<i>JPCB</i> <b>119</b>, 8406; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b02936">here</a>). The tetrahedrality, local density, Voronoi cell shape and others are considered, and the correlations between them are in general not terribly strong: they are each tending to measure different things. But in any event, the perturbations around the small hydrophobic solute are rather small relative to the bulk: there is nothing iceberg-like here, nor is there any sign of significant heterogeneity. I think it would be fair to say that, rather than implying that water structure is best defined as “X”, we should conclude that “water structure” is an ill-defined concept. The authors also conclude that angular distortions offer the best measure of fluctuations in water reorientation dynamics.
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I sense a meaty story in this one. Nascent membrane proteins emerging from the ribosome are assembled and integrated into the cell membrane with the aid of the translocon, a channel-like complex of proteins within the membrane. This complex has an hourglass shape and is filled with water, and the insertion of membrane proteins here has been considered as a simple process of hydrophobic partitioning. But it’s not so simple, according to Stephen White at the University of California at Irvine and colleagues (S. Capponi <i>et al., PNAS</i> <b>112</b>, 9016; 2015 – paper <a href="http://www.pnas.org/content/112/29/9016.abstract">here</a>). They have performed MD simulations of the bacterial SecY translocon complex, and find that the water inside is very different from the bulk phase, having retarded rotational dynamics and aligned dipoles: in other words, it is decidedly “anomalous water”, suggesting that the translocon can’t simply be regarded as a protein-conducting pore. So any hydrophobic partitioning is likely to be more subtle than has been supposed, and we need to consider some degree of functional modification of the water properties: as the authors put it, “what is the partitioning free energy of solutes between water in bulk and water in restraining confined spaces?”
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“If life can be considered as a massive self-assembly process, water seems to be a major driving force behind it.” There’s a nice way to begin a paper, and it’s how Vrushali Hande and Suman Chakrabarty of the CSIR National Chemical Laboratory in Pune start their simulation study of water ordering around hydrophobic polymers (<i>JPCB</i> <b>119</b>, 11346; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b03449">here</a>). They investigate specifically the notion introduced by Chandler and coworkers of a qualitative change in hydration at a length scale of around 1 nm. This depends, the authors say, on the conformation of the polymer. When it is extended, the tetrahedral ordering of the hydration shell is more or less insensitive to polymer chain length, because of the sub-nanometre scale of hydrogen bonding around the polymer chain. But in a collapsed conformation it’s a different story, with the hydration waters then dynamically coupled to fluctuations of the polymer. All the same, tetrahedral ordering doesn’t provide a strong signature of any order-disorder transition in the hydration layer, at least until chain lengths of around C40. But the authors say that this collapse itself is linked to fluctuations in the solvent in the manner discussed by Chandler <i>et al</i>., which can induce local dewetting.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYjBBLcUgqYHl5GgKZaHQQv7C8gupw9ikuFel17IqI8_RKAplrLSHzFNOl1O6yU4z0EXr9ehn2M6YxQ8q9Txk_Z_1ynyq3m0syMfWF_RawGQ7kKuAJA-AOszkLD3XwiSBxbek4Vx6pPDc/s1600/polymer+collapse.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhYjBBLcUgqYHl5GgKZaHQQv7C8gupw9ikuFel17IqI8_RKAplrLSHzFNOl1O6yU4z0EXr9ehn2M6YxQ8q9Txk_Z_1ynyq3m0syMfWF_RawGQ7kKuAJA-AOszkLD3XwiSBxbek4Vx6pPDc/s320/polymer+collapse.jpg" /></a>
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<i>The open and collapsed states of hydrophobic polymers in water, studied by Hande and Chakrabarty.</i>
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What is the state of water close to hydrophilic surfaces? There have been several experimental suggestions that this “interfacial water” has, over a nanoscale thickness, a viscosity several orders of magnitude greater than the bulk (e.g. Jinesh <i>et al., Phys. Rev. Lett.</i> <b>96</b>, 166103; 2006). Andrei Sommer at Ulm and colleagues have recently argued that this interfacial water can be modified by irradiation with near-IR laser light (A. P. Sommer <i>et al., Sci Rep.</i> <b>5</b>, 12029; 2015 – paper <a href="http://www.nature.com/articles/srep12029">here</a>). They now suggest that the gradient in viscosity that this would imply might explain why and how the rate of ATP synthesis changes in response to both reactive oxygen species and such irradiation. If ROS increase the hydrophilicity of the membrane in which the ATP synthase is embedded, they say, then this will increase the viscosity further and degrade the efficiency of this rotary device. By the same token, IR light decreases the viscosity and has a contrary effect on ATP synthesis. Note that the argument is only indirectly supported by the experiments described here, which are concerned only with measuring changes in the nanoindentation force for a diamond tip penetrating a water-coated hydrophilic metal surface due to laser irradiation, and interpreting them in terms of viscosity changes in the water film.
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The controversy around water’s putative liquid-liquid phase continues. There have already been responses to David Limmer and David Chandler’s suggestion that the metastable LL transition reported in previous theoretical work is just an unequilibrated state that would eventually convert to ice (<i>JCP</i> <b>135</b>, 134503; 2011 and <b>138</b>, 214504; 2013). But now in a <a href="http://www.arxiv.org/abs/1505.06432">preprint</a>, Frank Smallenburg and Francesco Sciortino say that, by modifying the bond flexibility of ST2 water, they can continuously tune the LL critical point until it moves into a regime where the liquid is more stable than ice – thereby, they say, negating any kinetic arguments for why this critical point is a phantom of the simulation technique
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The degree of covalency of the hydrogen bond in water has been much debated. Thomas Kuhne at Paderborn and colleagues propose that this can be quantified by measuring components of the magnetic shielding tensor of the water hydrogens in NMR (H. Elgabarty <i>et al., Nat. Commun</i>. <b>6</b>, 8318; 2015 – paper <a href="http://www.nature.com/ncomms/2015/150915/ncomms9318/full/ncomms9318.html">here</a>). They define covalency as the amount of electron density transferred between hydrogen-bonded molecules and the associated stabilization energy, which they calculate in <i>ab initio</i> simulations to be, respectively, around 10 milli-electrons and 15 kJ/mol. They describe a calibration of the relationship between these quantities and the hydrogen magnetic shielding tensor that would enable their experimental determination.
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The exchange of amide hydrogens in proteins with water can be used as a measure of protein structuring, flexibility, dynamics, and solvent exposure. But the mechanism by which it happens hasn’t been clear. Filip Persson and Bertil Halle show how even deeply buried parts of the polypeptide chain may become briefly exposed to water by conformational fluctuations (<i>PNAS</i> <b>112</b>, 10383; 2015 – paper <a href="http://www.pnas.org/content/112/33/10383.abstract">here</a>). Their simulations of the bovine pancreatic trypsin inhibitor are long enough to identify the elusive “open” state by which proton exchange happens: a state, they propose, that requires the N-H hydrogen to be within 2.6 Å of at least two water molecules, and not involved in any intramolecular hydrogen-bonding. As well as the donor water molecule, the second water molecule is needed to solvate and stabilize the transient imidate ion formed after proton extraction from N-H, before it acquires a replacement proton from this second molecule. This “open” state exists for around 100 ps on average in all the amide groups studied here.
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Bertil continues to probe conformational dynamics in an NMR study with Shuji Kaieda of water displacement within the cavity of a lipid binding protein (<i>JPCB</i> <b>119</b>, 7957; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b03214">here</a>). Conformational changes act to gate this water release, with fluctuations in a critical part of the protein determining the rate of passage of some highly ordered internal waters. The latter fall into three dynamical classes, with distinct survival times of the order of 1 ns (most of the waters are of this type), 100 ns and 6 μs.
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Functionally relevant conformational fluctuations are also studied in a preprint sent to me by Tomotaka Oroguchi and Masayoshi Nakasako of Keio University. Their MD simulations suggest that the functional motions of an enzyme (glutamate dehydrogenase) are dominated by nanoscale wetting/drying transitions of a small number of hydration water molecules in a hydrophobic pocket (HS1) of the active site, along with stepwise association and dissociation of water clusters in a cylindrical hydrophilic crevice (HS2). The interpretation of behaviour at the hydrophobic site is supported by measurements of the catalytic rate of a mutant in which this hydrophobicity is lower. The combination of changing hydration states at the two sites makes the enzyme act as something of a hydraulic machine. This offers a nice illustration of how the vague idea of water-lubricated conformational flexibility in proteins can be united with more precise notions of nanoscale wetting and dehydration transitions.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHf0xD0PPpmWFZJlJgLSDlksIdqqjGNHTJOKAOTrraRLNAM0dNcFjUy5luUy0aZhoRd778tfI3dTKn_aTN7584OW4sUGaXHVBG71OzVnJJF3sKNeOclMve2goN8bSre3W73I4RcO2jKPE/s1600/GDH_wetting.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhHf0xD0PPpmWFZJlJgLSDlksIdqqjGNHTJOKAOTrraRLNAM0dNcFjUy5luUy0aZhoRd778tfI3dTKn_aTN7584OW4sUGaXHVBG71OzVnJJF3sKNeOclMve2goN8bSre3W73I4RcO2jKPE/s320/GDH_wetting.jpg" /></a>
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<i>Snapshots of different wetting states for the hydrpphobic pocket HS1 of glutamate dehydrogenase, along with a heat map relating solvent occupancy of this cleft (Q) to the separation of the “jaws” (d).</i>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDkLWqbhwgWnsXKvj-rmBPFB8btjxGLceLYVw_M-KFhrLhNRoXhrqgGCT2wNs6TKfP5VcF1V00VRSmZcLn_GNrbd67vnJb4h6P38SDhbC52mYU9z3uIxbhn5pBNKNKDKoVSesy90oPbtk/s1600/GDH_machine.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgDkLWqbhwgWnsXKvj-rmBPFB8btjxGLceLYVw_M-KFhrLhNRoXhrqgGCT2wNs6TKfP5VcF1V00VRSmZcLn_GNrbd67vnJb4h6P38SDhbC52mYU9z3uIxbhn5pBNKNKDKoVSesy90oPbtk/s320/GDH_machine.jpg" /></a>
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<i>The “GDH machine”, driven by changes in hydration states in the hydrophobic (HS1) and hydrophilic (HS2) sites.</i>
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Ion channel selectivity is largely determined by electrostatic interactions with charged residues in the channel. But Vicente Aguilella and colleagues at the Universitat Jaume I in Castellón present calculations and simulations which challenge the idea that only solvent-accessible residues near the ion permeation pathway matter (E. García-Giménez <i>et al. JPCB</i> <b>119</b>, 8475; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b03547">here</a>). Looking in particular at bacterial porin OmpF, they say that many other charged residues, including buried ones, may affect the pore selectivity and that the dielectric properties of the protein therefore matter.
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How does trehalose protect proteins from urea-induced denaturation? Subrata Paul and Sandip Paul at the Indian Institute of Technology in Assam explore that question via MD simulations of the hydration of the simple protein model N-methylacetamide (<i>JPCB</i> <b>119</b>, 9820; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b01576">here</a>). They find that trehalose displaces urea from the vicinity of the amide, and that amide-water hydrogen bonds are replaced by amide-trehalose H-bonds; thus trehalose will reduce the propensity of water to H-bond with a protein backbone, which would otherwise stabilize the denatured state. The results also largely support the notion that urea denaturation occurs via direct interactions rather than indirect effects on “water structure”.
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Here is another introductory remark that encapsulates an issue rather splendidly: “If proteins had evolved to fold in a vacuum, thermodynamic experiments in the laboratory could have been straightforwardly interpreted by statistical energy landscape theory, just as model computer simulations with implicit solvent have been. Instead, the intimate involvement of the aqueous environment in the folding process made the uncovering of the principles of the energy landscape theory of protein folding a convoluted process.” This comes from a paper by Peyer Wolynes and colleagues (B. J. Sirovetz <i>et al., JPCB</i> <b>119</b>, 11416; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b03828">here</a>) in which a new model of protein folding (the associative memory, water mediated, structure and energy model, AWSEM) is used to map out the folding diagram for two proteins and explore hot, cold and pressure-induced denaturation. This model uses a coarse-grained force field that, among other things, captures water-mediated interactions. Using ubiquitin and λ-repressor as the test cases, the work shows that the model can supply a unified description of all of these cases that captures the key features of experimental measurements.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWSdzIrzkH4rhIy_CXOR4M6931XMjqkeGjqDvfYKfd3UlH9N5k2tIyM73Zj43zmB95zf5ntPS9ty5EcXHp9kDipcjjk8-3y3h3hbfp3Xrnj58YfTiN6IAP9T9ZD5mgnKD5qSPMe1O6tzA/s1600/ubiquitin_denatured.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhWSdzIrzkH4rhIy_CXOR4M6931XMjqkeGjqDvfYKfd3UlH9N5k2tIyM73Zj43zmB95zf5ntPS9ty5EcXHp9kDipcjjk8-3y3h3hbfp3Xrnj58YfTiN6IAP9T9ZD5mgnKD5qSPMe1O6tzA/s320/ubiquitin_denatured.jpg" /></a>
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<i>Representative structures of uniquitin in the native and denatured states in the AWSEM.</i>
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An interesting model system for studying water wires is described by Mihail Barboiu of the European Institute of Membranes in Montpellier (M. Barboiu <i>et al., JPCB</i> <b>119</b>, 8707; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b03322">here</a>). They look at self-assembled structures of a synthetic bola-amphiphile, which contain transverse pores that are hydrophilic, chiral and can contain helical water wires in which the waters are strongly orientationally ordered. Cations can permeate along these channels, offering a simple analogue of ion conduction through biomolecular water channels (for example, in gramicidin A). The authors say that selectivity of ion transport here is dominated by a subtle balance between the hydration and complexation energies of the ions.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijrqtV0kjyIuTm8hGtrAfiRzgL-2rknGRFFmnHBZoeCZbarwmocNFnEx8n6ZRvpPpnlV9bxPBont8VNLfW6O87utJnOepgCsZNe1eANSPGKY8jU-Eu5nr_3LzoLJA2rlGDV66XN245S8k/s1600/chiral+water+channels.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijrqtV0kjyIuTm8hGtrAfiRzgL-2rknGRFFmnHBZoeCZbarwmocNFnEx8n6ZRvpPpnlV9bxPBont8VNLfW6O87utJnOepgCsZNe1eANSPGKY8jU-Eu5nr_3LzoLJA2rlGDV66XN245S8k/s320/chiral+water+channels.jpg" /></a>
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<i>Looking down the chiral water channels in crystals of a bola-amphiphile.</i>
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In somewhat related territory, Manish Kumar at Penn State University and colleagues describe a new class of artificial water channels that self-assemble into membrane-like structures (Y.-X. Shen <i>et al., PNAS</i> <b>112</b>, 9810; 2015 – paper <a href="http://www.pnas.org/content/112/32/9810.abstract">here</a>). They call them peptide-appended pillar[5]arenes, which have a linked arene belt in the middle and short peptides extending above and below it, making a tubular structure. These molecules have been investigated before (summarized in Cragg & Sharma, <i>Chem. Soc. Rev.</i> <b>41</b>, 597; 2012), but those described here are more hydrophobic and will insert at rather high concentration into lipid membranes, making the membrane water-permeable (3.5x10^8 water molecules per s, comparable to aquaporins). Simulations suggest that the channels seem to fluctuate between filled and empty states of water in a wetting/dewetting transition.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOmJX632WH5aZB3ninmjvILbOJ9YFzMNBRYhR2B6kwA1YaAqeO9csIfkonNUNM3dg89t5puE9BRIUyieCai38RN0uRQg7LtZ_81e_B8pPAkdvdzYI0RRgYNahkx9dgDN8qW-IgZXgoSvU/s1600/pillararenes.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgOmJX632WH5aZB3ninmjvILbOJ9YFzMNBRYhR2B6kwA1YaAqeO9csIfkonNUNM3dg89t5puE9BRIUyieCai38RN0uRQg7LtZ_81e_B8pPAkdvdzYI0RRgYNahkx9dgDN8qW-IgZXgoSvU/s320/pillararenes.jpg" /></a>
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<i>Pillar[5]arenes (A and B), and their insertion into a lipid membrane (C). D shows the water permeability.</i>
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Something quite different from my colleague John Hallsworth at Queen’s in Belfast and his coworkers, who ask “Is there a common water-activity limit for the three domains of life?” (A. Stevenson <i>et al., Int. Soc. Microbial Ecol. J.</i> <b>9</b>, 1333; 2015 – paper <a href="http://www.nature.com/ismej/journal/v9/n6/full/ismej2014219a.html">here</a>). They report that halophilic Archaea and Bacteria, and some xerophilic fungi, can all sustain viability at water activities as low as about 0.61.Could this point to a common physicochemical/thermodynamic origin for such a limiting value? If so, could there be astrobiological implications? (A good time to be thinking about that!)
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Another unusual kind of contribution with prebiotic resonances comes from Atul Parikh of Nanyang Technological University in Singapore and coworkers, who report that giant vesicles filled with sugar solution and subjected to osmotic stress in a bath of lower sugar concentration may undergo damped cycles of expansion and contraction, accompanied by temporary rupture of the vesicle walls (K. Oglecka <i>et al., eLife</i> <b>3</b>, e03695; 2014 – paper <a href="http://elifesciences.org/content/3/e03695">here</a>). In the expanded phase, the vesicles are patchy, due to phase separation of cholesterol and phospholipids in the walls; in the contracted phase they are uniform. The researchers say that this might have offered a useful, even adaptive, response to the microenvironment for early protocells. There’s a nice phys.org story on the work <a href="http://phys.org/news/2014-10-emergent-behavior-environment.html">here</a>.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com13tag:blogger.com,1999:blog-7540687028464774748.post-24262956929339043782015-07-24T08:35:00.000-07:002015-07-24T08:35:24.495-07:00Goodbye to "biological water" (hello water in biology)Surely an essential read for any reader of this blog is a commentary by Pavel Jungwirth in <i>JPC Lett.</i> (<b>6</b>, 2449; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b01143">here</a>) called “Biological water or rather water in biology?” (which I only just realize now I can decide to interpret as an homage to this site – you can see which of these alternatives I prefer!). Pavel expresses the issue perfectly, saying that his piece has two main messages:
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“The first one, addressed to biologists and biochemists, who tend to focus their attention primarily to the biomolecules, is that water does matter.”
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“The second and arguably more important message is addressed to our community of physical chemists:… Although water… plays a key role in establishing the homeostasis, it is primarily the biomolecule itself which carries the biological function… As physical chemists who naturally tend to understand water better than biomolecules, we may sometimes have a tendency to overemphasize the role of the former at the expense of the latter.”
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In particular, Pavel suggests that the term “biological water” be dropped. He is quite right that this kind of terminology risks becoming a <i>deus ex machina</i>, if not indeed a kind of “vital force”, and I’d be happy never to see it again. This also gives me an opportunity to say explicitly that, while this blog aims to focus on all the important, often under-valued and occasionally amazing things that water does in the cell, there should be no doubt that proteins, DNA, lipids and carbohydrates are still the main players.
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I mentioned in an earlier post a study by Bob Evans at Bristol a study suggesting an explanation for the enhanced density fluctuations in water near a hydrophobic surface that David Chandler, Shekhar Garde and others have advanced as the driving force behind dewetting transitions. Bob and his coauthor Nigel Wilding at Bath have now published this paper (<i>Phys. Rev. Lett.</i> <b>115</b>, 016103; 2015 – paper <a href="http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.115.016103">here</a>). They argue that the fluctuations can be regarded as a divergence in the local compressibility associated with the approach to a critical (continuous) drying transition. Frankly, it seems rather splendid to have this phenomenon rooted in a general and well understood physical effect – and moreover one that is not at all specific to water or hydrogen-bonding networks.
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This seems to bear directly on what Rick Remsing, Amish Patel, Shekhar and others say in their latest paper on “pathways to dewetting” (R. C. Remsing <i>et al., PNAS </i><b>112</b>, 8181; 2015 – paper <a href="http://www.pnas.org/content/112/27/8181.abstract">here</a>). Their MD simulations of water confined in the nanospace between two square hydrophobic plates confirm that it undergoes enhanced density fluctuations that can nucleate a vapour tube connecting the plates of a radius greater than the critical radius needed for spontaneous growth to a dry state, according to standard nucleation theory. This means that the free-energy barrier to dewetting is lower than standard macroscopic theory would predict. That’s very striking and illuminating, but still doesn’t obviously say in itself where those enhanced fluctuations come from – which is what Bob’s paper seems to address. You should talk to each other, chaps! – it seems as though there could even be the prospect of tying this story together once and for all.
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Suzanne Zoë Fisher at Los Alamos National Laboratory and colleagues have used neutron scattering and NMR to characterize the details of the proton transfer system in human carbonic anhydrase, in which a water network linked to hydrophilic residues plays a key role (R. Michalczyk <i>et al., PNAS</i> <b>112</b>, 5673; 2015 – paper <a href="http://www.pnas.org/content/112/18/5673.abstract">here</a>). It’s a nice, thorough study which shows how the environment lowers the pKa of the Tyr7 residue bound to the water molecules.
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More water wires in a first-principles simulation study by Daniel Sebastiani at the University of Halle-Wittenberg and colleagues – but this time looking at their transient formation in pure water itself (G. Bekçioglu <i>et al., JPCB</i> <b>119</b>, 4053; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp5121417">here</a>). In their calculations they use hydroquinoline as a fluorescent probe to study proton transfer along the wires, and find that wires of up to six or seven water molecules, reaching 1.5 nm or so, may persist for up to a few picoseconds. These might facilitate proton transfer (here between donor and acceptor sites on the probe molecule) by a stepwise mechanism.
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Samir Kumar Pal at the Bose National Centre for Basic Sciences in Kolkata and colleagues report a nice model system for studying the dynamical coupling between a macromolecule and its hydration sphere (S. Choudhury <i>et al., JPCB</i> 10.1021/jp511899q – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp511899q">here</a>). They have used micelles with different degrees of packing rigidity as model macromolecules, and use FRET, polarization-gated fluorescence anisotropy and quasielastic neutron scattering to look at the dynamics of the micelles and their hydration shells. There is slower water motion around the less flexible micelles, consistent with the standard “slaving” picture of dynamical coupling.
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Some water of course may penetrate into amphiphile assemblies of this sort. It’s known that cholesterol reduces the permeability of lipid membranes to water, but it’s not clear why. Bilkiss Issack and Gilles Peslherbe at Concordia University in Montreal have studied the question with MD simulations (<i>JPCB</i> <b>119</b>, 9391; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp510497r">here</a>). The results imply that this is a thermodynamic and not a kinetic effect – water diffusion doesn’t vary much with cholesterol concentration, but the free-energy barrier to water penetration through a bilayer does increase with concentration, probably because cholesterol increases the hydrophobicity of the core region.
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Pooja Rani and Parbati Biswas at the University of Delhi say that intrinsically disordered proteins have a larger binding capacity for water than do globular proteins (<i>JPCB</i> 10.1021/jp511961c – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp511961c">here</a>). What’s more, their MD simulations show more tetrahedral ordering, and slower dynamics, of water around disordered protein segments. In a loose sense this seems consistent with the different water dynamics around IDPs observed by Martin Weik and colleagues using neutron scattering – which they see as a difference in degree rather than in kind.
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But modelling IDPs accurately using MD requires better water models, according to Stefano Piana of D. E. Shaw Research in New York and colleagues (<i>JPCB</i> <b>119</b>, 5113; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp508971m">here</a>). They say that most simulations produce IDP conformations that are too compact, but that they can do better using a new water potential called TIP4P-D, which includes a better representation of the dispersion forces between water molecules. There’s more optimization still to be done, but it’s presumably possible that such improvements aren’t unique to IDPs, even if they are particularly sensitive to them.
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Not unrelated is a study by Yuichi Ogawa and colleagues at Kyoto University of the coil-to-globule transition of a “model peptide”, poly(N-isopropylacrylamide) (K. Shiraga <i>et al., JPCB</i> <b>119</b>, 5576; 2015 – paper <a href="http://pubs.acs.org/doi/full/10.1021/acs.jpcb.5b01021">here</a>). They follow changes in the hydration state of the polymer during this conformational switch using attenuated total reflection spectroscopy, which is a new one on me but apparently probes changes in the dielectric response in the terahertz region, providing information about the hydrogen-bond network. The transition to globule form corresponds with a reduction in the average hydration number of each monomer from around 10 to about 6.5, and it seems that these changes happen mostly in hydrophobic regions of the polymer. The authors interpret these changes as (I don’t entirely follow the reasoning) changes not so much in the hydration state of the polymer as in the structure of the hydrogen-bond network, and so speculate that the conformational change involves not just alterations to polymer-water interactions but also water-water interactions.
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Time-dependent fluorescence Stokes shifts (TDFSS) are becoming a useful tool to look at water and protein dynamics, the usual approach being to measure the decay of tryptophan fluorescence as a probe of local dynamics. Jay Knutson at NIH and colleagues have used this method to look at relaxation processes in the protein monellin and their coupling to the solvent (J. Xu <i>et al., JPCB</i> <b>119</b>, 4230; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jpcb.5b01651">here</a>). They distinguish two emission processes, which they call genuine and pseudo-TDFSS, and show how to separate them; only the former tells us about the coupling of water and protein dipoles.
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One aspect of water’s cell behaviour that is less often discussed is hydrodynamics, which must evidently become important at the mesoscale. Of course, that’s the scale which is very hard to model – but here fluid motions are likely to influence things like protein relaxation and crowding. Fabio Sterpone at the Université Paris Diderot and colleagues present a coarse-grained protein model called OPEP that enables this when combined with a Lattice Boltzmann approach to the fluid kinetics (F. Sterpone <i>et al., J. Chem. Theor. Comput.</i> <b>11</b>, 1843; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fct501015h">here</a>). They demonstrate its use to look at, e.g. protein transport properties, amyloid aggregation and crowding.
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A new approach to modeling water is presented by Vlad Sokhan of the National Physical Laboratory in England and colleagues (V. P. Sokhan <i>et al., PNAS</i> <b>112</b>, 6341; 2015 – paper <a href="http://www.pnas.org/content/112/20/6341.abstract">here</a>). They say that they can incorporate many-body effects into a coarse-grained parametrization of the electronic structure, which, along with fairly standard point charges and short-range pair potentials, allows accurate prediction of all the bulk behaviour, from liquid-gas coexistence to criticality, freezing and the temperature of maximum density. It’s apparently relatively easy to implement, and they hope to use it to look at effects such as hydrophobic hydration and drying and water’s role in protein association.
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More to follow rather soon, I hope.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com13tag:blogger.com,1999:blog-7540687028464774748.post-27534891629127461822015-04-13T15:55:00.000-07:002015-04-13T15:55:08.097-07:00Hydrophobic or just solvophobic?As I mentioned in the previous post, the notion of a dewetting transtion – in effect, capillary condensation driven by enhanced density fluctuations – that drives hydrophobic attraction has yet to be fully integrated with the question of whether this is a generic solvophobic effect or something specific to water’s hydrogen-bonded network. David Chandler’s picture of a dewetting transition occurring between extended hydrophobic surfaces for a lateral size scale of around 1 nm or more has tended to focus on the impossibility of maintaining the integrity of the H-bonded network in this geometry. But it may be that the density depletion and enhanced fluctuations on which this picture is predicated are more general features of solvophobicity. Rick Remsing and John Weeks at the University of Maryland speak to this question in a preprint that aims to dissect this hydrophobic interaction into components related to hydrogen bonding and to longer-ranged dispersion and electrostatic forces between the solvent molecules (<a href="http://www.arxiv.org/abs/1502.05220">http://www.arxiv.org/abs/1502.05220</a>). Their conclusions are so nicely summarized in the paper that I can’t do better by paraphrasing them:
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“We employ short ranged variants of the SPC/E water model to show that small scale solvation and association in water is governed by the energetics of the hydrogen bond network alone. However when the solute is large and the hydrogen bond network is broken at the hydrophobic interface, water behaves in a manner qualitatively similar to a simple fluid, with unbalanced LJ attractions dominating the solvation behavior.”
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For example, without LJ attractions in the solvent, there is no dewetting-induced hydrophobic attraction of two fullerene molecules. (This implies that the crossover between “small” and “large” solutes lies somewhere between the sizes of methane and C60.) In other words, dewetting here is nothing other than regular (albeit barrier-less) capillary evaporation of a solvent, and not a “water effect” at all. Which, if it’s right, means that we might want to think about speaking of a “hydrophobic interaction” at small scales but a “solvophobic interaction” at large scales. But I’d like also to know how this fits with Ronen Zangi’s study indicating that there’s actually a repulsion between fullerenes in water, mentioned in an <a href="http://waterinbiology.blogspot.nl/2014/11/hydrophobic-or-not.html">earlier post</a>. In other words, how potential-dependent is all this?
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They’ve been busy. In another contribution, Remsing and Weeks add another variant to the many efforts to develop hydrophobicity scales for biomolecules. This one is based on electrostatics, which has the advantage of being able to predict water-mediated hydrophilic interactions as well as hydrophobic ones (<i>JPCB</i> jp509903n; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp509903n">here</a>). They begin with a nice description of efforts so far, making the fundamental distinction between “surface-based” methods which aim to use the biomolecular surface properties alone, and “water-based” methods in which the effects of surface topography and neighbouring chemical functionality on the hydrogen-bond network of the local hydration sphere are taken into account. Their new method calls into the latter category, but is computationally inexpensive as it aims to characterize the long-wavelength collective electrostatic response of the water to the surface in question. Not only does this distinguish between hydrophilic and hydrophobic surfaces, but it accounts for different types of hydrophilic surfaces, e.g. those the polarize the water molecules in different orientations. This allows them to identify situations where the approach of two hydrophilic surfaces might induce a water-mediated interaction because of the commensurate polarization of the water network.
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That water penentrates into carbon nanotubes, despite its hydrophobic nature, has been confirmed both in simulations and in experiments. In a preprint (<a href="http://arxiv.org/abs/1501.0608">http://arxiv.org/abs/1501.0608</a>), Hemant Kumar and colleagues at the Indian Institute of Science in Bangalore ask whether this is driven by entropy or energy. Previous studies have given conflicting answers, but on the basis of MD simulations using the two-phase thermodynamic method Kumar et al. conclude that both energy (the carbon-oxygen LJ interaction) and entropy (for low occupancy, at least) support the filling process. This seems consistent with the findings of J. P. Huang at Fudan University in Shanghai and colleagues that water flows several times faster through non-straight (zigzag) carbon nanotubes than through straight ones, owing to the greater LJ interactions in kinked channels (T. Qiu <i>et al., JPCB</i> <b>119</b>, 1496; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp511262w">here</a>).
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhli0n7c9-owH_wlUR-s8CVBNULlSIAcKT9db5bTVk8_mMlQCJOekkpHwcdz_bSeNwkGlnndbnOJKxKzXwZY6TirHFgRqmcIi2Onat8fy8C0pfUDRn_7p7pTqQkq83v-u_ZzihhlIHEjz4/s1600/kinked_nanotube.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhli0n7c9-owH_wlUR-s8CVBNULlSIAcKT9db5bTVk8_mMlQCJOekkpHwcdz_bSeNwkGlnndbnOJKxKzXwZY6TirHFgRqmcIi2Onat8fy8C0pfUDRn_7p7pTqQkq83v-u_ZzihhlIHEjz4/s320/kinked_nanotube.jpg" /></a>
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When a solute particle is excited (electronically, vibrationally, rotationally), how does the (water) solvent relax to the perturbation? Rossend Rey at the Polytechnic University of Catalonia and James Hynes at Colorado have examined this question using linear response theory, and conclude that most of the absorbed energy is transferred to hindered rotations (librations) of the water molecules – and that mostly in the first hydration shell (<i>JPCB</i> jp5113922; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp5113922">here</a>).
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The M2 proton channel of influenza virus A is the target of several flu drugs. These appear to bind to the channel and disrupt the proton transport, which seems to involve water clusters in the channel. By calculating the energetics of pore blockers at different sites in M2, Michael Klein at Temple University and coworkers offer insights into the mechanisms of drug action that might guide the identification of new types of inhibitor (E. Gianti <i>et al., JPCB</i> <b>119</b>, 1173; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp506807y">here</a>). The general principle is to dehydrate the pore by replacing the water clusters with the ligand scaffold, and the results here show that this is most effectively done when the ligand scaffold mimics the water-cluster contour, while also preserving the interactions that the cluster made with the protein.
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Another water-containing channel is explored by Ai Shinobu and Noam Agmon at the Hebrew University of Jerusalem, and I like their opening line: “Internal water molecules in proteins are conceivably part of the protein structure”. Quite so. They look at the lone water molecule in the “barrel” of the proton-conducting green fluorescent protein, using MD simulations to examine how water exchange occurs following photoexcitation, which opens up the channel transiently (<i>JPCB</i> <b>119</b>, 3464; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp5127255">here</a>). The water molecule is shifted by the formation of a water wire through a temporary “hole in the barrel” connecting the chromophore with the bulk: a weak spot between strands of the β-barrel. This wire provides a route for protons to leak out of the channel, and the authors think that this might in fact supply the dominant mechanism for proton escape from the protein. The water motion, meanwhile, involves interactions with hydrogen-bonding residues that result first in sub- and then super-diffusive motion.
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How conformationally stable are proteins when dehydrated for storage? One way to find out is to look at water adsorption isotherms as a function of humidity for different conformations. This is what Pablo Debenedetti and coworkers at Princeton have done for the Trp-cage mini-protein using simulations of different protein matrices: crystal, powder, and thermally denatured powder (S. B. Kim <i>et al., JPCB</i> <b>119</b>, 1847; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp510172w">here</a>). All three matrices display so-called type II adsorption isotherms, in which there is hysteresis between adsorption and desorption across most of the humidity range. The isotherms are all of similar shape, showing little sensitivity to the degree of ordering in the proteins. Moreover, all show similar changes in swelling behaviour and hydrogen-bonding content as a function of humidity, except for the degree of intra-protein H-bonding, which unsurprisingly depended on the degree of folding in the monomers.
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A great deal of attention is now being focused on proteins that have no great degree of conformational regularity in the first place: intrinsically disordered proteins, such as the tau protein which regulates microtubule formation in the nervous system. Dysfuntions in tau can lead to protein aggregation and fibril formation of the sort associated with neurodegenerative diseases such as Alzheimer’s. Martin Weik at Grenoble and coworkers have used neutron scattering and MD simulations to compare the dynamical coupling of protein and solvent through the protein dynamical transition (at 240 K) for the tau IDP and a representative globular protein, the maltose binding protein (G. Schirò <i>et al., Nature Commun.</i> <b>6</b>, 6490; 2015 – paper <a href="http://www.nature.com/ncomms/2015/150316/ncomms7490/full/ncomms7490.html">here</a>). There is a general notion that the dynamical transition corresponds with the onset of hydration-water translational motion on the protein surface. But although IDPs also show a dynamical transition, they have considerably more solvent-accessible surface than globular proteins, so it is by no means clear that one can expect the same kind of water-protein coupling to apply. But it seems that it does. Martin and colleagues find that in both cases the onset of water translational diffusion seems to coincide with that of large-amplitude protein conformational fluctuations, of the sort needed for functional behaviour. Thus this connection seems to be independent of the protein’s folding state.
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What effect do osmolytes such as urea (a denaturant of globular proteins) have on IDPs? That question is explored by Zachary Levine and colleagues at UCSB using a combination of simulations and experiments (<i>PNAS</i> <b>112</b>, 2758; 2015 – paper <a href="http://www.pnas.org/content/112/9/2758.abstract">here</a>). They find that both urea and trimethylamine N-oxide (TMAO) affect the structure of tau by shifting the distribution of existing conformations rather than by adding any new ones. The osmolytes do so by altering the balance between hydrogen-bonding and salt-bridge interactions in the individual IDPs. In doing so, urea suppresses aggregation, while TMAO promotes the formation of compact oligomers. The mechanism of the latter is subtle, stemming from changes in hydration of the IDP in the presence of TMAO in such a way as to promote aggregation entropically by releasing TMAO and water from the protein surfaces. These predictions of the simulations are borne out by experiments.
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Urea can denature RNAs too. Alexander MacKerell at Maryland and colleagues have investigated why (K. Kasavajhala <i>et al., JPCB</i> <b>119</b>, 3755; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2F jp512414f">here</a>). The general idea has been that urea forms H-bonds and stacking interactions with the nucleotide bases. That’s a view that is supported by these <i>ab initio</i> calculations, which show that stacking via dispersion forces as well as H-bonding create cage-like complexes around the bases. For example, guanine may become surrounded by 5 urea molecules and 12 waters, pretty decisively trapping it in an unfolded conformation. Direct interactions, you see.
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MacKerell also has an interesting paper with E. Prabhu Raman on the energetics of protein-ligand binding (<i>JACS</i> <b>137</b>, 2608; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2F ja512054f">here</a>). They have looked in particular at the roles of water in the binding site, and especially the classical view that the “hydrophobic effect” in ligand binding is due to the reduction of nonpolar solvent-exposed area at the binding interface and the concomitant release of more “highly structured” water from this location. To calculate changes in solvation energy as a ligand binds, they use something called Grid Inhomogeneous Solvation Theory (GIST), described by Nguyen <i>et al.</i> in <i>J. Chem. Phys. </i><b>137</b>, 044101 (2012). They calculate the various thermodynamic contributions to the binding energy for propane and methanol in several different binding pockets of the proteins Factor Xa and P38 MAP kinase. While they find that the entropy of reorganization of water in the binding pockets favours ligand binding, much as the traditional picture of an entropically driven hydrophobic effect would suggest, the picture is actually rather complex, with subtle interplay between direct protein-ligand interaction energies (even in nonpolar sites) and loss of water interaction energies that can sometimes compensate and lead to a rather small binding enthalpy. Sometimes the enthalpic and entropic changes can oppose (compensate) each other, sometimes they reinforce one another. The general message seems to be that, much as some earlier studies have shown, it is difficult to generalize about the respective contributions to the binding thermodynamics.
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More on antifreeze proteins: Aatto Laaksonen and colleagues at Stockholm University show that representatives of the two major classes of AFPs (“hyperactive” and “moderately active”) have different effects on the nature of the ice-water interface when they are bound there (G. Todde <i>et al., JPCB</i> <b>119</b>, 3407; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2F jp5119713">here</a>). For the former class, they study the snow flea AFP; for the latter, the winter flounder AFP. Both AFPs increase the thickness of the interfacial region (defined as the region where water diffusion varies from 10 to 90% of the bulk liquid value), with the hyperactive AFP having the greatest effect (widening by 25-40%). This protein has ~25% more hydrophobic surface (the ice-binding side) than the wfAFP, but also 60-70% more hydrophilic surface; the authors think that it’s the first of these differences that counts the most.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHGw1uKxhOICmeybSh9cItcXeeIOWhsLmR0oOadBweLpbanUGcFDke_r5_curPAhzQPPQmlKunYoJidh-Sj3dW7ZLCeHV9ZjzKUHeDQzydAIZkDQfnhd6bswsIUqSEeewA3mrLnlGj1f8/s1600/AFP.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgHGw1uKxhOICmeybSh9cItcXeeIOWhsLmR0oOadBweLpbanUGcFDke_r5_curPAhzQPPQmlKunYoJidh-Sj3dW7ZLCeHV9ZjzKUHeDQzydAIZkDQfnhd6bswsIUqSEeewA3mrLnlGj1f8/s320/AFP.jpg" /></a>
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The snow flea (a) and winter flounder (b) antifreeze proteins bound at the ice-water interface.
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Ariel Fernandez has reported further evidence that the protein regions he calls dehydrons – parts of the backbone where hydrogen bonds in the backbone are “imperfectly wrapped” and thus solvent-exposed – may play not just a structural but also a chemical role (<i>FEBS Letters</i> <b>589</b>, 967; 2015 – paper <a href="http://www.febsletters.org/article/S0014-5793%2815%2900140-4/abstract">here</a>). He has previously argued that water molecules in dehydron regions can act as proton acceptors because of the way that confinement prevents them from orienting their dipoles perfectly with the prevailing electric fields. Now, using quantum calculations, he expands on how this behaviour makes dehydrons activators of nucleophilic groups, and looks at some biochemical consequences, in particular for cancer-related mutations of certain kinases. The nucleophilicity induced by the dehydron, he says, turns the kinase constitutively (and hazardously) active for phosphorylation.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com37tag:blogger.com,1999:blog-7540687028464774748.post-64895601441142340282015-03-19T02:20:00.002-07:002015-03-19T02:20:40.950-07:00JCP special issue on biological waterThe main news this time round must be the “special topic” issue of <i>J. Chem. Phys.</i> on “biological water”, edited by Gerhard Hummer and Andrei Tokmakoff (<a href="http://scitation.aip.org/content/aip/journal/jcp/141/22/section?heading=SPECIAL+TOPIC%3a+BIOLOGICAL+WATER">here</a>; see their preface <a href="http://scitation.aip.org/content/aip/journal/jcp/141/22/10.1063/1.4901337">here</a>). I’m not going to go through all the contributions, nor invidiously to pick out any ones in particular – needless to say, it’s a treasure trove, and well worth browsing.
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A completely new motif for ice binding in an antifreeze protein has been identified by Peter Davies and colleagues at Queen’s University in Kingston, Ontario, in a midge native to Lake Ontario (K. Basu <i>et al., PNAS</i> <b>112</b>, 737; 2015 – paper <a href="http://www.pnas.org/content/112/3/737.abstract">here</a>). It is a small protein of just 79 residues, and contains a 10-residue coil crosslinked by a disulfide bond, which presents seven tyrosine chains in a flat array for ice binding. The protein, which has no known homologues, seems to be a relatively “cheap” means of protecting the midges from occasional night frosts when they emerge in the spring.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYJjLXRpbZwfK4u9K_QEpha594c6Jf2pBNWMG1GD_1UEuOSG0SMnw-P8iEz05IDa9qdaPXIvrkqimDgMUjbD_JHGtENRAKYhgSXBjH-O5ybLzn64tryMPLzpFu3HQ-56MYATRwl6ULQXo/s1600/midge_AFP.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgYJjLXRpbZwfK4u9K_QEpha594c6Jf2pBNWMG1GD_1UEuOSG0SMnw-P8iEz05IDa9qdaPXIvrkqimDgMUjbD_JHGtENRAKYhgSXBjH-O5ybLzn64tryMPLzpFu3HQ-56MYATRwl6ULQXo/s320/midge_AFP.jpg" /></a>
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The idea that protein denaturants such as guanidinium cations and urea act via direct interactions with the protein is explored by Sandeep Patel and colleagues at the University of Delaware, who use MD simulations to look at the orientations of these molecules close to hydrophobic residues and how these affect solvent fluctuations in the vicinity (D. Cui <i>et al., JPCB</i> <b>119</b>, 164; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp507203g">here</a>). They find a correlation between the stability of the molecular arrangement at the interface (e.g. parallel or perpendicular orientations of the denaturant) and the degree of fluctuation induced – implying that the effects of the denaturants may be related to their tendency to introduce malleability in the local hydration shell, with consequences for hydrophobic interactions.
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Intracellular lipid-binding proteins (iLBPs) are central to fatty-acid uptake, transport and metabolism. They have an intriguing structure, in which a β-barrel contains a large water cluster. Shigeru Matsuoka and colleagues at Osaka University have attempted to figure out what the role of these waters is, using MS simulations of human-heart-type fatty-acid binding protein (FABP3), a typical iLBP (D. Matsuoka <i>et al., JPCB</i> <b>119</b>, 114; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp510384f">here</a>). They observe two conformations. The empty cavity is wide open, with a relatively ordered hydrogen-bond network inside it. But when the ligand is bound, some of the waters exit through a “back portal” while others provide a hydrogen-bonded latch, connecting to highly conserved hydrophilic residues, that “seals” the cavity with the fatty acid (stabilized by hydrophobic interactions with the interior) inside.
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In an arxiv preprint (1412.2698 – paper <a href="www.arxiv.org/abs/1412.2698">here</a>), Martin Wolf and colleagues at Augsburg present dielectric measurements of hydration water dynamics of lysozyme in frozen solution, ordinary solution and a hydrated powder. They claim to find clear evidence for bimodal dynamics, with a crossover that supports the notion of a fragile-to-strong transition in the metastable “No Man’s Land” regime.
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(Incidentally, did I detect in Twitter some skepticism about how so many of these studies present their results as N=1 samples consisting of lysozyme or HIV protease? If so, it’s a fair concern, but you have to start somewhere. As Wolf and colleagues acknowledge, further studies are needed here to determine the generality.)
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The fact that I write every month for Nature Materials makes it all the more unforgiveable that I failed to spot the paper there by Wang <i>et al.</i> in 2013 showing how water may play a vital structural role in bone apatite (<i>Nat. Mater.</i> <b>12</b>, 1144 – paper <a href="http://www.nature.com/nmat/journal/v12/n12/full/nmat3787.html">here</a>). By way of atonement, let me point to a nice contribution by Neeraj Sinha at the Center of Biomedical Research in Lucknow and colleages who describe a solid-state NMR method for investigating the nature of collagen hydration in the bone matrix (R. K. Rai <i>et al., JPCB</i> <b>119</b>, 201; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp511288g">here</a>). They say that the hydration in situ seems to be significantly different from that of extracted collagen, and adds to the idea that water plays a big part in determining and modifying the mechanical properties.
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We need new flu drugs, agreed? Bill DeGrado at UCSF and colleagues report a new strategy for designing inhibitors of flu viruses that bind in two variants of the M2 proton channels (WT and S31N), where a network of water molecules assists proton transport (Y. Wu <i>et al., JACS</i> <b>136</b>, 17987; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja508461m">here</a>). For these two strains, in which the inhibitor binds with different orientations, the initial results suggest that the antiviral activity should be comparable to the existing antiviral amantadine.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1oppA_hXMDeHkAmatlaBJSvKFOIoUYh8B0wSetkLmr__i2mop80oG-unLvvubmXpdyiEIpZa3ccoUpStQOtZ90_ItfwaAAAA8PKAKe9vkBtBqmUk-oQ6iOnEVsiLbdMmHvHcO90fTfho/s1600/WT_channel.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh1oppA_hXMDeHkAmatlaBJSvKFOIoUYh8B0wSetkLmr__i2mop80oG-unLvvubmXpdyiEIpZa3ccoUpStQOtZ90_ItfwaAAAA8PKAKe9vkBtBqmUk-oQ6iOnEVsiLbdMmHvHcO90fTfho/s320/WT_channel.jpg" /></a>
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The role of hydration waters in the sequence-specific bending flexibility and conformational stability of DNA is studied in a paper by Jerzy Leszczynski at Jackson State University and colleagues (T. Zubatiuk <i>et al., JPCB</i> 10.1021/jp5075225 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp5075225">here</a>). They look specifically at A-tracts of B-DNA, which resist deformations and so might be important in the organization of nucleosomes. They find that this stiffening is influenced by the specific patterns of structural water within both the major and minor grooves
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Tunneling and delocalization of protons in a hydrogen-bonded network in the active site of ketosteroid isomerase is described in ab initio simulations by Thomas Markland and colleagues at Stanford (<i>PNAS</i> <b>111</b>, 18454; 2014 – paper <a href="http://www.pnas.org/content/111/52/18454.abstract">here</a>). They say that this leads to a boost in the acidity of the site by around four orders of magnitude compared with the classical situation. There are no actual waters in the site in this case, but the general implication seems clear enough.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjc-anr4dVfAwpyv4cbPXxdLQEQ1DmSLJCZHN3aHLD75zzHYDxhvbTsm_58UqXc0SJh9iJ4SggL5XXJRt_ZgmrxJC9gexZR3KZUoPSJ-WzOpvxaGnPczKPpxj91atjTwWDMmHs51EWwjIU/s1600/proton_delocalization.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjc-anr4dVfAwpyv4cbPXxdLQEQ1DmSLJCZHN3aHLD75zzHYDxhvbTsm_58UqXc0SJh9iJ4SggL5XXJRt_ZgmrxJC9gexZR3KZUoPSJ-WzOpvxaGnPczKPpxj91atjTwWDMmHs51EWwjIU/s320/proton_delocalization.jpg" /></a>
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Another nice example of “functional water” at an active site: Vivek Sharma at the Tampere University of Technology in Finland and colleagues say that an organized cluster of water molecules in cytochrome c oxidase helps to steer proton transfer in the right direction, so that the electron transfer in the reduction of oxygen to water can be coupled to proton pumping across the membrane (<i>PNAS</i> <b>112</b>, 2040; 2015 – paper <a href="http://www.pnas.org/content/112/7/2040.abstract">here</a>). Their simulations indicate that the waters reorganize in a redox-dependent way so as to coordinate electron transfer with proton transfer along the requisite path (see diagram of the two states below).
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCnFtixPsKO4RpzkLRo7SRhrmcKvybGQhQD6BtVsowAov-R9cKI7gV9uKm3FKwZbBjJblYOeRv-2Q4wUT2k0Zf5TpkpdEN3VHfBeB8JzQDXRXYBiv3IG5bZqg7dA_zFZypryqtAxJWwNg/s1600/cyto+c+proton+paths.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhCnFtixPsKO4RpzkLRo7SRhrmcKvybGQhQD6BtVsowAov-R9cKI7gV9uKm3FKwZbBjJblYOeRv-2Q4wUT2k0Zf5TpkpdEN3VHfBeB8JzQDXRXYBiv3IG5bZqg7dA_zFZypryqtAxJWwNg/s320/cyto+c+proton+paths.jpg" /></a>
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There is increasing reason to believe that hydrophobicity is a context-dependent property. That conclusion might be read into the findings of Dor Ben-Amotz and colleagues at Purdue on how the presence of a charged group such as carboxylate or tetraalkylammonium alters the hydration structure around an adjacent aliphatic chain (J. G. Davis <i>et al., JPCB</i> jp510641a – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp510641a">here</a>). They found in previous work (<i>Nature</i> <b>491</b>, 582; 2012) there seems to be a change in the hydration structure of aliphatic alcohols at a chain length of around 1 nm, consistent with the proposal of such a crossover by David Chandler and colleagues. Using Raman spectroscopy and simulations, they now see a similar structural change for aliphatic carboxylic acids with different chain lengths, but that this transition is suppressed when the carboxylic acids are deprotonated. The effect is stronger for tetraalkylammonium ions – that is, the perturbation created by the charged head group extends several methylene groups down the aliphatic tail. So it would seem that these charged head groups alter the hydrophobic hydration in ways that neutral hydrophilic groups do not.
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This fits very nicely with recent work by Sam Gellman, Nicholas Abbott and colleagues at Wisconsin-Madison, who find that the hydrophobic interactions of methyl-terminated self-assembled monolayers, as measured by chemical force microscopy and single-molecule force measurements for docking of the nonpolar domains of peptides, are altered by the inclusion of some cationic amine and guanidinium groups among the SAM (C. D. Ma <i>et al., Nature</i> <b>517</b>, 347; 2015 – paper <a href="http://www.nature.com/nature/journal/v517/n7534/full/nature14018.html">here</a>). Curiously, protonated amine groups enhanced the hydrophobic interactions, while charged guanidinium groups suppress them. Gellman and colleagues reach much the same conclusion as Dor’s team: that the results are consistent with the idea that “solvation shells are susceptible to the influence of neighbouring atoms, especially strongly charged ones.” There’s a nice News and Views piece accompanying the paper by Shekhar Garde (<i>Nature</i> <b>517</b>, 277 – <a href="http://www.nature.com/nature/journal/v517/n7534/full/517277a.html">here</a>).
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How does dewetting between two hydrophobic surfaces happen? The classic picture is that this is capillary condensation, a first-order process that requires the formation of a nucleus of a critical size – say, a vapour tube bridging two planar hydrophobic surfaces. But Richard Remsing at the University of Pennsylvania and coworkers report simulations in which dewetting seems to circumvent this classical mechanism: fluctuations of the confined water give rise to a cavity larger than the size of a critical nucleus, which then grows spontaneously (R. Remsing <i>et al.</i>, arxiv 1502.05436 – paper <a href="http://arxiv.org/abs/1502.05436">here</a>). This certainly fits with earlier suggestions by the Chandler group that dewetting is driven by solvent fluctuations.
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I wonder, though, if we have an adequate picture of how these fluctuations fit within a standard picture of confined fluids. Where do they come from, and are they specific to water or a consequence of solvophobicity more generally? I have been talking to (admission of interest: my one-time PhD supervisor) Bob Evans at Bristol about this, who pointed me to a paper in press with <i>J. Phys. Cond. Matt.</i> with Maria Stewart which hopes to shed light on the issue. They point out that even for simple Lennard-Jones fluids close to solvophobic walls there is an enhancement, over just a molecular diameter or two, of the local compressibility. This, they say, looks very much like the “enhanced fluctuations” that David Chandler, Shekhar Garge and others have reported for water at hydrophobic surfaces. In other words, this local compressibility, analogous to the surface susceptibility in an Ising model that serves as an indicator of the approach to a critical wetting or drying transition – offers a properly defined thermodynamic measure of what previously has been a rather vague, hand-waving concept. And it implies that there is nothing here that is unique to water.
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How much do quantum effects that allow for electronic polarization matter to the energetics of ligand-receptor binding calculations, relative to molecular mechanics calculations that neglect them? Adrian Mulholland and colleagues at Bristol address this question by looking at the binding of water molecules within the cavity of the influenza viral protein neuraminidase, a target for antivirals such as oseltamivir and peramivir (C. J. Woods <i>et al., JPCB</i> <b>119</b>, 997; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp506413j">here</a>). They consider this system because of the recognized importance of bound water molecules in drug design, and in particular the known function of a water molecule in oseltamivir binding. Structural studies of ligand-neuraminidase complexes have revealed two kinds of important “structural” waters: one in a hydrophilic site, the other a hydrophobic one. They find that in going from molecular modeling to <i>ab initio</i> calculations, the difference in binding energy due to water polarization can be as much as 1 kcal/mol, and is greater for the hydrophilic water.
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Laurence Pratt at Tulane University and his coworkers have dissected the role of intermolecular forces on hydrophobic interactions (M. I. Chaudhar <i>et al.</i>, arxiv preprint 1501.02495 – paper <a href="http://arxiv.org/abs/1501.02495">here</a>). They find that for hydrated argon atoms, including realistic solute attractive forces substantially weakens the hydrophobic attractions relative to the situation without them (as assumed in Pratt-Chandler theory formulated in 1977 for hard spheres: <i>JCP </i><b>67</b>, 3683). Among other things, it’s pretty remarkable that Laurence has returned to reconsider the idea after almost 40 years!
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This is not directly about hydration, but it’s involved: I have a story <a href="http://www.rsc.org/chemistryworld/2015/03/program-ready-weed-out-tough-drug-leads-ligand-receptor">here</a> in <i>Chemistry World</i> about a new computational method for calculating the free energies of ligand binding to a wide range of protein receptors (L. Wang <i>et al., JACS</i> <b>137</b>, 2695; 2015 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja512751q">here</a>). The authors claim that it comes within 1 kcal/mol of the measured binding energies for most of the cases studied. As far as hydration is concerned, Robert Abel at Schrodinger, the company that developed the method, says to me that “These simulations use explicitly solvated molecular dynamics. So, molecular hydration affects should be well-described. Such an example of a ligand displacing a water from a cavity is described in in figure 4 sub-panel C and at the bottom second column of page 2699 of the manuscript.”
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com16tag:blogger.com,1999:blog-7540687028464774748.post-55592742104191172772014-12-08T02:11:00.001-08:002014-12-17T04:07:04.363-08:00What to think about KauzmannI guess you can tell when I’m on travel, because that is when so many of these posts tend to get done – on this occasion, on a visit to the rather wonderful Chemical Heritage Foundation in Philadelphia (and yes, had I had more time then I should surely have liked to do some more visiting in the locale, since I know some readers were nearby!).
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“Restoring Kauzmann’s 1959 explanation of how the hydrophobic factor drives protein folding” is quite a big claim. But what Robert Baldwin at Stanford means by making this claim in the title of his <i>PNAS</i> paper (<i>PNAS</i> <b>111</b>, 13052; 2014 – paper <a href="http://www.pnas.org/content/111/36/13052.abstract">here</a>) is not that, as Kauzmann argued, hydration water is a kind of ordered, ice-like clathrate, but rather that the driving force of hydrophobic attraction is ultimately entropic, being due to the release of relatively constrained waters. Baldwin argues that a dynamic but relatively ordered hydration shell due primarily to van der Waals attraction can equally account for the hydration energetics: why, for example, the hydrophobic free energy depends on the solvent-accessible surface area of the nonpolar interface of hydrophobes. What I still find a little puzzling about this analysis, however, is the apparent implication that there was any doubt about the existence of non-bulk-like hydration shells around hydrophobic groups. That, surely, is clear by now; what seems less agreed is whether or not these shells have waters with retarded dynamics, stronger hydrogen-bonding and so forth.
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This issue is also directly confronted in a paper by Wilbee Sasikala and Arnab Mukherjee of the Indian Institute of Science Education and Research in Pune (<i>JPCB</i> <b>118</b>, 10553; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp502852f">here</a>). They calculate the translational and rotational entropy of single water molecules as a function of their distance from hydrophobic solutes and find that, intriguingly, the entropy gradually increases with distance for small (>0.746 nm) hydrophobes but that the translational entropy decreases with distance for larger hydrophobes. The rotational entropy still increases with distance in this latter case, so that the crossover for the sum of the two in fact occurs at solute sizes of around 1.5 nm – consistent with David Chandler’s suggestion of a crossover in styles of hydrophobic hydration at around this scale. The increase in translational entropy close to large hydrophobes seems to be related to the relatively larger number of dangling H-bonds in that case.
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These questions are also touched on from a different direction in a paper by Robert Harris and Montgomery Pettitt (<i>PNAS</i> <b>111</b>, 14681; 2014 – paper <a href="http://www.pnas.org/content/111/41/14681.abstract">here</a>) in which they examine the energetics of cavity formation for a nonpolar van der Waals solute inserted into water. Although their calculations of the free-energy perturbation for a series of alkanes fits the standard idea that the solvation free energy depends linearly on surface area (as Baldwin notes), nevertheless the contributions to this trend for each atom in the alkanes are not simply additive but depend on correlations with the neighbouring atoms. Or to put it another way, the various contributions to the free energy change can’t be calculated by assuming a constant surface tension for the cavity interface; there are thus subtle changes in the water density around the solute that a complete theory of hydrophobic hydration will need to take into account.
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As described by David Chandler and his coworkers, the dewetting transition that may drive hydrophobic attraction between extended surfaces is triggered by unusually large-amplitude fluctuations. This picture has often been advanced for the case of purely hard-core hydrophobic surfaces. Richard Remsing and Amish Patel at the University of Pennsylvania have investigated whether that picture is modified for the case of realistic solutes with attractive van der Waals interactions with the solvent (<a href="http://www.arxiv.org/abs/1410.1614">http://www.arxiv.org/abs/1410.1614</a>). They find that, when the attraction is felt in the hydration-shell alone (that is, not in the solute core), it makes essentially no difference to the water density fluctuations.
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There is something of the Kauzmann spirit in the convenience of the explanation for crowding effects that explains them in terms of entropic effects: namely, that crowding agents such as glucose and PEG exert their influence via excluded-volume effects due to hard-core repulsions. Simon Ebbinghaus and colleagues at Bochum challenge this view in a paper that argues for a role of enthalpic effects too (M. Senske <i>et al., JACS</i> <b>136</b>, 9036; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja503205y">here</a>). They study the thermodynamics of ubiquitin folding in the presence of cosolutes such as sugars, PEG and salt, using CD spectroscopy and DSC. They find that the temperature dependence of the heat capacity change on unfolding has an important role, which implies some enthalpic influence. They suggest that, for crowding agents like glucose and dextran, this influence might be exerted by cosolute-induced distortions of the hydrogen-bonded hydration network around the protein, i.e. it is solvent-mediated. This suggests a new framework for understanding crowding effects in terms of a balance between entropic and enthalpic contributions.
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It has been suggested that water molecules trapped in internal cavities of thermophilic proteins might contribute to their enhanced thermal stability. Might they provide a hydrogen-bonded network that helps to stabilize the molecule and inhibit the formation of internal voids as an initial stage in denaturation? Fabio Sterpone at the University Paris Diderot and his coworkers investigate this question for the hyperthermophilic domain of a protein from <i>S. solfataricus</i>, using MD simulations and free-energy calculations to compare it with a homologous domain from an <i>E. coli </i>protein (O. Rahaman <i>et al., JPCB</i> ASAP jp507571u – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp507571u">here</a>). Although under ambient conditions the internal hydration for the thermophilic protein is more favourable than for the mesophilic one, at the high temperatures at which the former operates the cavities are largely empty anyway. However, fluctuations in the number of buried waters appear to be intimately connected to the conformational fluctuations of the protein: the more hydrated cavities of the thermophilic protein seem to provide access to multiple conformational states, belying the common notion that such proteins are more rigid than mesophilic homologues.
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[n.b. I have just come across <a href="http://arxiv.org/abs/1412.1514">this preprint</a>, which, while not discussing thermophiles, is extremely relevant to the issue in its analysis of the role of internal cavities, and their hydration state, for protein conformational flexibility.]
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Martina Havenith and her coworkers at Bochum have previously provided evidence from THz spectroscopy that rather long-ranged gradients in solvent dynamics may play an important role in the binding of substrates in an enzyme’s active site as it forms the transition-state complex. Now they report something even more remarkable: that coupling of solvent and protein dynamics exhibit correlations on timescales that exceed the duration of a single catalytic cycle, indicating coupling that is not accounted for within conventional Michaelis-Menten steady-state theory (J. Dielmann-gessner <i>et al., PNAS</i> advance online publication 10.1073/pnas.1410144111 – paper <a href="http://www.pnas.org/content/early/2014/11/24/1410144111.abstract">here</a>). These couplings are substrate-specific, and they contribute to the enzyme’s reactivity. In calling water “more than a bystander”, I have to say that I had not imagined that its participation would extend so deeply. I suppose one must assume that MM kinetics remain a good approximation to what transpires in most cases, but this is a striking illustration of what a delightful collaboration of solvent, protein and substrate is entailed in the fuller picture.
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Barry Sharpless’s work on “on-water” reactions – the acceleration of various organic reactions when they happen at the interface of water and an organic solvent (S. Narayan <i>et al., Angew. Chem. Int. Ed.</i> <b>44</b>, 3275; 2005) – was extremely interesting but never fully explained. One idea was that transition states were being stabilized by dangling hydrogen bonds at the interface. Thomas Kühne at Paderborn and his coworkers have now examined this idea for the case of a Diels-Alder reaction via quantum-chemical MD simulations, and find that while the effect dos occur, it seems to be rather less significant than has often been supposed – the number of H-bonds to the transition state is only marginally increased at the interface compared to the homogeneous situation (K. Karhan <i>et al.</i>, <a href="http://www.arxiv.org/abs/1408.5161">http://www.arxiv.org/abs/1408.5161</a> (2014)).
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The release of a proton from photo-excited retinal in bacteriorhodopsin – the initial stage of the molecule’s photocycle – is accompanied by a twist of the retinal photoproduct. Is this twist governed by the intrinsic properties of retinal or by interactions with the protein/solvent environment? Marcus Elstner at the Karlsruhe Institute of Technology and colleagues study this question using quantum-chemical MD (T. Wolter <i>et al., JPCB</i> ASAP jp505818r – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp505818r">here</a>). The answer is complex, especially in its temperature dependence, but it does seem that a twisted retinal conformer is somewhat stabilized by interactions with the protein side chains and water molecules in the active site. It seems that relaxation of the twisted chromophore back to its planar state could involve translocation of one water molecule from the extracellular to the cytoplasmic side of the complex – but that can’t yet be confirmed either way from these calculations.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiy3RRRMk-5EJR1mYZ3o20SWSUTbdoqU-Y0pWLNbtiBq_vWQNydD4SxyXtNHRzVnDyb6GIRGvV1x3U6bdsqV6BKWZR5uEfOmILSvNId1-7Za8eG5XSjkSQ79rGF1onAmGpgO-KI4ZuVq-Q/s1600/retinal.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiy3RRRMk-5EJR1mYZ3o20SWSUTbdoqU-Y0pWLNbtiBq_vWQNydD4SxyXtNHRzVnDyb6GIRGvV1x3U6bdsqV6BKWZR5uEfOmILSvNId1-7Za8eG5XSjkSQ79rGF1onAmGpgO-KI4ZuVq-Q/s320/retinal.jpg" /></a>
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There seems to be a rather more clear mechanism by which active-site water plays a functional role in the related case of rhodopsin, according to simulations by Yaoquan Tu and colleagues at the KTH Royal Institute of Technology in Stockholm (X. Sun <i>et al., JPCB</i> <b>118</b>, 10863; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp505180t">here</a>). They find that a rearrangement of the hydrogen-bonded network around the Schiff base of rhodopsin, due to movement of one particular water molecule, might be responsible for the switch from the inactive to the constitutively active state, mediating proton transfer from the base to the Glu113 group.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhINocMb5pkyV7g3UHmobCCV33VEfgB45VV343T-GBI4V3sAtitRfvBGES_jKwf-kTq482I0wkMF52VvfS0DmH57l0OxjZ6O14cfm5LJ0xeIhX3x-HKpeM5QFp7LgSAnicE75IJJOWt4mE/s1600/rhodopsin.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhINocMb5pkyV7g3UHmobCCV33VEfgB45VV343T-GBI4V3sAtitRfvBGES_jKwf-kTq482I0wkMF52VvfS0DmH57l0OxjZ6O14cfm5LJ0xeIhX3x-HKpeM5QFp7LgSAnicE75IJJOWt4mE/s320/rhodopsin.jpg" /></a>
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<i>[Proposed water-mediated mechanism for activation of rhodopsin. You won’t be able to see much from this image alone, I guess – the text of the paper explains the details indicated by the red arrows. But it’s the IW6 hydration site towards the top of the active site that is proposed as the crucial switch.]</i>
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“Is urea a structure-breaker?” is the provocative question posed by Niharendu Choudhury and colleages at the Bhabha Atomic Research Centre in Mumbai (D. Bandyopadhyay <i>et al., JPCB</i> <b>118</b>, 11757; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp505147u">here</a>). You might be tempted to respond “Is that really the right question?”, but this is in a sense the researchers’ point: the considerable debate around the mechanism of urea’s denaturant properties has often been conditioned by notions of the breaking (or otherwise) of water structure – the so-called indirect effect on macromolecular structure. Yet is there any real evidence for it? Using MD simulations, Choudhury and colleagues conclude that, even at high concentrations, urea does not significantly disrupt the tetrahedral structure of water. Rather, it replaces water rather neatly in the hydrogen-bonded network. The authors admit that this does not yet really pronounce on the situation with macromolecules present, in terms of the nature and balance of solvent-solute-cosolute interactions. The question of whether any of this should be broached in terms of alleged “chaotropicity” is one to which I will return shortly…
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How hydration properties affect the behaviour of intrinsically disordered proteins has become a focus of considerable attention recently. Sanjoy Bandyopadhyay at the Indian Institute of Technology in Kharagpur and colleagues have investigated this issue using MD simulations of an IDP, amyloid beta, in comparison with the globular protein ubiquitin (J. C. Jose <i>et al., JPCB</i> <b>118</b>, 11591; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp505629q">here</a>). They find that the hydration water for the IDP is marginally less strongly coupled to the protein dynamics, and more bulk-like, than it is for UBQ. The water dynamics are more heterogeneous, apparently because of the conformational fluctuations of the protein. To return to the questions above, this arguably implies that there should be a smaller entropic driving force for hydrophobic association of the IDP – to put it another way, the protein’s surface is rendered relatively less hydrophobic.
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The conventional view of antifreeze proteins (and glycoproteins) as acting via direct binding of ice at their surfaces was recently supplemented by the observation of long-ranged (up to 2 nm from the surface) retardation of water dynamics (S. Ebbinghaus <i>et al., JACS</i> <b>132</b>, 12210; 2010). This picture is supported by MD simulations by Anand Narayanan Krishnamoorthy and colleagues at the University of Stuttgart (<i>JPCB</i> <b>118</b>, 11613; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp507062r">here</a>). They find that hydrogen-bonding groups – hydroxyl in threonine, disaccharides – at the protein surfaces are mostly responsible not only for direct water binding but also for the long-range dynamical perturbation. Osmolytes, including chaotropes such as urea and (especially) kosmotropes such as hydroxyectoine, enhance this dynamical effect. Meanwhile, Alexander MacKerell at the University of Maryland and coworkers also find in MD simulations that carbohydrate groups on AFGPs not only engage in hydrogen-bonding with the solvent but also modify the tetrahedral arrangement and the dynamics of water molecules as far as 12Å from the surface – but only at low temperatures (<250 K) (S. S. Mallajosyula <i>et al., JPCB</i> <b>118</b>, 11696; 2014 – paper <a href="http://">here</a>). They propose that the dynamical effect is in fact the dominant influence on the antifreeze behaviour.
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The best way to characterize the hydrophobicity of amino acid side chains has been much debated. Timir Hajari and Nico van der Vegt at TU Darmstadt extend the emerging focus on context-dependence of the issue by computing solvation free energies for the side chains in a way that factors in the effects of the peptide backbone (<i>JPCB</i> <b>118</b>, 13162; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp5094146">here</a>). They find that the backbone effects are far more significant for nonpolar than for polar side chains, in the former case reducing the hydrophobicity relative to what is found for the isolated amino acids. This might support the view that intramolecular hydrogen-bonding in the peptide is a more important driving force for protein folding than are hydrophobic interactions.
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Adam Perriman, Stephen Mann and their collaborators at Bath recently described a technique for preparing solvent-free protein liquids by coating the surfaces with electrostatically bound polymer surfactants (Perriman & Mann, <i>ACS Nano</i> <b>5</b>, 6085; 2011). Now they show that lipases prepared this way remain catalytically active despite having only 20-30 water molecules per molecule, which is of the order of 2% of what is needed to cover the solvent-accessible area (A. P. S. Brogan <i>et al., Nature Commun.</i> <b>5</b>, 5058: 2014 – paper <a href="http://www.nature.com/ncomms/2014/141006/ncomms6058/full/ncomms6058.html">here</a>). What is more, the proteins remain active up to temperatures of at least 150 C.
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Huaqiang Zeng of the Institute of Bioengineering and Nanotechnology in Singapore have created synthetic molecules based on pyridine that form helical structures with a pore about 2.8Å threading through them, which they hope might mimic the water-conducting channels of aquaporins (W. Q. Ong <i>et al., Chem. Commun.</i> <b>47</b>, 6416; 2011). Now they report that these constructs can be threaded by a water wire that permits not only proton transport but also osmotically driven water-molecule transport across lipid membranes in the presence of a proton gradient (H. Zhao <i>et al., JACS</i> <b>136</b>, 14270; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja5077537">here</a>).
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To what extent the state of hydrated protons is influenced by quantum effects has been quite widely studied, but Ali Hassanali at the Abdus Salam International Centre for Theoretical Physics in Trieste and coworkers revisit the question using state-of-the-art quantum chemical methods (F. Giberti <i>et al., JCPB</i> <b>118</b>, 13226; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp507752e">here</a>). They find that the classic Eigen and Zundel ions still dominate, but that there can be “wild fluctuations” in which the proton is extended over long proton wires involving 2-5 water molecules. These fluctuations reduce the effective hydrophobicity of the hydrated proton.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com10tag:blogger.com,1999:blog-7540687028464774748.post-52758532301006526552014-11-12T04:30:00.000-08:002014-11-12T04:30:31.163-08:00Hydrophobic or not?You thought buckyballs were the archetypal hydrophobic substance? Me too. But Li et al. have found in molecular simulations that the interaction of two C60 molecules in water has a repulsive contribution for the solvent: water actually seems to push the molecules apart (Li <i>et al., Phys. Rev. E</i> <b>71</b>, 011502, 2005; <i>J. Chem. Phys.</i> <b>123</b>, 204504; 2005). The same seems to be true of two carbon nanotubes when they come into close proximity with a particular alignment of their axes (Uddin <i>et al., Polymer</i> <b>52</b>, 288; 2011; Ou <i>et al., JPCB</i> <b>116</b>, 8154; 2012).
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How can this be possible? How can buckyballs be hydrophobic and at the same time apparently attracted to waters more than the waters are attracted to themselves? Ronen Zangi has recently addressed this question using molecular dynamics simulations (<i>J. Chem. Phys.</i>, in press). He points out that buckyballs lie right at the 1-nm crossover point predicted by David Chandler and colleagues for different modes of hydrophobic hydration. But it seems that they act more like large rather than small hydrophobes, in that it’s not possible for the water to rearrange so as to preserve the hydrogen-bonding network as it can for small hydrophobic molecules.
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However, buckyballs aren’t like a pair of hydrophobic plates. They are of course curved, convex surfaces, and we know that hydrophobic solvation is sensitive to curvature (Wallqvist & Berne, <i>JPC</i> <b>99</b>, 2885; 1995). Ronen finds that, because the actual contact area of two buckyballs is rather small, the favourable free energy change for association can’t be attributed to strong solute-solute interactions, as it is for two graphene sheets say.
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So the various influences here on the free energy of association are subtle. However, the crucial point is that, as the buckyballs come together, some of the hydration water changes character. The waters in the primary hydration spheres are already somewhat compromised, having on average a smaller number of hydrogen bonds than those in the bulk (these are shown in grey below). But when the buckyballs are only a few nanometers apart, there is a new class of water molecules in between them that are even more depleted of hydrogen bonding (shown in orange). And the key point is that, unlike the case of flat plates in contact, some of these anomalous water molecules remain even when the buckyballs are in contact.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivaky3U-Jb8bYj_xOss-oD5rmcnZSJB4HHgpTaYXEdrcQvEwTcaidPTcgHplatIheV2cz8PAyGyxdyqIU9ODE2ser66jZrwKibv0-VzafmJkEKKtAK53O4phe_gRpa0PJZnT0iLz1tr_Q/s1600/Zangi_fullerenes.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEivaky3U-Jb8bYj_xOss-oD5rmcnZSJB4HHgpTaYXEdrcQvEwTcaidPTcgHplatIheV2cz8PAyGyxdyqIU9ODE2ser66jZrwKibv0-VzafmJkEKKtAK53O4phe_gRpa0PJZnT0iLz1tr_Q/s320/Zangi_fullerenes.jpg" /></a>
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So there is a complex reckoning here of the entropic and enthalpic effects, coming from the fact that the various factors are not simply additive because of the particular scale and geometry of the hydrophobic interaction. Ronen concludes that “bucky-balls can serve as an example in which hydrophobic interaction cannot be deduced from hydrophobic solvation”. Or to put it another way, the effective pair interaction of the solute is not hydrophobic, in that solvent contributes a repulsive influence, and yet the solvation properties are hydrophobic because of the qualitative difference between the solvent-separated and fully associated particles. This, I think, is one of the best illustrations I have seen that hydrophobicity is a very slippery concept.
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Martina Havenith has written a nice Perspective for <i>JACS</i>, with Valeria Conti Nibali, on the use of THz spectroscopy to study biomolecular hydration (<i>JACS</i> <b>136</b>, 12800; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja504441h">here</a>). In particular, they discuss recent work on ligand binding and antifreeze proteins which points to the existence of a gradient in water dynamics towards the active sites, acting as a “hydration funnel”. The concept is nicely illustrated in this graphic:
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNG-CtZdi2GVeCy4Ozi6ZnjujukUsIszMz7265oEq7I_S6dWYg_WeL7yaWBIImizzuuyd_TdFEIjfcgqrBJAkX5U-QPq32vxhzQqeGl5GXEQGU_MDHOY8va9p57ekkUvgY-Uta-qtpiBA/s1600/hydration_funnel.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhNG-CtZdi2GVeCy4Ozi6ZnjujukUsIszMz7265oEq7I_S6dWYg_WeL7yaWBIImizzuuyd_TdFEIjfcgqrBJAkX5U-QPq32vxhzQqeGl5GXEQGU_MDHOY8va9p57ekkUvgY-Uta-qtpiBA/s320/hydration_funnel.jpg" /></a>
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You won’t be surprised to hear me cheer on the final conclusion: “So far, in all these applications, the solvent is still a strongly underestimated and mostly neglected element of the multilateral partnership in biomolecular function.”
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Intrinsically disordered proteins tend to form loose but collapsed globules that trap some water. Some of these, such as kappa-casein, have charged and basically hydrophilic residues, and their collapsed conformations trap a fair amount of water. Shruti Arya and Samrat Mukhopadhyay of the Indian Institute of Science Education and Research in Mohali have studied the dynamics of this water within globules of kappa-casein using time-resolved fluorescence spectroscopy to measure the solvation time of a fluorescent dye probe (<i>JPCB</i> <b>118</b>, 9191; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp504076a">here</a>). They find that the water relaxation times are three orders of magnitude slower than the bulk, and an order of magnitude slower that that typically found at protein surfaces. In other words, they say, it seems to form a highly ordered network within the disordered globule. They speculate that the entropic gain on release of this water light explain the oligomer formation that initiates the formation of amyloid fibrils from IDPs.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtmu4LmMHTqGhsJEAeCHgqVkMkevm87hmRJVvsavTX4XA5hRuXa9QgX2S7L_Q3eXQNaHlq1hcFFu4QctgNoLxfyeCwe-uCJyBnYsOlELhg-G-niSttHFy5wYKjm9PI4DdvVRpqA1lwHRU/s1600/IDP_water.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhtmu4LmMHTqGhsJEAeCHgqVkMkevm87hmRJVvsavTX4XA5hRuXa9QgX2S7L_Q3eXQNaHlq1hcFFu4QctgNoLxfyeCwe-uCJyBnYsOlELhg-G-niSttHFy5wYKjm9PI4DdvVRpqA1lwHRU/s320/IDP_water.jpg" /></a>
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A similar approach of adding a dye-sensitized group (an aza-Trp) to ribonuclease T1 enables Wei-Chih Chao and colleagues of National Taiwan University to examine the water dynamics in this protein, and specifically in the connecting loop region of the molecule (W.-C. Chao <i>et al., JPCB</i> ASAP jp503914s – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp503914s">here</a>). They find that the decay dynamics can be fitted with a two-component model, leading them to propose two conformational forms, which they call the loop-open and loop-close(d?) forms. Simulations support this idea and suggest that interconversion of the two conformers involves changes in the water network around the substituted Trp group, with water being squeezed out of the loop-close form. What I don’t get too clearly – my fault, I’m sure – is how/if these conformational changes relate to enzymatic function.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtjRmTjcGXApObZKz7vqpxwchFp5fBxPY3IHZKQSdIondaWfpbgt1Hf3ShxIvKr0NrSF18gHMIUIjqVh8J6AnHM9NmhxRCSv1qHSa_OCImsSOoLr6knx-c9L2kivQubSgRICYL60EjJBY/s1600/RNase_T1.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtjRmTjcGXApObZKz7vqpxwchFp5fBxPY3IHZKQSdIondaWfpbgt1Hf3ShxIvKr0NrSF18gHMIUIjqVh8J6AnHM9NmhxRCSv1qHSa_OCImsSOoLr6knx-c9L2kivQubSgRICYL60EjJBY/s320/RNase_T1.jpg" /></a>
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Domains of membrane proteins with different dynamics have different hydration dependence, according to Jun Wang and colleagues of the Wuhan Institute of Physics and Mathematics (Z. Zhang <i>et al., JPCB</i> <b>118</b>, 9553; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp503032h">here</a>). They use NMR to follow the dynamics of the protein chains in diacylglycerol kinase, and find that while the highly mobile regions are highly sensitive to changes in hydration – the fast, large-amplitude motions are suppressed below 20% hydration – the dynamics of the more rigid domains are insensitive to hydration. This, I daresay, is what one might expect given that the rigid domains are those embedded in the lipid membrane while the mobile domains generally extend beyond it. But is this hydration dependence an epiphenomenon of the demands for folding and packing the respective regions, I wonder, or essential to those structural differences?
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I recently wrote a feature for <i>Chemistry World</i> about the internal structures of quiescent cells and spores (<a href="http://www.rsc.org/chemistryworld/2014/05/suspended-animation">here</a>, but behind a paywall I fear), which looked to some extent into the question of what the state of the solvent in these cells is. That is now probed too by Charles Rice at the University of Oklahoma and colleagues, using deuterium NMR to look at water dynamics in bacterial (<i>B. subtilis</i>) spores (A. W. Friedline <i>et al., JPCB</i> <b>118</b>, 8945; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp5025119l">here</a>). They conclude that the water in the cytoplasm is in a mixture of states: there is some water that is mobile and accessible to proton exchange with the external environment, and also some that is more rigid and inaccessible to exchange. Some of the latter seems to be “bound water” associated with hydrated biomolecules, but some is sequestered in an essentially rigid core, which is however not ice-like. This raises questions of whether such water is a passive consequence of the dormancy of the cell (for example because of the relative lack of molecular motion such as that driven by transport motor proteins), or an active aspect of that shutdown, which perhaps helps to protect the molecular ingredients. And is it gel-like, glassy, or…? An interesting contribution to an unfolding story.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6iQR_K7HZ1S_cT9c0Jkh9P8KTgPabZhaIE4fhJNsvnlXTaVpOnX5G4ML0VbcIokd2X8yETwiyJhMCf3nOv8TUmEsW3cXrsh8MYPgTu0Xm0h1RQshyphenhyphen2frYtk0qP4vX9560mXl5jjWoRPA/s1600/spore_water.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEh6iQR_K7HZ1S_cT9c0Jkh9P8KTgPabZhaIE4fhJNsvnlXTaVpOnX5G4ML0VbcIokd2X8yETwiyJhMCf3nOv8TUmEsW3cXrsh8MYPgTu0Xm0h1RQshyphenhyphen2frYtk0qP4vX9560mXl5jjWoRPA/s320/spore_water.jpg" /></a>
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What do alcohols do to water? In particular, does an increasingly long aliphatic tail increasingly disrupt “water structure”? Well actually, no, according to the X-ray Raman scattering study of Iina Juurinen and colleagues at the University of Helsinki (I. Juurinen <i>et al., JPCB </i><b>118</b>, 8750, 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp5045332">here</a>). They see no substantial difference in the effects on either the hydrogen-bond network of the solvent as a whole, nor in the tetrahedrality of the alcohols’ solvation water, in progressing from methanol to ethanol and 1-propanol. This supports the earlier conclusions for methanol alone by Dixit <i>et al.</i> (<i>Nature</i> <b>416</b>, 829; 2002), who found that the total number of hydrogen bonds is unchanged in adding the alcohol to water.
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And what drives the association of glycine oligomers in water (such systems being sometimes considered simple models of intrinsically disordered proteins)? Montgomery Pettitt at the University of Texas in Galveston and colleagues explore that issue through simulation of Gly5 (D. Karadur <i>et al., JPCB</i> <b>118</b>, 9565; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp503358n">here</a>). They conclude that the aggregation is not driven by hydrogen-bonding but by electrostatic interactions between the partially charged atoms. Gly5 can’t really be considered hydrophobic, so hydrophobic interactions don’t obviously play a part, although interestingly the researchers see some features often associated with them.
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Some brief glimpses. Harsha Annapureddy and Liem Dang at PNNL in Washington present a summary of their attempts to understand water exchange in the solvation shells of ions using molecular simulations, for example by calculating the potentials of mean force (<i>JPCB </i><b>118</b>, 8917; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp502922c">here</a>). Giuseppe Bellavia and colleagues at the University of Lille explore how glycerol further enhances the denaturant properties of trehalose by rigidifying the (still liquid) solvent matrix (G. Bellavia <i>et al., JPCB</i> <b>118</b>, 8928; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp500673b">here</a>). Timothy Duignan and colleages at ANU calculate ion solvation energies at the air-water interface and say that their findings can reproduce the surface tensions of electrolyte solutions (T. Duignan <i>et al., JPCB</i> <b>118</b>, 8700; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp502887e">here</a>). And on a similar Hofmeister theme, Ferenc Bogár at the University of Szeged and coworkers report MD simulations of the effect of various salts on the interfacial tension between water and a small model protein (F. Bogár <i>et al., JPCB</i> <b>118</b>, 8496; 2014 - paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp502505c">here</a>).
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OK, with apologies to those of you who have sent me papers, I will leave it here for now and deal with them in the next post – and I’m still only caught up to early August… Oh, and I should just add that I thoroughly enjoyed this recent <a href="http://nanobubble2014.csp.escience.cn/dct/page/1">conference on nanobubbles</a> in Shanghai, hosted by the Shanghai Institute of Applied Physics. And that offers me an excuse for a parting remark from Confucius that some of you might find reassuring: “the intelligent find joy in water.”
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com11tag:blogger.com,1999:blog-7540687028464774748.post-56674140424799730792014-09-01T06:00:00.000-07:002014-09-02T03:28:50.193-07:00Life after GordonFrom time to time I wonder to myself if the number of folks reading this blog can be counted on the fingers of one hand – but judging from the kind comments I received at the wonderful Water Gordon Conference in July, I would need at least my toes too. More importantly, it seems to be appreciated; Shekhar Garde was even kind enough to advertise it in the <a href="http://www.nytimes.com/2014/07/20/opinion/sunday/shekhar-garde.html">New York Times</a>, which makes me smile somewhat at the bemusement it might have elicited in some NYT readers who perhaps tried it out. In any event, you have persuaded me to keep it up; indeed, to begin the next post on the flight home [but not to finish it then, I fear…]
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I spoke at the meeting about some of the myths of “water structure” and their origins. Jacob Israelachvili has previously referred to this “structure” as a <i>deus ex machina</i> that can be enlisted to explain anything. However, not all such explanations need be a leap of faith. For example, the notion that water inside the cavity of the chaperonin GroEL might be non-bulk-like, because of confinement and interactions with the hydrophobic cavity walls and the GroES lid, is not obviously unlikely. Song-I Han at UCSB and colleagues explore this idea in a very nice experimental paper in which they use magnetic-resonance methods to probe the water inside the GroEL-GroES complex of E. coli (J. M. Franck <i>et al., JACS</i> <b>136</b>, 9396; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja503501x">here</a>). They conclude that the density and translational dynamics of the cavity water is in fact not significantly different from the bulk. There’s a caveat that they can’t fully probe the water at the bottom of the cavity, but all the same these findings support the idea that GroEL is a “passive” cavity in which folding is much the same as it is in bulk solution.
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Had I the presence of mind to have looked at Nuno Galamba’s (University of Lisbon) paper on water around hydrophobic solutes (<i>J. Phys. Chem. B</i> <b>118</b>, 4169; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp500067a">here</a>) before my talk, I’d certainly have referred to it, since it supports my contention that dynamics might be more fruitful than alleged “structural” effects to understand how water is modified in such circumstances. His MD simulations suggest that the slowdown in orientational dynamics in the hydration spheres of small hydrocarbons is due primarily to the decline in hydrogen-bond acceptor switches, due to excluded-volume effects, rather than to any changes in “water structuring”, such as greater tetrahedrality.
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Ariel Fernandez has advanced a very provocative claim in his continuing investigation of dehydrons, structural “defects” at protein surfaces where amide-carbonyl hydrogen bonds are imperfectly hydrated due to nanoscale confinement. These sites have a net polarization arising because the water molecules are too constrained to fully align with the electrostatic field at the protein surface. This charge is negative, says Fernandez, and may behave as a proton acceptor, i.e. it has chemical functionality. He now suggests that this basicity of dehydrons may become manifest as catalytic activity, citing the high concentration of dehydrons specifically at the active site of HIV protease (<i>J. Chem. Phys.</i> <b>140</b>, 221102; 2014 – paper <a href="http://dx.doi.org/10.1063/1.4882895">here</a>). In other words, these structural defects turn the hydration water itself into a kind of catalytic assistant of protein function. It’s a fascinating idea, though I daresay many will want to see experimental or at least computational proof that the plausibility argument that Ariel advances actually stacks up.
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Sandeep Patel, Phillip Geissler, Pavel Jungwirth and several others (forgive me for the incomplete list) have been considering how ions near the air-water interface may have specific effects on the interfacial fluctuations – a new wrinkle, perhaps, on how ions induce Hofmeister-type ion-specific effects, since such modification of fluctuations might also be expected at hydrophobic aqueous interfaces. Patel now looks more closely at this idea for the case of halide ions interacting with hydrophobin II (D. Cui <i>et al., J. Phys. Chem. B</i> <b>118</b>, 4490; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp4105294">here</a>). Their simulations imply that iodide is more surface-stable than chloride – consistent with what one might expect from its greater “hydrophobicity” – and that it induces more pronounced interfacial fluctuations. In contrast, there are no significant differences in behaviour of the two ions at hydrophilic interfaces – suggesting that ion-specific effects are sensitive to the nature of the surfaces with which the ions are interacting.
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More on this topic comes from Tahei Tahara and colleagues at RIKEN’s Molecular Spectroscopy Lab in Saitama (S. Nihonyanagi <i>et al., JACS</i> <b>136</b>, 6155; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja412952y">here</a>). They use vibrational SFG spectroscopy to look at how counterions affect interfacial water vibrations (specifically the OH band) at charged interfaces. Here the effects seem to depend on the charge of the surfaces: at positively charged surfaces (of surfactant monolayers), the OH intensity decreases in the order of the halide Hofmeister series, whereas at negative surfaces there seems to be no such effect of the counter-cations. This seems to reflect the tendency of halides to be absorbed at the interface, whereas cation effects seem to operate via changes in the hydrogen-bond strength of the interfacial water. In other words, Hofmeister effects seem to have a different mechanism for anions and cations.
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I guess there is, broadly speaking, some resonance here with a study by Yoshikata Koga at UBC in Vancouver and colleagues, who look at differences in the molecular organization of cation and anion hydration spheres (T. Morita <i>et al., J. Phys. Chem B</i> <b>118</b>, 8744; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp504245c">here</a>). They use a thermodynamic methodology they have developed previously which involves addition of a cosolvent 1-propanol. They make the interesting proposal that there are five different classes of solute, which one might regard as a rather more sophisticated and physically meaningful variant of the chaotrope/kosmotrope picture. Crudely speaking, cations such as Na+ and K+ simply acquire a tight hydration shell while leaving the water beyond it unperturbed, while anions have a stronger influence with some hydrophobic character. I must say that I like this idea of trying to salvage a useable qualitative classification scheme from the confusion of the chaotrope/kosmotrope view.
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Several measures of hydrophobicity have been proposed for amino acid residues, but they aren’t always consistent. There seems to be an emerging view that this is because hydrophobicity and hydrophilicity are context-dependent parameters. That idea is supported by work from Sara Bonella and colleagues at Sapienza University in Rome (S. Bonella <i>et al., J. Phys. Chem. B</i> <b>118</b>, 6604; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp500980x">here</a>). They assess hydrophobicity in simulations based on the orientiation of water molecules at a certain distance from the amino acid in question, and say that a single quantity is not sufficient to characterize it. Rather, they suggest a three-parameter index, the components of which emerge from the statistical analysis of water orientation in ways that seem clear enough but which I can’t easily see how to summarize. The authors say that this method seems to work for predicting which regions of membrane proteins are the transmembrane sections.
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Lei Zhou and Qinglian Liu at Virginia Commonwealth University say that adding a layer of explicit water on the surface of proteins whose normal modes are being calculated to predict anisotropic B-factors in their crystallographic structures improves the agreement with experiment (<i>J. Phys. Chem. B</i> <b>118</b>, 4069; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp4124327">here</a>). It’s a nice illustration of the intimate coupling of protein and solvent.
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It’s possible to engineer a buried ion pair in the hydrophobic interior of a protein without significant structural reorganization of the rest of the protein. That’s the conclusion of a study by Bertrand Garcia-Moreno E. of Johns Hopkins and colleagues (A. C. Robinson <i>et al., PNAS</i> <b>111</b>, 11685; 2014 – paper <a href="http://www.pnas.org/content/111/32/11685.abstract">here</a>). They have re-engineered staphylococcal nuclease (SNase) so that it incorporates an ionizable Glu-Lys pairing (2.6 Å apart) in its interior. Although the Coulomb interaction of these largely unscreened charges is appreciable, it is not enough to offset the dehydration of the buried charges. However, two water molecules are able to penetrate deeply into the core to provide some hydration, and one of these seems able to participate in a water wire to facilitate proton transport to and from the buried ion pair. As a result, the pair is accommodated well without disrupting the protein’s structure significantly. This is useful to know because such buried ion pairs participate in some important enzymatic processes, including proton transfer and electron transfer – so there is no obvious reason why this sort of catalytic capability might not be engineered artificially into proteins.
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More on the mode of operation of osmolytes: Francisco Rodríguez-Ropero and Nico van der Vegt at the TU Darmstadt say, on the basis of MD simulations, that urea stabilizes the folded state of PNiPAM via direct interactions (<i>J. Phys. Chem. B</i> <b>118</b>, 7327; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp504065e">here</a>). The urea molecules enter the first hydration shell thanks to vdW interactions with the hydrophobic isopropyl groups of the polymer, creating an entropic driving force for folding via the formation of this “urea cloud”.
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Irisbel Guzman and Martin Gruebele at Illinois offer a nice review of methods (especially fast relaxation imaging) for probing protein folding <i>in vivo</i>, where interactions with other proteins, aggregation and macromolecular crowding effects can be important (<i>J. Phys. Chem. B</i> <b>118</b>, 8459; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp501866v">here</a>).
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And Fabio Sterpone at the Université Paris Diderot and colleagues provide a nice review of the coarse-grained OPEP protein model for investigating all manner of cell phenomena ranging from DNA complexation and amyloid formation to crowding and hydrodynamics – the latter applied, for example, to protein unfolding (F. Sterpone <i>et al., Chem. Soc. Rev.</i> <b>43</b>, 4871; 2014 – paper <a href="http://pubs.rsc.org/en/content/articlelanding/2014/cs/c4cs00048j#!divAbstract">here</a>).
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Sambhu Datta at the Indian Institute of Technology and coworkers propose a comprehensive quantum-chemical treatment of the solubility of CO2 in water that includes a consideration of how hydrogen-bonding changes alter phonon energies in the fluid (T. Sadhukhan <i>et al., J. Phys. Chem. B </i><b>118</b>, 8782; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp505237s">here</a>). They say may explain how it is that RuBP in chloroplasts seems able to significantly enhance the gas solubility, increasing the rate of photosynthesis.
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For anyone who wants to check out the full details (and can read French), Guillaume Jeanmairet has made available (<a href="http://arxiv.org/abs/1408.7008">http://arxiv.org/abs/1408.7008</a>) his PhD thesis on a computationally inexpensive DFT treatment of water (see G. Jeanmairet <i>et al., J. Phys. Chem. Lett.</i> <b>4</b>, 619; 2013).
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com10tag:blogger.com,1999:blog-7540687028464774748.post-82383247337211840542014-06-23T10:05:00.001-07:002014-06-23T10:05:31.584-07:00Catching up in the RuhrThe direct-interaction picture of the action of denaturants receives some support from a study by Santosh Kumar Jha and Susan Marqusee of UC Berkeley (<i>PNAS</i> <b>111</b>, 4856; 2014 – paper <a href="http://www.pnas.org/content/111/13/4856.abstract">here</a>). They look at the denaturing activity of guanidinium chloride on RNase H using FRET, UV CD and kinetic measurements. They find that the initial stage of unfolding involves a fast transition to a dry molten globule, showing that it entails denaturant interactions that do not affect the solvent-accessible surface area or disrupt the hydrophobic core. It is hard to square this with any idea that GdmCl acts, at least initially, via some kind of destabilization of hydrophobic interactions.
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Benjamin Schuler at the University of Zurich and coworkers also use FRET to study solvation effects on conformational changes, in this case looking at the temperature-dependent collapse of five intrinsically disordered proteins (R. Wuttke <i>et al., PNAS</i> <b>111</b>, 5213; 2014 – paper <a href="http://www.pnas.org/content/111/14/5213.abstract">here</a>). These proteins become more compact as the temperature is raised. Naively this might argue for a hydrophobic, entropically driven mechanism of collapse, but the researchers argue that it’s not that simple, not least because the effect is strongest for the most hydrophilic IDP. They say that this implies a dominant contribution from temperature-dependent solvation changes for charged and polar residues, although it seems the details of that phenomenon remain to be elucidated.
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There are, broadly speaking, two kinds of IDPs. One type (group a) is completely disordered, the other (group b) has regions of defined secondary structure connected by disordered stretches. Nidhi Rawat and Parbati Biswas of the University of Delhi have compared the dynamics of intermolecular and intramolecular hydrogen bonds for the two cases using MD (<i>J. Phys. Chem. B</i> <b>118</b>, 3018; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp5013544">here</a>). They find that both exhibit rather similar dynamics, in both cases with the intramolecular H-bonds rather longer-lived than the intermolecular ones. But the former are somewhat more persistent in group b IDPs – perhaps as one would expect from their higher degree of structure.
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Terahertz spectroscopy as a means of understanding picosecond and nanometre-scale hydration dynamics have been pioneered by Martina Havenith and her coworkers at Bochum (from where I am at this very moment returning, if the extraordinary summer storms permit…). But it has been challenging to correlate particular spectral features in this frequency range with particular molecular-scale motions. By combining THz measurements with ab initio MD simulations conducted by Dominik Marx, the Bochum group has now been able to make this connection for the case of glycine, using heavy water to identify distinct intramolecular and intermolecular vibrations, rotations and translations involving interfacial water (J. Sun <i>et al., JACS</i> <b>136</b>, 5031; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja4129857">here</a>).
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhyro-WPPH3lfdbB7hZbmQzVIvIxegOVSe3ARrf5My46i8A009SyKFvqRbaVZZqOosf4qFoPxkxZTLOuC3HK0o8OZDhnE7qIqLIl9IuXr0wXj0p1V0aEwQNoKFCks3gTWeZ2u2sWn-XU6U/s1600/Unwetter-in-Deutschland.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhyro-WPPH3lfdbB7hZbmQzVIvIxegOVSe3ARrf5My46i8A009SyKFvqRbaVZZqOosf4qFoPxkxZTLOuC3HK0o8OZDhnE7qIqLIl9IuXr0wXj0p1V0aEwQNoKFCks3gTWeZ2u2sWn-XU6U/s320/Unwetter-in-Deutschland.jpg" /></a>
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Proof that the RESOLV summer school in Bochum was electrifying...
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It was a pleasure to meet Roland Winter again on this trip. His group at Dortmund, with collaborators in Maryland, have used neutron spin echo spectroscopy to study solvent effects on the formation of amyloid fibrils by (bovine) insulin, which happens in the presence of sodium chloride (M. Erlkamp <i>et al., J. Phys. Chem. B</i> <b>118</b>, 3310; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp500530h">here</a>). They find that solvent conditions (pH, salt concentration) that promote aggregation support self-diffusion of insulin, which suggests the absence of strong concentration gradients, whereas when fibril formation is suppressed, diffusion displays the collective character diagnostic of strong concentration fluctuations. Does this seem counterintuitive to you? It does to me. But I think I see the point that stronger fluctuations imply a ‘softer’, low-compressibility system in which intermolecular interactions are rather weak.
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Ariel Fernández has previously argued (<i>J. Chem. Phys.</i> <b>139</b>, 085101; 2013) that the normal picture of the electrostatics of hydration first developed by Debye, in which water dipoles tend to align themselves with the electrostatic field, can break down at protein surfaces when sub-nanometre curvature and/or chemical heterogeneity produces constraints and frustration, leading to defects in the matrix of water-water interactions. These in turn introduces an anomalous polarization orthogonal to the electric field. During protein folding, water molecules that introduce these anomalies are driven away from the interface to minimize electrostatic energy, leaving water-exposed hydrogen-bonding groups on the protein backbone called dehydrons. In a preprint, Fernández now argues that this energy minimization drives the folding process, and that it leads to the healing of packing defects as the protein folds. The torque exerted by the protein’s electrostatic field on the water molecules at these defects inhibits water reorientation. Fernández suggests that antifreeze proteins have a particularly high density of such defects, and the resulting hindrance of water reorientation prevents the nucleation of ice at these sites.
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More active water networks: Kakali Sen and Walter Thiel at the MPI für Kohlenforschung at Mülheim find using MD and quantum chemical simulations that the mechanism of the P450 enzyme CPY107A1, which catalyses a hydroxylation, involves two water networks at the active site (<i>J. Phys. Chem. B</i> <b>118</b>, 2810; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp411272h">here</a>). At least one of them, based around residue E360, is involved in proton transfer to enable activation of molecular oxygen at the Fe(II) reactive site.
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And again: a water wire supports proton translocation in Complex I, in which this proton pumping is redox-driven by being coupled to the movement of electrons from NADH to quinones: the first step in the mitochondrial and bacterial respiratory process. That’s the conclusion of a simulation study by Gerhard Hummer at NIH and colleagues (V. R. I. Kaila <i>et al., PNAS</i> <b>111</b>, 6988; 2014 – paper <a href="http://www.pnas.org/content/111/19/6988.abstract">here</a>). The results are based on the crystal structure of Complex I from <i>E. coli</i>, and they imply that the water channel is formed by the cooperative hydration of three antiporter-like subunits within the membrane domain of the complex. The researchers argue that their results “suggest that water-gated transitions may provide a general mechanism for proton-pumping in biological energy conversion enzymes”, such as bacteriorhodopsin and cytochrome c oxidase.
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OK, so we know that hydrated proteins can undergo a glass-like transition at low temperatures. But can essentially dry proteins do the same thing? That question is explored by Anna Frontzek at the A. F. Ioffe Physical Technical Institute of the Russian Federation in St Petersburg and colleagues (A. Frotnzek <i>et al</i>., <i>J. Phys. Chem. B</i> <b>118</b>, 2796; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp4104905">here</a>). They look at BSA at a hydration of just 0.04 and find anomalous relaxational dynamics around 250 K, indicative of a glass-like transition even in the absence of significant hydration water.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com7tag:blogger.com,1999:blog-7540687028464774748.post-75591230031524877492014-05-09T03:57:00.002-07:002014-05-09T03:57:11.444-07:00The things internal waters get up toI’d not previously come across guanine quadruplexes (GQs) before seeing the paper by Van Ngo and colleagues of the University of Southern California (<i>J. Phys. Chem. B</i> <b>118</b>, 864; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp408071h">here</a>). These structures have been seen in human telomeres, where they can form from single-stranded DNA, but their biological role is still unclear. Telomeric GQs are stabilized by monovalent cations such as sodium, potassium and ammonium, and they have been shown capable of conducting such ions along their axis, suggesting that they can be exploited as artificial ion(-selective) channels. Ngo and colleagues investigate this process of ion conduction using MD. They find that the central channel of a GQ can host a single-file chain of water molecules, and that the passage of ions along this channel is accompanied by water molecules being “knocked out” of the chain and escaping the channel. It seems that sodium ions can move along the axis at scarcely any energetic cost, whereas for potassium there is a barrier of about 4 kcal/mol for progression from one binding site to the next. Potassium is, however, the optimal fit inside the GQ core, and so these ions are more likely to be selectively bound, while sodiums are more readily conducted.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhg7tilgfFN1ti6uAg46QgRgilRwSlsDa4lMRGQc8cAGNUKN42t5ekEjqCN-IveMfe57FnuGRfcRJxg0JcYBquVihtd4V1JoRVP9lbC1TYZ2w10S55mykDt9ItT7Z3tiPR4tRIqUFZ6ZmM/s1600/GQ_channel.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhg7tilgfFN1ti6uAg46QgRgilRwSlsDa4lMRGQc8cAGNUKN42t5ekEjqCN-IveMfe57FnuGRfcRJxg0JcYBquVihtd4V1JoRVP9lbC1TYZ2w10S55mykDt9ItT7Z3tiPR4tRIqUFZ6ZmM/s320/GQ_channel.jpg" /></a>
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The ion channel and water chain
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGAfUEWySIdz6V35fPsPCMbT7vkwS9Nh8pg_YhvpgNaj4WckWmaqaR9n_iwTMaQ58yGZVsmXFRluvxI2uze7zo6ojGXc0vmK91cRi8DfX6-QpGCVkNNqyJCiY235t9dxx-QyNs3TUaTBo/s1600/GQ_sodium.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhGAfUEWySIdz6V35fPsPCMbT7vkwS9Nh8pg_YhvpgNaj4WckWmaqaR9n_iwTMaQ58yGZVsmXFRluvxI2uze7zo6ojGXc0vmK91cRi8DfX6-QpGCVkNNqyJCiY235t9dxx-QyNs3TUaTBo/s320/GQ_sodium.jpg" /></a>
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How sodium ions move down the chain
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Some time ago, Bertil Halle and Johan Qvist reported NMR results showing that the effect of temperature on water dynamics in the hydration shell of a hydrophobic small solute is non-monotonic (<i>JACS</i> <b>130</b>, 10345; 2008). A molecular-scale explanation for this has never really been developed. That’s the objective of a paper by Damien Laage at the ENS in Paris and colleagues (E. Duboué-Dijon <i>et al., J. Phys. Chem. B</i> <b>118</b>, 1574; 2014 - paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp408603n">here</a>). They have previously accounted for the retarded water dynamics in the hydration shell on the basis of excluded-volume effects that hinder local rearrangements of the hydrogen-bond network. This is the starting point for the new work (in which the solute is TMAO), but it alone is not sufficient to explain the temperature dependence. Rather, the researchers need to include an additional perturbation that describes the difference between structural fluctuations in the shell and in the bulk: at low temperatures, the constraints created by the interface with the solute impose a lower degree of structuring in the shell than is possible in the bulk.
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Damien has followed this with a subsequent paper with Aoife (that’s “Eefa” to you non-Celts) Fogarty, in which they probe the reorientational dynamics of individual waters in the hydration shells of four different proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme and ubiquitin (J. Phys. Chem. B jp409805p – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp409805p">here</a>). Despite their many differences, all of these proteins have rather smiliar hydration-shell dynamics, which the authors suggest is an indication of how the dynamics are determined by rather general features of surface chemistry and topology, which induced excluded volume effects and hinder the approach of new hydrogen-bond acceptors within the hydration network. Fluctuations of the protein surface provide an additional source of dynamic heterogeneity. The authors also explore the effects of water confinement, for example within clefts and cavities of partially hydrated subtilisin.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxT8ezp-sahvjG_whPVsnMHJqrgnEdoRlLo5DN0kqUtWkl5KtFzL9vmo6paYVkQax9wZrRGT0M4guGctysHxRIliG3OvtDi6sP8yuFD6XTExaBY3or2ELBzQWRxodoKo-ojrJyiClV01o/s1600/reorientational_dynamics.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxT8ezp-sahvjG_whPVsnMHJqrgnEdoRlLo5DN0kqUtWkl5KtFzL9vmo6paYVkQax9wZrRGT0M4guGctysHxRIliG3OvtDi6sP8yuFD6XTExaBY3or2ELBzQWRxodoKo-ojrJyiClV01o/s320/reorientational_dynamics.jpg" /></a>
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The water reorientational times mapped onto the surfaces of the respective proteins.
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More roles for internal water molecules at ligand binding sites: Dario Estrin of the University of Buenos Aires and colleagues find that a water molecule close to the heme group of a group of mutated forms of the thermostable hemoglobin can influence the energy barriers for ligand entry and exit through steric hindrance (J. P. Bustamante <i>et al., J. Phys. Chem. B</i> <b>118</b>, 1234; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp410724z">here</a>).
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It seems that internal waters may also be critical for the functioning of ion channels. Michael Green and colleagues at CUNY report quantum calculations on the KV1.2 potassium channel which suggest that water molecules hydrating the ion in the channel, but not visible in X-ray structures, have a determining influence on the path of the ion (A. M. Kariev <i>et al., Biophys. J.</i> <b>106</b>, 548; 2014 – paper <a href="http://www.cell.com/biophysj/abstract/S0006-3495%2813%2905758-5">here</a>). Without an internal water network (for example, in a mutant form of the channel), the ion can get ‘stuck’, and the conductivity is much reduced. The authors also argue that protonation of the His418 residue by water is essential for gating, which might explain the observation that deuterated water slows down the gating.
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How does water govern the conformations adopted by unfolded proteins? That question has gained urgency thanks to the discovery of intrinsically disordered proteins. One fact seems clear: the unfolded conformations are not arbitrary or ergodic. Reinhard Schweitzer-Stenner and colleagues at Drexel University have conducted circular dichroism and NMR studies of small peptides to get an insight into the thermodynamic factors involved, and particularly into the role of enthalpy-entropy compensation (S. E. Toal <i>et al., J. Phys. Chem. B</i> <b>118</b>, 1309; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp500181d">here</a>). They find that this compensation is virtually perfect, in that there is a linear relationship between the ΔH and ΔS of solvation for glycine-terminated poly-proline, with the two cancelling exactly (ΔG=0) at about 295 K. In other words, while solvent reorganzation contributes to both the enthalpy and entropy of solvation in this (near-physiological) temperature range, it doesn’t really affect the conformational equilibria at all.
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What is denaturation, anyway? Is it the same thing, regardless of how it occurs? Not according to Bruce Berne at Columbia and colleagues, who report simulations of ubiquitin which show that chemically-induced and force-induced (pulling) denaturation produce quite different states (G. Stirnemann <i>et al., PNAS</i> <b>111</b>, 3413; 2014 – paper <a href="http://www.pnas.org/content/111/9/3413.abstract">here</a>). Denaturation promoted by urea produces a partly extended state with many non-native contacts, while force-unfolding creates a fully extended state with no contacts. That is perhaps what one might expect, but the full details of the conformational differences, such as differences in the dihedral angles, revealed here are not at all obvious.
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Understanding the fibrous structure of cellulose in plant cell walls might be crucial to the efficient conversion of biomass to biofuels. Goundla Srinivas at Oak Ridge and colleagues say that an explicit solvent model might be needed to adequately model the transition between the crystalline and amorphous states of cellulose, and they present a coarse-grained approach for doing this (G. Srinivas <i>et al., J. Phys. Chem. B</i> <b>118</b>, 3026; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp407953p">here</a>).
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I have not previously come across the rhodopsin called channelrhodopsin, which differs from the light-driven ion-pump rhodopsins in that it enables passive cation conductance. How it does so is the subject of a paper by Hideki Kandori of Nagoya Institute of Technology and coworkers (S. Ito <i>et al., JACS</i> <b>136</b>, 3475; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja410836g">here</a>). They say that, as with pumps such as bacteriorhodopsin, the conductance depends on a network of water molecules around the chromophore. Their FTIR spectra reveal that nine distinct water vibrational bands are implicated in the passage of cations, which they rationalize in terms of a network incorporating four bound waters around the Schiff base (shown below).
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnqkra9oavSI2YR_TBTbQXQ_o7DQac2UmcjdacYUesXHjOVO9yLLnfURLfHidCTGXECRj-cbC4Nu7Ixd7dnodqk1Bc-JtAoZuG9cgA9fF-TEp4eVNHjmvtMGK-UaQx8iZPrpovkuSZ-q0/s1600/ChR_water_network.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhnqkra9oavSI2YR_TBTbQXQ_o7DQac2UmcjdacYUesXHjOVO9yLLnfURLfHidCTGXECRj-cbC4Nu7Ixd7dnodqk1Bc-JtAoZuG9cgA9fF-TEp4eVNHjmvtMGK-UaQx8iZPrpovkuSZ-q0/s320/ChR_water_network.jpg" /></a>
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But it seems it’s not always so easy to figure out what internal water networks are up to. There is a water-filled pore threading through enzymes called family 48 cellulases, which exist primarily in bacteria and catalyse the hydrolysis of cellulose. Evidently that process consumes water, and it’s been thought that the pore might provide a channel for replenishing water at the active site. But this may not be the case, according to John Brady at Cornell and coworkers (M. Chen <i>et al., J. Phys. Chem. B</i> <b>118</b>, 2306; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp408767j">here</a>). They have studied one of these enzymes, Cel48A from <i>Thermobifida fusca</i>, with both simulations and experimental site-directed mutagenesis, in particular looking at the effect of inserting hydrophobic groups into the pore region to disrupt the water channel. When this is done experimentally, the mutants don’t fold properly. And in the simulations, while hydrophobic residues can prevent water from filling the pore, it could find other ways of diffusing to the active site. So whether or not the water channel is functional remains unresolved.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlJTaZupDr92HYSgpyYBP5bb0m9wrL3_WQq5NekNH837nISOIw3iIntQ4G9iP0moTMr-qTN8wVSwQvbVI7khc9HNordqFP9W39sLYu4Kcu9f_Y4moERKXcqY54yME4c2F2pFtPaID3x20/s1600/Ch48.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhlJTaZupDr92HYSgpyYBP5bb0m9wrL3_WQq5NekNH837nISOIw3iIntQ4G9iP0moTMr-qTN8wVSwQvbVI7khc9HNordqFP9W39sLYu4Kcu9f_Y4moERKXcqY54yME4c2F2pFtPaID3x20/s320/Ch48.jpg" /></a>
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Side view (left) and top view (middle) of the water pore structure in Cel48A, illustrating the division of the pore into rings 1, 2, 3, 4, and 5, coloured blue, red, green, orange, and yellow. On the right, only the five rings are illustrated as coloured van der Waals surfaces, along with the substrate chain.
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How to quantify the hydrophobicity of protein residues is a long-standing question, and it is now clear that this depends on the structural context in which the residue finds itself. Amish Patel at U. Penn. and Shekhar Garde at Rensselaer Polytechnic Institute report a method for assigning a value of hydrophobicity that takes account of this context, based on the hydration free energy for cavity formation around the residue in question (<i>J. Phys. Chem. B</i> <b>118</b>, 1564; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4081977">here</a>). They report its use for the protein hydrophobin II, for which they provide a “hydrophobicity map” (here using a benzene-shaped “probe”, which explains the hexagonality of these images). The shape of the probe matters – a map using a small spherical probe looks slightly different from these ones.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgmkO0LMo27JLPrjLwyE45LlXz5ZelI6almVCi-3JlnFaqKoDvTZbjUuHjirkxtwyIe6xsEdCkvSr4Jured36YLJyADtE6QKpjoU1x1dcoQjfFrqX_6onF3PhjwdKMmIvtfsaP4bfXKPig/s1600/hydrophobicity_map.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgmkO0LMo27JLPrjLwyE45LlXz5ZelI6almVCi-3JlnFaqKoDvTZbjUuHjirkxtwyIe6xsEdCkvSr4Jured36YLJyADtE6QKpjoU1x1dcoQjfFrqX_6onF3PhjwdKMmIvtfsaP4bfXKPig/s320/hydrophobicity_map.jpg" /></a>
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Hydrophobicity map for hydrophobin II, from two directions
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A different approach to the same end is described by Jürgen Hubbuch at the Karlsruhe Institute of Technology and coworkers (S. Amrhein <i>et al., J. Phys. Chem. B</i> <b>118</b>, 1707; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp407390f">here</a>). They too attempt to develop a hydrophobicity scale that takes account of the residue’s position on the protein surface, and compare it with experiments using UHPLC. Their approach also uses (presumably hydrophobic) probe or ‘tracer’ molecules that are sensitive to the topological constraints around a given residue, quantified by a modified radial distribution function.
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Water self-diffusion in salt solutions is anomalous with respect to the pure bulk (e.g. J. S. Kim <i>et al., J. Phys. Chem. B </i><b>116</b>, 12007; 2012). Yun Ding at ETH and colleagues show that this can be explained using ab initio MD simulations, and that it does not need any notion of “structure-making/breaking” (<i>PNAS</i> <b>111</b>, 3310; 2014 – paper <a href="http://www.pnas.org/content/111/9/3310.abstract">here</a>). The ions “do not disrupt the [water] network in any significant manner”, they say. Rather, the molecular explanation is subtle, involving dynamic and electronic heterogeneity of the water molecules on diffusional timescales. I can’t help thinking that there is a moral here about the sometimes dangerous allure of physically intuitive explanations – the fact seems to be that on occasion a simple picture is merely simplistic.
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The ab initio study of the geometry of the hydrogen-bond network in liquid water by Thomas Kühne and Rustam Khalliullin at the University of Mainz, on which I <a href="http://www.rsc.org/chemistryworld/2013/02/water-structure-tetrahedral-controversy-xas-xafs">reported some while back</a>, has now been extended by these authors with a comparison to the network geometry in hexagonal ice (<i>JACS</i> <b>136</b>, 3395; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja411161a">here</a>). The results essentially support the previous picture, namely that “the traditional description of liquid water is fundamentally correct [but] for a significant fraction of molecules the hydrogen-bonding environments are highly asymmetric with extremely weak and distorted bonds”.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com5tag:blogger.com,1999:blog-7540687028464774748.post-25676564354298763672014-03-12T02:22:00.000-07:002014-03-12T02:22:26.695-07:00Weird antifreeze<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijqX37nZK7Uc4KKFFYfPviYP57TfPVdWcTWVHoMftMUMluvrnBQRn6XtAgu444Z3i1EKEpK8LKQRlPqFCpReJxX2ltoMJTdDQ6W18VvmWKxc8_8XC3rnRDJ_eixRgpzUi-ZchgMc0pB-4/s1600/F3.medium.gif" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEijqX37nZK7Uc4KKFFYfPviYP57TfPVdWcTWVHoMftMUMluvrnBQRn6XtAgu444Z3i1EKEpK8LKQRlPqFCpReJxX2ltoMJTdDQ6W18VvmWKxc8_8XC3rnRDJ_eixRgpzUi-ZchgMc0pB-4/s320/F3.medium.gif" /></a>
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The oddest finding I’ve seen recently has to be the crystal structure of the fish antifreeze protein Maxi reported by Peter Davies of the Queen’s University in Kingston, Canada, and colleagues (T. Sun <i>et al., Science</i> <b>343</b>, 795; 2014 – paper <a href="http://www.sciencemag.org/content/343/6172/795">here</a>). This is a four-helix bundle with an interior, mostly hydrophobic channel filled with more than 400 water molecules, crystallographically ordered into a clathrate-like network of mostly five-membered rings. It seems that this ordered network extends outward through the gaps between the helices, helping to create an ordered later of water molecules on the outer surface that enables Maxi to bind to ice crystals and hinder their growth. Commenting on this work, Gerhard Hummer has called the water network a kind of molecular Velcro that holds the coils together. I have described this work in more detail in a <a href="http://www.rsc.org/chemistryworld/2014/02/ice-core-antifreeze-protein-inner-workings-flounder-clathrate">news story</a> for <i>Chemistry World</i>.
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Water molecules buried deep within a protein’s interior can have extremely slow dynamics. That fact acquires functional significance in potassium channels, according to Marc Baldus of Utrecht University and coworkers (M. Weingarth <i>et al., JACS</i> <b>136</b>, 2000; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja411450y">here</a>). These channels have remarkably slow recovery rates from the non-conductive to the conductive form, especially given that the macromolecular rearrangements involved don’t appear to be large. Using NMR and MD simulations, Baldus <i>et al.</i> find that there are several buried, ordered waters with long residence times behind the selectivity filter region of the channel, and that the recovery pathway involves exchange of these with bulk water.
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Warren Beck and colleagues at Michigan State have used guanidinium as a probe of the coupling of a protein – here zinc-substituted cytochrome c – to its hydration shell (J. Tripathy <i>et al., J. Phys. Chem. B</i> <b>117</b>, 14589; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp404554t">here</a>). They attribute the fluorescence Stokes shift response in the presence of Gdm ions to the enhanced flexibility of the protein-solvent network caused by direct binding of Gdm+ to the protein surface.
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A far more idealized case of osmolyte effects on hydration is reported by Jens Smiatek of the University of Stuttgart, who considers how the hydration of charged model spheres is altered by urea and hydroxyectoine (<i>J. Phys. Chem. B</i> <b>118</b>, 771; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp410261k">here</a>). The agenda here is the molecular mechanisms of so-called chaotropic and kosmotropic influences of osmolytes – whether, for example, these involve direct solute-cosolute or indirect (‘structure-making/breaking’) effects. It’s hard to generalize, however, about the results, other than perhaps to say that indirect effects seem to be minor and that the direct interactions of the cosolutes depends on the nature (here charge) of the solute surface. Smiatek concludes that the interactions are more complex than has often been assumed, and that “a general theory for kosmotropic and chaotropic behavior is far from being fully understood… [o]ne reason is the observed specific dependence on the considered solute surface characteristics.”
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Similar issues are also explored by Abani Bhuyan and coworkers at the University of Hyderabad (P. Sashi <i>et al., J. Phys. Chem. B </i><b>118</b>, 717; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp4111103">here</a>). They use methanol titration to look at cosolvent effects on the alcohol-induced unfolding of cytochrome c at different pH, and thus differing degrees of side-chain ionization. They find that, with increasing protein charge, increasing amounts of water molecules are associated with the peptide chain, presumably because charge repulsion causes expansion of the folded state. Correspondingly larger amounts of hydration water are thus excluded by the methanol as the unfolding proceeds.
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Specific ion (Hofmeister) effects on the diffusion of water at the hydration surface of a lipid bilayer are reported by Songi Han and colleagues at UCSB (J. Song <i>et al., JACS</i> <b>136</b>, 2642; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja4121692">here</a>). They use Overhauser nuclear dynamic polarization to monitor water diffusion in the 2-3 layers close to the surface of a lipid vesicle, and find that various ions can have an accelerating or retarding effect that is in line with the Hofmeister series. They put the case nicely: “The concept of ions generally altering the bulk water structure, in the absence of molecular surfaces, does not seem plausible in explaining the effects of ions at the molecular level on surfaces in electrolyte solutions. However, it has been discussed in the literature that the ion’s effect on the local hydration water structure directly surrounding the ions can differ depending on the ion type”. That’s the case they make, and moreover propose a general mechanism: “This suggests that the origin of the Hofmeister ions may be the balancing between macromolecule−water and macromolecule− macromolecule interaction through the modulation of the effective surface hydrophilicity and hydrophobicity mediated by specific ions in dilute solution.”
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Why, though, are water molecules generally retarded at lipid membrane surfaces in the first place? It has been suggested that the water molecules might form bridges between the lipid head groups that stabilize the membrane. This ideas is explored by Eiji Yamamoto and colleagues at Keio University in a preprint <a href="http://www.arxiv.org/abs/1401.7776">http://www.arxiv.org/abs/1401.7776</a>. Their MD simulations indicate that water undergoes subdiffusion at a membrane surface due to binding and unbinding of the molecules in bridging conformations. The authors point out that these retarded dynamics of water might be biologically efficacious in increasing the efficiency of biomolecular binding reactions at the membrane.
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In a water monolayer confined between two parallel graphene sheets, ions can induce the formation of long fluctuating chains of hydrogen-bonded molecules that can extend for up to 30 or so molecules, according to simulations by Petr Král and colleagues at the University of Illinois at Chicago (I. Strauss <i>et al., JACS</i> <b>136</b>, 1170; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja4087962">here</a>). These chains can bridge two ions of opposite charge, and remain locked in place even at room temperature.
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Water passing through carbon nanotubes has been found previously to have a high, almost frictionless flow rate and collective dynamics. Thomas Sisan and Seth Lichter at Northwestern now argue from MD simulations that, when the nanotubes are particularly narrow, this flow can occur in the form of solitons (<i>Phys. Rev. Lett.</i> <b>112</b>, 044501; 2014 – paper <a href="http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.112.044501">here</a>). The solitons are composed of defects in the single-file water chain that convect mass.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com3tag:blogger.com,1999:blog-7540687028464774748.post-78873188122939797902014-01-23T02:20:00.002-08:002014-01-23T02:20:59.969-08:00Does bulk water get crowded out of cells?Although terahertz spectroscopy has become an important tool for studying biomolecular hydration, its interpretation is not straightforward. To resolve some of the ambiguities, Robert Donnan and colleagues at Queen Mary College in London have used MD to compute the vibrational density of states for several hydrated proteins of varying size, looking in particular at the distance and timescales probed by THz (O. Suchko <i>et al., J. Phys. Chem. B</i> <b>117</b>, 16486; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp407580y">here</a>). They find that for all the cases studied – lysozyme, BPTI, TRP tail and TRP-cage – the hydration layer is 10 Å thick, and displays similar dynamics. Differences in the solvation dynamics for these systems seemed to stem primarily from highly retarded water molecules in the proteins’ interiors.
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What dominates the solvation free energies of peptides? One view is that it is the free energy needed to create a cavity in the solvent. But this may be offset to at least some degree by the electrostatic interactions of polar groups with the water, and/or by the van der Waals interactions. To examine this balance, Montgomery Pettitt at the University of Texas at Galveston and colleagues have performed MD calculations for flexible alanine oligomers (H. Kokubo <i>et al., J. Phys. Chem. B</i> <b>117</b>, 16428; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp409693p">here</a>). They find that, for rigid peptides the free-energy gains from vdW interactions more than compensate for the cost of cavity formation as the oligomers get longer. But when the solutes are flexible and allowed to collapse, this situation reverses – implying that van der Waals interactions provide a significant driving force for the collapse. It seems not yet clear, however, what role intramolecular interactions play in the collapse, since the fluctuations in that component of the free energy are large.
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The role of water in the complexation of DNA-binding agents is examined for the case of the minor-groove binder netropsin by Edwin Lewis of Mississippi State University and colleagues (J. P. Ramos <i>et al., J. Phys. Chem. B</i> <b>117</b>, 15958; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp408077m">here</a>). Specifically, they use calorimetry to look at how binding is affected by osmolytes (TEG and betaine), which introduce an osmotic pressure on the hydration water. The results support the earlier idea that there are two distinct binding modes of netropsin, and allow quantification of the water molecules that seemingly hydrate the bound molecule: 31 and 19 molecules for the two cases. Moreover, in the latter case at least one water molecule seems to remain trapped at the binding site, mediating the interaction with netropsin. The addition of the osmolytes, which exert broadly similar effects, has much the same effect on complexation as a reduction in the temperature.
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At high concentrations, protein solutions have been found to exhibit liquid-liquid phase separation into solutions of different protein concentration. Such highly concentrated solutions are relevant to some medical conditions, such as sickle-cell anaemia and Alzheimer’s, and also to technological processes such as protein purification and storage. Johannes Möller of the TU Dortmund and colleagues relate this phase behaviour to that in protein solutions at high pressure (J. Möller <i>et al., Phys. Rev. Lett.</i> <b>112</b>, 028101; 2014 – paper <a href="http://prl.aps.org/abstract/PRL/v112/i2/e028101">here</a>). Using SAXS from lysozyme solutions, they find that the liquid-liquid phase separation is in fact re-entrant at high pressure. They attribute this behaviour to the effect of pressure on solvent-mediated protein-protein interactions, and conclude that pressure might be used as a means of controlling protein aggregation and crystallization.
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Another possible influence on protein dynamics and function at high concentrations is crowding. Kevin Kubarych and his collaborators at the University of Michigan have been studying this matter for some time, and their latest paper (J. T. King <i>et al., JACS</i> <b>138</b>, 188; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja407858c">here</a>) reports the interesting observation of a dynamical transition above a certain crowding threshold. Above this limit for lysozyme (induced by the polymeric crowding agent PEG-400, or by protein self-crowding), ultrafast 2D-IR spectroscopy reveals a significant slowdown in hydration dynamics on picosecond timescales. The authors suggest that this is a kind of jamming transition between hydration shells of the protein molecules extending out to 15-20 Å, i.e. to separations of 3-4 nm, which are certainly of the order of those found between macromolecules in cells. In other words, the transition reflects a collective frustration of rearrangements of the overlapping hydration shells. According to this picture, one would anticipate most regions of a cell to be in the “over-crowded” regime, with little “bulk-like” water. The same abrupt dynamical transition was not seen, however, in the authors’ previous studies using the small-molecule crowding agent glycerol, for which the dynamical slowdown was more gradual.
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Models of the air-water interface – including models of hydrophobic hydration that invoke an interface of that nature adjacent to the hydrophobic surface – can’t in general easily accommodate a good description of long-wavelength density fluctuations, according to an analysis by Suriyanarayanan Vaikuntanathan and Phillip Geissler at the Lawrence Berkeley National Laboratory (<i>Phys. Rev. Lett.</i> <b>112</b>, 020603; 2014 – paper <a href="http://prl.aps.org/abstract/PRL/v112/i2/e020603">here</a>). They show that discretizing the interface, as in a lattice model, effectively suppresses long-range fluctuations, even to the extent of suppressing a roughening transition, above some critical value of the interaction potential. The authors show how one can accommodate the resulting nonlinearities, which for example allows them to describe the shape dependence of interfacial free energies.
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Thomas DeCoursey of Rush University and Jonathan Hosler of the University of Mississippi Medical Center offer an intriguing discussion of the current understanding of (as the authors somewhat provocatively put it, the “philosophy of”) voltage-gated proton channels (<i>J. R. Soc. Interface</i> <b>11</b>, 20130799; 2014 – paper <a href="http://dx.doi.org/10.1098/rsif.2013.0799">here</a>). The paper includes an overview of such issues as proton hopping along water wires, and mechanisms for proton selectivity (for example, exclusion of alkali metal ions) and for the suppression of proton transport in aquaporins.
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Christopher Fennell at Oklahoma State University and colleagues have previously developed a computationally inexpensive water model called the semi-explicit assembly (SEA) model, which does a good job of calculating the solvation free energies of polar and nonpolar solvents (Fennell <i>et al., PNAS</i> <b>108</b>, 3234; 2011). They now extend the SEA model to a version they call field-SEA, which can handle ions and charged solutes with no additional computational overhead (L. Li <i>et al., J. Phys. Chem. B</i> jp4115139; 2014 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4115139">here</a>).
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com10tag:blogger.com,1999:blog-7540687028464774748.post-5523414839104976682013-12-12T01:57:00.000-08:002013-12-12T01:57:36.707-08:00Enthalpy/entropy compensationThe weak forces that govern protein-protein association and aggregation are of course intimately connected with hydration, partly for example via hydrophobic interactions but also through the electrostatic consequences of water removal at the interfaces. These effects are examined in a continuum solvent model by Sergio Hassan at the NIH in Bethesda and colleagues (A, Cardone <i>et al., J. Phys. Chem. B</i> <b>117</b>, 12360; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4050594">here</a>). They use the model to examine the barnase-barstar complex, and say that it could be extended to multi-protein systems.
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A rather exquisite water-mediated mechanism of enzymatic activity is reported by Qiang Cui at Wisconsin-Madison and colleagues (P. Goyal <i>et al., PNAS</i> <b>110</b>, 18886 – paper <a href="http://www.pnas.org/content/110/47/18886.abstract">here</a>). They describe a computational study of cytochrome c oxidase, which uses oxygen reduction to pump protons across a membrane. During this process a glutamate residue is believed to act as a temporary proton donor. Cui and colleagues show that the proton affinity of this Glu is controlled by the degree of hydration in an internal hydrophobic cavity, which is itself governed by protonation of a substituent on the heme group 10Å away, triggering movement of a loop gating the cavity’s entrance.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYaK9ai_nSz2Ev0QtfvxbJbXxsDntyt4jfA39u7csLP9xRp8kCZ0kKvxUkhe6xjosqv_9-lv-_a3IEddmQ8CZbdunMqHzbc1UYbTOuQi7nK-rT4t1fkbZY1OeRWGPkq5mgQ8qsAU7IRDM/s1600/Cui_et_al.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjYaK9ai_nSz2Ev0QtfvxbJbXxsDntyt4jfA39u7csLP9xRp8kCZ0kKvxUkhe6xjosqv_9-lv-_a3IEddmQ8CZbdunMqHzbc1UYbTOuQi7nK-rT4t1fkbZY1OeRWGPkq5mgQ8qsAU7IRDM/s320/Cui_et_al.jpg" /></a>
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Enthalpy/entropy compensation in protein-ligand binding is the topic of a nice study by George Whitesides’ group in a special issue of the <i>European Physical Journal</i> (doi:10.1140/epjst/e2013-01818-y – paper <a href="http://epjst.epj.org/articles/epjst/abs/first/st13002/st13002.html">here</a>). The group examines this issue further in a paper in JACS (B. Breiten <i>et al., JACS</i> <b>135</b>, 15579; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja4075776">here</a>), where they look at the human carbonic anhydrase system that they have also studied earlier (see P. W. Snyder <i>et al., PNAS</i> <b>108</b>, 17889; 2011). This new paper expands on that earlier work, in which a series of ligands modified with various thiazole-based sulfonamides was used to probe the effects of solvent rearrangements within the binding cavity. They find that the changes in the free energy of binding, and the contributions from enthalpy and entropy, are largely determined by the rearrangements or displacements of water, and voice a telling conclusion: “This water- centric view of ligand binding – and H/S-compensation – cannot be rationalized by the lock-and-key principle and suggests that the molecules of water surrounding the ligand and filling the active site of a protein are as important as the structure of the ligand and the surface of the active site.”
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Myoglobin binds various ligands, such as O2, CO and NO, in an internal cavity. It also binds water in internal sites, but crystallographic studies have given conflicting views on where these cavities are and how occupied they are. Shuji Kaieda and Bertil Halle at Lund have used deuteron and 17O magnetic relaxation dispersion spectroscopy to probe these hydration sites and the dynamics of the water molecules occupying them (<i>J. Phys. Chem. B</i> <b>117</b>, 14676; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp409234">here</a>). They find that the waters come and go on a microsecond timescale in all four sites, despite their significant separation, and conclude that these dynamics share a global mechanism involving transient penetration of the protein by hydrogen-bonded chains that may intermittently ‘flush’ the cavity network.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTItkOX2lHT-CsKBIX4EmdSA9HgzY8NCAEUnxQzC5GejSuqHkWCsApKwinc1QyQiy8YquMn5ZSoWpJAGBlbBzc3M7BgV5pA8tQVEcCsD4277ibgpIGL54URnQ-FvNLFl56xssmYEAl0S0/s1600/Halle_Mb.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjTItkOX2lHT-CsKBIX4EmdSA9HgzY8NCAEUnxQzC5GejSuqHkWCsApKwinc1QyQiy8YquMn5ZSoWpJAGBlbBzc3M7BgV5pA8tQVEcCsD4277ibgpIGL54URnQ-FvNLFl56xssmYEAl0S0/s320/Halle_Mb.jpg" /></a>
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5K4hAStOvMa6qXC7X_SFmWaqpA82CIXWkl17Nq3bZAx5Vyg8UZDcT9YfH_CVqtSH4TKzg9w4P5aXifmZijHxWr1IT-q-t3meOb2bYNMGKudvLTJNZgp7FnbzxN3cGYbHWHK-x2vmym98/s1600/Halle2.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi5K4hAStOvMa6qXC7X_SFmWaqpA82CIXWkl17Nq3bZAx5Vyg8UZDcT9YfH_CVqtSH4TKzg9w4P5aXifmZijHxWr1IT-q-t3meOb2bYNMGKudvLTJNZgp7FnbzxN3cGYbHWHK-x2vmym98/s320/Halle2.jpg" /></a>
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More on small-molecule solute perturbations to protein structure: Warren Beck and colleagues at Michigan State University report fluorescence spectroscopic measurements on zinc-substituted cytochrome c in the presence of guanidinium ions, in an effort to discover why Gdm+ perturbs the protein dynamics by making it apparently more flexible (J. Tripathy <i>et al., J. Phys. Chem. B</i> <b>117</b>, 14589; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp404554t">here</a>). They conclude that part of this response comes from a change in structure of the protein’s hydration shell because of direct binding of Gdm+ to the protein surface.
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How do magnesium ion channels attain their high specificity in the presence of high concentrations of calcium? Todor Dudev at the Academia Sinica and Carmay Lim at National Tsing Hua University in Taiwan say that the differences in the metals’ hydration shells are the key (<i>JACS</i> <b>135</b>, 17200; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja4087769">here</a>). Their calculations suggest that the hexacoordinated magnesium ions polarize the bound water more strongly, resulting in stronger ion-water-protein interactions.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhc_hyd2AF3OaVbTW3mNezSGaLgV0pMxt9WcUBfTQgsn0io6WqhymTNI9Zyu6QLXcqR185OkxLLMaXAU2pKhpnbyV6n7tf0NtRDTKBITTOxAngBNIxrMnQqPjhkvHyzu_450K-00UErHqE/s1600/magnesium_channel.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhc_hyd2AF3OaVbTW3mNezSGaLgV0pMxt9WcUBfTQgsn0io6WqhymTNI9Zyu6QLXcqR185OkxLLMaXAU2pKhpnbyV6n7tf0NtRDTKBITTOxAngBNIxrMnQqPjhkvHyzu_450K-00UErHqE/s320/magnesium_channel.jpg" /></a>
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How water diffuses at the surface of a lipid membrane has been studied before, but it can be hard to ensure that just the water molecules immediately at the interface are probed. Robert Bryant at the University of Virginia Charlottesville and colleagues claim to be able to do that using magnetic relaxation dispersion spectroscopy for phospholipid vesicles in deuterated water (K. G. Victor <i>et al., J. Phys. Chem. B</i> <b>117</b>, 12475; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp407149h">here</a>). They report that the water molecules explore the interface via essentially two-dimensional diffusion over the vesicle surface, with a translational correlation time that seems relatively long: about 70 ps. This modified dimensionality of water motions, they say, stems from an excluded-volume effect.
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The molecular basis of anaesthesia is still unclear, although it seems to involve low-affinity binding of the anaesthetic to proteins. Hai-Jing Wang of UNC and colleagues say that hydration water plays a crucial role in this process (H.-J. Wang <i>et al., J. Phys. Chem. B</i> <b>117</b>, 12007; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp407115j">here</a>). They use NMR to look at the binding of volatile halogenated alkanes (known anaesthetics) to BSA, which has binding pockets for such molecules. They find that binding occurs only once the hydration level of the protein surpasses a critical threshold. The molecular details of what this hydration water does remain to be elucidated, but Wang et al. suppose that the threshold hydration level is needed to “establish a favourable free-energy landscape for the binding of anaesthetics to the pre-existing binding sites.”
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Peter Rossky and Lauren Kapcha at Texas at Austin have introduced a new hydrophobicity scale for protein constituents that works at the level of individual polar and non-polar atoms rather than classifying each residue as a whole (<i>J. Mol. Biol</i>. 10.1016/j.jmb.2013.09.039 – paper <a href="http://www.ncbi.nlm.nih.gov/pubmed/24120937">here</a>). They say that it gives an appropriate measure of hydrophobicity in cases where a residue-based approach fails – without being any more computationally intense – and that it shows that this atomistic level of detail is therefore sometimes indispensable.
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Another computational challenge is addressed by Sergio Pantano of the Institut Pasteur de Montevideo in Uruguay and coworkers (H. C. Gonzalez <i>et al., J. Phys. Chem. B</i> <b>117</b>, 14438; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4079579">here</a>). They describe a way to combine the common SPC, TIP3P and SPC/E atomistic water models with a coarse-grained model called WatFour or WT4, demonstrating its effectiveness via (among other things) simulations of the β1 domain of streptococcal protein G.
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There’s a curious and interesting paper by Akira Yamakata of the Toyota Technical Institute in Nagoya and colleagues on the observation of hydration shells of ions being destroyed by electrochemical control of the ions’ binding to an electrode surface (A. Yamakata <i>et al., JACS</i> <b>135</b>, 15033; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja408326d">here</a>). The researchers use a platinum electrode rendered hydrophobic by coverage with a CO monolayer, and use time-resolved IR spectroscopy to monitor the hydration shells of tetrapropylammonium (Pr4N) and sodium ions as they are pulled onto the surface by the electric field. They can monitor the destruction of the hydration shells as this happens, and say that while that of Pr4N is rather easily destroyed at high field so that the ion interacts directly with the CO layer, the shell of sodium is more rigid and remains intact.
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Lawrence Pratt and colleagues at Tulane University use simulations to demonstrate that the hydrophobic interactions between hard-sphere solutes in water are more attractive and endothermic than is predicted by the molecular-scale Pratt-Chandler theory (M. I. Chaudhari <i>et al., PNAS</i> 10.1073/pnas.1312458110 – paper <a href="http://www.pnas.org/content/early/2013/11/27/1312458110.abstract">here</a>). This shows what an improved theory will have to shoot at.
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Peter Hamm and coworkers at the University of Zurich have used 2D Raman-THz spectroscopy to probe collective intermolecular modes of pure liquid water, and conclude that there are different types of hydrogen-bonded networks – albeit only on a very short (100-fs) timescale, which is not compatible with controversial proposals for persistent heterogeneity of these networks like that of Anders Nilssen <i>et al.</i> (J. Savolainen <i>et al., PNAS</i> 10.1073/pnas.1317459110 – paper <a href="http://www.pnas.org/content/early/2013/11/27/1317459110.abstract">here</a>). This seems to add to the growing view that this apparent controversy is best seen as a question of the different timescales being examined, and that at room temperature any ‘two-state’ picture is very rapidly averaged away.
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Finally, a curiosity about the macroscopic mechanical roles of water in plants. Peter Fratzl of the Max Planck Institute of Colloids and Interfaces in Potsdam and colleagues look at how changes in hydration can produce stresses and movement in plants via swelling and shrinkage (L. Bertinetti <i>et al., Phys. Rev. Lett.</i> <b>111</b>, 238001; 2013 – paper <a href="http://">here</a>). The free energy needed for such actuation can be considered to be provided, at least in part, by the formation of new hydrogen bonds. The authors propose a model that allows them to estimate the free energy made available by water absorption into woody plant tissue, and find that (except in the case of nearly dry tissue) it amounts to about 1.2 kT per water molecule, suggesting that the water bound to the macromolecules in the tissue acquires about one additional hydrogen bond for every eight molecules. Frankly, I don’t fully understand the arguments here: the authors say that “This would suggest that the main driving force for water absorption in non living plant tissues is a phase transition of water to a liquid state, characterized by a stronger H-bond network, occurring when H2O is confined within the macromolecular components of the wood cell wall material.” I’m going to have to get back to you on that.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com2tag:blogger.com,1999:blog-7540687028464774748.post-39787246081905261002013-11-14T02:15:00.002-08:002013-11-14T02:15:36.521-08:00Using water for drug designAlfonso García-Sosa at the University of Tartu in Estonia has published a paper getting to grips with precisely the question that I have long wanted to see addressed: how to employ water molecules in design strategies for drug binding (<i>J. Chem. Inform. Model.</i> <b>53</b>, 1388; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ci3005786">here</a>). He has analysed over 2,000 crystal structures of hydrated and non-hydrated ligand-receptor complexes (including many drugs), and finds that bridging water molecules are an effective strategy for tight binding. He concludes that such a binding mechanism could be beneficially targeted, and that “if a tightly bound, bridging water molecule is observed in the binding site, attempts to replace it [in a designed drug that binds competitively] should only be made if the subsequent ligand modification would improve also its ligand efficiency, enthalpy, specificity, and pharmacokinetic properties.” This is just the kind of large-scale study that is needed to extract the advantages or otherwise, and the effective modes, of using water molecules in ligand design.
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It seems increasingly likely that the mechanism of hydrophobic association, once considered in terms of a static picture involving expulsion of ‘bound’ water, is in fact associated with dynamical effects, in particular the fluctuations in the hydrogen-bonded network around the hydrophobes. That view is emphatically supported in a paper by Aljaz Godec and Franci Merzel of the National Institute of Chemistry in Ljubljana, working with Jeremy Smith at Oak Ridge (<i>Phys. Rev. Lett.</i> <b>111</b>, 127801; 2013 – paper <a href="http://prl.aps.org/abstract/PRL/v111/i12/e127801">here</a>). Their MC simulations of two hydrophobic particles (of about the size of a methane molecule) coming together shows that crossing over the desolvation barrier to the associated state involves a large collective fluctuation in hydration water in which the intervening hydrogen-bonded clusters are mostly displaced from the inner to the outer hydration shell. As the authors conclude, “a complete description of hydrophobic association can be obtained only by explicitly considering collective fluctuations involving many-body correlations between water molecules.”
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The observation by Amish Patel, Shekhar Garde and their colleagues that hydrophobic association is faster near a hydrophobic surface, which I have mentioned before in this blog, is fleshed out in detail by these researchers in a new paper (S. Vembanur <i>et al., J. Phys. Chem. B</i> <b>117</b>, 10261; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4050513">here</a>). The key issue is that the interfacial water, like that at the air-liquid interface, is more easily displaced, lowering the desolvation barrier to association. Naturally, this means that hydrophobic surfaces might be used to catalyse aggregation processes. I wonder if it might also help to explain Barry Sharpless’s observations some years back of an increase in organic reaction rates at the air-water interface?
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Water diffusion close to lipid membranes is not like that close to solid surfaces, Roland Netz at the Free University of Berlin and colleagues say (Y. von Hansen <i>et al., Phys. Rev. Lett.</i> <b>111</b>, 118103; 2013 – paper <a href="http://prl.aps.org/abstract/PRL/v111/i11/e118103">here</a>). Their MD simulations reveal that, whereas at solid surfaces water diffuses faster laterally than perpendicularly, at lipid membranes the opposite is true. This seems to be because the lipids present a rough surfaces, with some head groups protruding from the leaflets, so that lateral diffusion takes place amidst a rough free-energy landscape and is correspondingly hindered. As a result, lateral motion in the fluid phase at the membrane surface involves a distinct perpendicular component to the trajectories: water molecules wander in local energy traps before moving up and away an then “descending” elsewhere.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiV9bHySauJC5yfsZGJ6jyPPyU05Fi3k9evsoqMtJtneK2jb4mScbFjHWp2O9xvPPGtdZD3_DagDsRDrpUy2OMVmg0F1Txp0gZZ4GUO67RafN4qil4J3unFStYNZDqyfQcvK8dsTc9vItk/s1600/lipid_membrane_diffusion.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiV9bHySauJC5yfsZGJ6jyPPyU05Fi3k9evsoqMtJtneK2jb4mScbFjHWp2O9xvPPGtdZD3_DagDsRDrpUy2OMVmg0F1Txp0gZZ4GUO67RafN4qil4J3unFStYNZDqyfQcvK8dsTc9vItk/s320/lipid_membrane_diffusion.jpg" /></a>
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The dynamics of interfacial water at lipid membranes is also probed by Kevin Kubarych and colleagues at the University of Michigan using IR spectroscopy (D. G. Osborne <i>et al., J. Phys. Chem. B</i> jp4049428 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4049428">here</a>). They infer this from the spectral diffusion of a labelled cholesterol derivative in the membrane, which reflects the dynamics of its hydration water, and find that these dynamics are three times slower than those of the same molecule in bulk water. The paper largely establishes this as a nice tool that might be used to look at variations in water dynamics at different locations in a membrane.
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One explanation for the apparent long-ranged hydrophobic interaction measured between adsorbed monolayers in the surface force apparatus invokes electrostatic interactions between the restructured monolayers themselves (see, for example, Jacob Klein’s work: <i>Phys. Rev. Lett.</i> <b>96</b>, 038301; 2006 and <b>109</b>, 168305; 2012). Max Berkowitz and colleagues at UNC investigate this idea using a lattice model to look at how a surfactant coated charged (mica) surface might become reconfigured into heterogeneous structures (C. Eun <i>et al., J. Phys. Chem. B</i> jp405979n – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp405979n">here</a>). They find that indeed an initially uniform surfactant monolayer can become transformed into a non-uniform surface covered with patches of surfactant bilayer separated by patches of bare (water-covered) mica. This simple model system might help to understand not just Klein’s studies but also the somewhat related issue of formation of lipid rafts in mixed-lipid membranes.
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Another ongoing discussion is the mechanism by which osmolytes stabilize proteins. Piotr Bruzdziak and colleagues at Gdansk University of Technology in Poland examine that issue by using IR spectroscopy and DSC to study the effects of various osmolyes (TMAO, Gly, NMG, DMG) on the stability of lysozyme (P. Bruzdziak <i>et al., J. Phys. Chem. B</i> <b>117</b>, 11502; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp404780c">here</a>). In contrast to many recent simulation studies of this problem, the authors here conclude that the osmolyte-protein interaction is indirect, the osmolytes “enhancing” water structure with a consequent “tightening” of protein folding.
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OK, why not touch on another controversial topic too: the molecular basis for the dormancy of bacterial spores, and in particular whether this involves an ‘altered state’ of water. That’s addressed in a preprint (<a href="arxiv.org/abs/1309.5033">arxiv.org/abs/1309.5033</a>) by Bertil Halle at Lund and colleagues, using deuteron magnetic relaxation dispersion to look at the state of water in spores of <i>B. subtilis</i>. Two models for the structure of the core aqueous phase have been proposed: a gel, in which mobile water permeates a macromolecular network, and a glass, in which everything inside the cells (including water) forms a solid amorphous phase. The NMR results clearly support the former picture – the water remains mobile, albeit with rotational motion about 15 times slower than the bulk.
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Calcium release-activated calcium (CRAC) channels play an important role in cell signalling, and their dysfunction is associated with cardiac arrythmia and immunodeficiency problems. Thanks to a recent crystal structure of the pore region of a CRAC channel, Michael Klein and colleagues at Temple University have been able to investigate the mechanism of ion permeation through simulations (H. Dong <i>et al., PNAS</i> <b>110</b>, 17332; 2013 – paper <a href="http://www.pnas.org/content/110/43/17332.abstract">here</a>). They say that a central hydrophobic region of the channel is the crucial region for switching on and off, and that it is the hydration of this region that controls ion transport: a small change in the number and orientation of water molecules here significantly alters the local electrostatic field. In other words, this is another channel that is water-regulated.
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Moving onto another channel: the high water permeability of aquaporins may be a result of an optimization of shape at the pore entrance to minimize viscous dissipation, according to a study by Laurent Joly of the University of Lyon 1 and colleagues (S. Gravelle <i>et al., PNAS</i> <b>110</b>, 16367; 2013 – paper <a href="http://www.pnas.org/content/110/41/16367.abstract">here</a>). Their finite-element calculations suggest that the hour-glass profile of the pore is particularly efficient at reducing dissipation, and that the optimal opening angle of 5-20 degrees is in the range of those observed in the proteins.
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Aquaporins have of course a well resolved crystal structure, but many membrane proteins are intrinsically disordered, especially in the regions that extend beyond the lipid membrane and into the extracellular matrix. Songi Han of UCSB and colleagues suggest that hydration dynamics – in their case as measured by Overhauser dynamic nuclear polarization NMR – can provide a proxy for at least locating these extended protein segments (C.-Y. Cheng <i>et al., PNAS</i> <b>110</b>, 16838; 2013 – paper <a href="http://www.pnas.org/content/110/42/16838.abstract">here</a>). The technique relies on the apparent existence of a gradient of diffusion dynamics up to 3 nm away from the membrane surface (really?). The authors can seemingly also use the technique to look at protein structure parallel to the membrane surface, as in the case of an amyloid-forming protein called alpha-synuclein associated with Parkinson’s disease. They report a sinusoidal variation in water retardation close to the lipid surface which they interpret as the result of the alpha-S coiled into an alpha helix embedded laterally in the membrane with its axis about 1-3 Å below the phosphate head groups, while the C-terminus end floats freely and disordered above the membrane surface.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhktcC7K_DetaJSZ42QgTptAKsclW-kAUR76hJfaY-lXuSRoOsF9MImjJrc3goHfawXUVIRL_mV4xcpVx7H_bGhRe_VTDLJYWNaA4WKOgC1MR9GpuuGQ-Ukmd4c9vh9tMSwmq5zxNd1-4A/s1600/alpha-synuclein.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhktcC7K_DetaJSZ42QgTptAKsclW-kAUR76hJfaY-lXuSRoOsF9MImjJrc3goHfawXUVIRL_mV4xcpVx7H_bGhRe_VTDLJYWNaA4WKOgC1MR9GpuuGQ-Ukmd4c9vh9tMSwmq5zxNd1-4A/s320/alpha-synuclein.jpg" /></a>
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Water dynamics generally found to be retarded in the vicinity of proteins. But NMR measurements on crystals of the protein Crh (protein catabolite repression Hpr) have indicated that water in the crystals may remain mobile down to at least -30 C – in other words, it seems more mobile than bulk water at these temperatures (Böckmann <i>et al., J. Biomol. NMR</i> <b>45</b>, 319; 2009). How can this be? To answer that question, Anja Böckmann of the University of Lyon, who did the NMR wirk, has collaborated with Wilfred van Gunsteren at ETH Zurich and colleagues to conduct MD simulations of the crystalline form of Crh (D. Wang <i>et al., J. Phys. Chem. B</i> <b>117</b>, 11433; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp400655v">here</a>). They find that indeed while retarded dynamics of hydration water are seen at 291 K, at 200 K (close to the glass transition) the rotational and translational mobility of this water is greater than in bulk. But while introducing artificial perturbations such as rigidifying the protein or switching off protein-solvent electrostatics does induce some enhanced mobility of either translation or rotation, the cause of the overall water mobility at this temperature remains obscure.
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While on the subject of glassy low-temperature behaviour, Thomas Loerting of the University of Innsbruck and colleagues have reported a second glass transition in amorphous ice at 116 K, which they say is related to the coexistence of two highly viscous metastable liquid-like phases: a low-density phase with a glass transition of 136 K and a high-density phase which undergoes this second glass transition at 116 K (K. Amann-Winkel <i>et al., PNAS</i> <b>110</b>, 17720; 2013 – paper <a href="http://www.pnas.org/content/110/44/17720.abstract">here</a>). Thus, they say, the putative HDL and LDL “can both be observed experimentally” – although the results don’t directly address the question of whether the two can be interconverted by a first-order liquid-liquid transition ending at a critical point.
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A stark and rather remarkable reminder of how much still remains to be understood about the hydrogen bond is provided by Michele Ceriotti at Oxford and colleagues (<i>PNAS</i> <b>110</b>, 15591; 2013 – paper <a href="http://www.pnas.org/content/110/39/15591.abstract">here</a>). Their <i>ab initio</i> simulations that incorporate nuclear quantum effects show that the protons in water’s hydrogen bonds undergo fluctuations that take them towards the oxygen acceptor atoms for significant fractions of time, sometimes leading to spontaneous proteolysis. What’s more, these events are strongly correlated among neighbouring hydrogen bonds, so that perturbations to the hydrogen-bonded network seem likely to modulate this distinctly non-classical effect in significant ways.
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The discussion continues of how ions alter the dynamics of water in their hydration shells. MD simulations by Ana Vila Verde and Reinhard Lipowsky at the MPI for Colloids and Interfaces in Potsdam look at the effect of ion pairs (here magnesium sulphate and caesium chloride) to see to what extent the slowdown of water dynamics in cooperative between the anion and cation (<i>J. Phys. Chem. B</i> <b>117</b>, 10556; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4059802">here</a>). They find that the cooperative slowdown can be intense (especially for ions of high charge density), but only in the first hydration shell. I note their comment “our results do not support the notion that the Hofmeister series is due primarily to long-range effects of ions on water properties. Instead, they point to the possibility that models of ion solvation may focus primarily on the first hydration layer without excessive loss of accuracy.”
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Directional transport of water through a carbon nanotube connecting two reservoirs, driven by electric fields, has been reported in simulations by several teams over the past few years. Hangjun Wu of Zhejiang Normal University in Jinhua and colleagues now add another instance (X. Zhou <i>et al., J. Phys. Chem. B</i> <b>117</b>, 11681; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp405036c">here</a>). They show that a vibrating charge that deforms the nanotube away from its halfway point (thus introducing the asymmetry that underpins the ratchet-like effect) will create a directional flux of water. But the direction of that flux is dependent on the displacement of the nanotube wall, and can even change sign when the displacement gets very large.
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Daryl Eggers at San José State University continues to develop his picture of solvation water as a reactant in solution equilibria. With Brian Castellano he considers what happens when one includes in the thermodynamic treatment of binding equilibria a representation of how water is perturbed next to solutes (so that it is not ‘equivalent’ on both sides of the equilibrium) (B. M. Castellano & D. K. Eggers, <i>J. Phys. Chem. B</i> <b>117</b>, 8180; 2013) – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp402632a">here</a>). The spirit of the exercise is nicely encapsulated thus: “When water is viewed as a coreactant, it becomes apparent that the traditional equation for the standard-state Gibbs free energy of binding represents an unbalanced equation.” In fact, this means that the equilibria and binding constants become concentration-dependent. Perhaps this might account for discrepancies between different ways of experimentally measuring the enthalpy changes of some reactions.
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To what extent can the vibrations of liquid water be decomposed into essentially single-molecule bending and stretching OH modes, plus intermolecular contributions? Less than was thought, according to Andrei Tokmakoff, currently at the University of Chicago, and colleagues (K. Ramasesha <i>et al., Nat. Chem</i>. <b>5</b>, 935; 2013 – paper <a href="http://www.nature.com/nchem/journal/v5/n11/full/nchem.1757.html">here</a>). Their studies using ultrafast 2D IR spectroscopy show that there is strong mixing between all of these modes, so that all the vibrations have some collective component. This will require some significant rethinking of relaxation and energy dissipation in water.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com3tag:blogger.com,1999:blog-7540687028464774748.post-19432086634703211212013-10-10T06:00:00.000-07:002013-10-10T06:00:19.960-07:00In praise of the NobelsAll the three recipients of this year’s Chemistry Nobel Prize – Martin Karplus, Arieh Warshel and Michael Levitt – have of course played some part in the general exploration of water’s roles in molecular biology. But Levitt in particular has been inspirational. It was what he wrote with Mark Gerstein in <i>Scientific American</i> in 1998 that, more than anything else, persuaded me there was a story to be unfolded about the importance of water in biology:
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“When scientists publish models of biological molecules in journals, they usually draw their models in bright colors and place them against a plain, black background. We now know that the background in which these molecules exist – water – is just as important as they are.”
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Much of the popular discussion of the Nobel award has centred around the technical computational aspects of these guys’ work, almost as though they deserve praise as programmers. But it is comments like this one that reveal the deep chemical insight behind all that computer stuff. This why I view the decision with deep satisfaction.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com3tag:blogger.com,1999:blog-7540687028464774748.post-4859720370648052302013-10-07T01:40:00.000-07:002013-10-07T01:40:48.244-07:00Water and protein foldingDoes water drive protein folding? That’s the title of a paper by Yutaka Maruyama and Yuichi Harano at Osaka University (<i>Chem. Phys. Lett.</i> <b>581</b>, 85; 2013 – paper <a href="http://www.sciencedirect.com/science/article/pii/S000926141300866X">here</a>), and as you’d expect from a title like that, they conclude that the answer is at least partly affirmative. They combine MD simulations and 3D-RISM solvation theory to calculate thermodynamic quantities involved in protein folding, and conclude that while hydration energy favours the denatured state (but is largely offset by the intramolecular interactions of the protein on folding), hydration entropy favours the folded state. In this sense, water contributes significantly to the stability of the collapsed conformation.
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A perhaps more dramatic claim along these lines is made by Ariel Fernandez, now at the Argentinian Institute of Mathematics in Buenos Aires (<i>J. Chem. Phys.</i> <b>139</b>, 085101; 2013 – paper <a href="http://jcp.aip.org/resource/1/jcpsa6/v139/i8/p085101">here</a>). He presents a model of electrostatic interactions between the protein surface and water dipoles, which suggests a principle that Ariel calls minimal episteric distortion: the protein-water interface adopts a configuration that minimizes the energetic cost of disrupting dipole interactions of the hydrogen-bonded matrix. In other words, the native fold is the one that corresponds to this minimally perturbing topology: the protein structure is the one that is least at odds with the structure of the surrounding water. As Ariel has put it, “The paper shows that the full interfacial free energy can be computed/interpreted in two different but equivalent ways: a) as elastic energy arising from the perturbation of the hydrogen-bond matrix of water, or b) as electrostatic energy stored in the anomalous polarization of water (interactions between dipoles forced not to behave in Debye manner and protein charges).” And crucially, if this interfacial free energy is omitted from the folding computations, an incorrect fold results because the structure is then “at odds with the solvent”.
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John Weeks at the University of Maryland was one of the architects of the Lum-Chandler-Weeks hypothesis (<i>J. Phys. Chem. B</i> <b>103</b>, 4570; 1999) that the hydration of small and large hydrophobes is qualitatively different, with a crossover scale of around 1 nm, and that the latter is dominated by interfacial free energies and the breaking of hydrogen bonds. (This was itself an extension of a proposal by Frank Stillinger in 1973.) Now Weeks, together with Richard Remsing at Maryland, has attempted to refine this idea by considering what roles van der Walls dispersion forces and electrostatic interactions might have in this business. Using MD simulations with the SPC/E water model, they confirm the original idea that solvation and association of small hydrophobes is dominated by hydrogen-bonding, but find that for large hydrophobes (where hydrogen bonds are broken at the interface) the attractions are dominated by Lennard-Jones dispersion forces, with water now behaving more like an ordinary liquid (<i>J. Phys. Chem. B</i> jp4053067 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4053067">here</a>). The crossover length scale is set by the hydrogen-bond network itself, occurring when the solute is too large for this network to remain intact. This paper seems to offer an important extension of LCW/Stillinger, while showing that the basic ideas expressed in those earlier works are sound.
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Further support for this picture comes from Guillaume Jeanmairet and colleagues at the École Normale Supérieure in Paris. They have recently presented a now molecular density-functional theory of water (<i>J. Phys. Chem. Lett.</i> <b>4</b>, 619; 2013). In a preprint, they have now applied it to the hydration of hydrophobes of various sizes (G. Jeanmairet <i>et al</i>., <a href="http://www.arxiv.org/abs/1307.7237">arxiv.org/abs/1307.7237</a>). They find that the original theory doesn’t work so well, in terms of predicting solvation free energies, when applied to large hydrophobes, but that supplementing it by introducing a hard-sphere component that reproduces the van der Waals picture of liquid-vapour coexistence in bulk rescues the model. This seems to be, they say, very much in line with the Lum-Chandler-Weeks picture of a crossover between “volume-driven” hydrophobic hydration at small scales and a surface-driven picture, dominated by interfacial free energies, at larger scales.
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Rahul Sarma and Sandip Paul of the Indian Institute of Technology in Guwahati Assam have been rather extensively investigating the origins of osmolyte effects on protein stability using MD simulations. In their latest paper (<i>J. Phys. Chem. B</i> <b>117</b>, 9056; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp405202j">here</a>) they look at the stabilizing effect of trimethylamine-N-oxide (TMAO) against the pressure-denaturation of proteins. They find that TMAO enhances the hydration number of a coiled peptide more than its extended state under pressure, whereas the opposite is seen in its absence. Partly this is an indirect effect: solvation of TMAO reduces the ‘crowding’ of water molecules at high pressure that drives them towards the relative freedom they find in the hydration shell of the extended peptide. There is also a direct effect due to the relative inefficiency with which TMAO interacts with the unfolded peptide.
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Alkaline phosphatase enzymes are able to catalyse the hydrolysis of a range of different phosphate and sulphate substrates. What accounts for this promiscuity? Through first-principles simulations, Guanhua Hou and Qiang Cui at the University of Wisconsin-Madison show that this class of enzymes can support different types of transition state in the same active site (<i>JACS</i> <b>135</b>, 10457; 2013 - paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja403293d">here</a>). The differential placement of water molecules in the active sites is implicated in some of this, although the details are complicated and apparently as yet case-specific: there is no general picture emerging yet of how these and other enzymes engineer their promiscuity.
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Another water molecule playing a functional role in enzyme catalysis is identified by Walter Thiel and colleagues at the MPI für Kohlenforschung in Mülheim (B. Karasulu <i>et al., JACS</i> <b>135</b>, 13400; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja403582u">here</a>). They look at the three-molecule water bridge that exists in the active site of a lysine-specific demethylase (which is involved in demethylation of histones), showing how it is stabilized by interactions with the surrounding residues and how it assists proton transfer.
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWWbhjBG6hycl6IooYhd1OA8Bo4SoIygMLY7XTus_dkCxLOrn7fgMpkQav9iYwMQRZhkVm1Tz0AQ4qJ6SJ6MXiv7biMO4C-f8rjfjCVTMgwG3224oVR0MYVA4NqZXOwvIZAJ5OSO2Gl_E/s1600/lysine_demethylase.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjWWbhjBG6hycl6IooYhd1OA8Bo4SoIygMLY7XTus_dkCxLOrn7fgMpkQav9iYwMQRZhkVm1Tz0AQ4qJ6SJ6MXiv7biMO4C-f8rjfjCVTMgwG3224oVR0MYVA4NqZXOwvIZAJ5OSO2Gl_E/s320/lysine_demethylase.jpg" /></a>
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Electrowetting – switching surfaces between hydrophobicity and hydrophilicity with electric fields – has useful applications in microfluidics and ink-jet printing, and might enable voltage-gating of flow through nanochannels. This provides the motivation for a study by Alenka Luzar at Virginia Commonwealth University and her colleagues of the effect of electric fields on water dynamics at the interfaces of a slit-like nanopore (M. von Domaros <i>et al., J. Phys. Chem. C</i> <b>117</b>, 4561; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp3111259l">here</a>). They recognize that the application of a field across the pore breaks the symmetry so that the water dipoles tend to be aligned in opposite directions with respect to the surfaces at each interface – this becomes, they say, the electrical equivalent of a chemical Janus interface. Their simulations indicate that the water density in the first hydration layer is lower for the “incoming” than for the “outgoing” field, and that the response times for orientational dynamics can be up to two orders of magnitude different (in the picosecond regime) – an effect that ought to be visible to, for example, dielectric spectroscopy.
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Pavel Jungwirth, Damien Laage and their colleagues have looked at how hydrated ions affect water dynamics (G. Stirnemann <i>et al., JACS</i> <b>135</b>, 11824; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja405201s">here</a>). Their simulations indicate that in dilute solution, effects on water reorientational dynamics are short-ranged and ion-specific: both retardation and acceleration may be seen, depending on the interaction strengths. But in concentrated solution, where hydration shells overlap, the effect is always a retardation and is not ion-specific. They suggest that this might explain the apparent discrepancy between the studies of water dynamics by NMR (at low salt concentration) and by infrared and THz spectroscopy (e.g. Huib Bakker), which must use high salt concentrations.
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Niharendu Choudhury and colleagues at the Bhabha Atomic Research Centre in Mumbai offer a new view of the local solvation environment in pure water (<i>J. Phys. Chem. B</i> <b>117</b>, 8831; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp404478y">here</a>). They say that, by considering the hydration shell of each molecule to be composed only of other waters hydrogen-bonded to it, they can explain the density anomaly without recourse to polyamorphism of the liquid state. I confess that I’ll need to digest this paper more to see where it really diverges from previous treatments; in essence it seems to posit three order parameters, namely a tetrahedral order parameter in the first hydration shell, an orientational order parameter in the second shell, and the number of hydrogen bonds. I think the point is that the first two can be subsumed in the third, and that distortions to the tetrahedral coordination arise at higher temperatures from the incursion of non-hydrogen-bonded molecules into the first shell. The resulting analysis restores a picture of water structure in terms of fluctuations in a homogeneous fluid, rather than requiring the kind of heterogeneities posited by Anders Nilsson.
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Ali Hassanali at ETH and coworkers have uncovered what seems to be an extraordinary complexity and subtlety in motion of protons through water (A. Hassanali <i>et al., PNAS</i> <b>110</b>, 13723; 2013 – paper <a href="http://www.pnas.org/content/110/34/13723.abstract">here</a>). (See also commentary by Edelsys Codorniu-Hernández and Peter Kusalik of the University of Calgary <a href="http://www.pnas.org/content/110/34/13697.extract">here</a>.) Their first-principles simulations show that there is a great deal more to it than Grotthuss hopping. For a start, the process is very heterogeneous in time: both proton and hydroxide diffusion happen in bursts of activity followed by periods of quiescence. These motions involve medium-range correlations between the movements of many protons, which the authors characterize in terms of the connected-ring structure of the hydrogen-bonded network. The result is that protons can jump over a wide range of length scales, and not merely hope from one molecule to the next. The authors point out that “the fundamental aspects raised in this re- port are likely to open up new directions in the role of the water network in phenomena associated with the hydration of ions and macromolecules such as proteins and DNA.”
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Making water modelling easier: Vijay Pande at Stanford and colleagues have simplified the AMOEBA polarisable model of water to a version they call inexpensive or iAMOEBA, which introduces a direct polarization approximation that removes the need to calculate polarization iteratively (L.-P. Wang <i>et al., J. Phys. Chem. B</i> <b>117</b>, 9956; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp403802c">here</a>). Any shortfall in the polarization energy introduced by the approximation can be recovered by parametrization, so that the model accurately reproduces the water/ice phase diagram, dielectric properties and so forth.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com2tag:blogger.com,1999:blog-7540687028464774748.post-54397514106974007562013-08-20T01:36:00.000-07:002013-08-20T01:36:04.919-07:00Spectral tuning and pumping in rhodopsinsInert gases in water will under some conditions not exhibit the expected hydrophobic attraction but will form a solvent-separated pair. Yuri Djikaev and Eli Ruckenstein at SUNY at Buffalo rationalize this observation in the course of developing a new approach to describing hydrophobic hydration (<i>J. Phys. Chem. B</i> <b>117</b>, 7015; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp312631c">here</a>). They derive an analytical expression for the number of hydrogen bonds each water molecule has as a function of its distance from the hydrophobic particle, and find that the hydration energy can be positive even for apolar particles if they are small enough, thanks to van der Waals interactions.
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On the other hand, two guanidinium ions can form a like-charge ion pair in water, as reported by Richard Saykally and colleagues at Berkeley from XAS measurements (O. Shih <i>et al., J. Chem. Phys.</i> <b>139</b>, 035104; 2013 – paper <a href="http://jcp-bcp.aip.org/resource/1/jcpbcp/v7/i7/p07B616">here</a>). Their calculations indicate that the ions form a stacked arrangement through pi* interactions.
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It is very nice to see that Bruce Berne and colleagues are extending the work on drying transitions in protein assembly to their potential role in molecular recognition and ligand binding (J. Mondal <i>et al., PNAS</i> <b>110</b>, 13277; 2013 – paper <a href="http://www.pnas.org/content/110/33/13277.abstract">here</a>). Their simulations of an idealized hydrophobic particle being bound in a cavity indicate that the latter can fluctuate between wet and dry states, which have distinct kinetic binding profiles.
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More on water’s liquid-liquid transition: Yaping Li and colleagues at the University of Arkansas see such a first-order transition between HDL and LDL, with an associated critical point, in simulations using the so-called Water potential from Adaptive Force Matching for Ice and Liquid (WAIL), which they argue is a particularly reliable potential because it is not biased by fitting to experimental data (Y. Li <i>et al., PNAS</i> <b>110</b>, 12209; 2013 – paper <a href="http://www.pnas.org/content/110/30/12209.abstract">here</a>).
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And in a preprint apparently heading for the Eur. Phys. J., Hajime Tanaka presents a new model of the liquid state based on an order parameter that describes bond orientational ordering, which he says explains many of the anomalies of tetrahedrally bonded liquids (including a liquid-liquid transition) (<a href="http://www.arxiv.org/abs/1307.0621">arxiv.org/abs/1307.0621</a>). This huge and ambitious paper also provides accounts of glass formation and fragility, quasicrystal formation and other metastable crystallized states.
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Somewhat related in exploring tetrahedral order in water is a preprint destined for Chem. Phys. Lett. by Marcelo Carignano of Northwestern University and colleagues, who have compared this aspect of water structure along with hydrogen-bond lifetimes and diffusion coefficients in simulations with four different water potentials (SPC/E, TIP4P-Ew, TIP5P-Ew, Six-site) (<a href="http://www.arxiv.org/abs/1307.3611">arxiv/1307.3611</a>). They find that there are significant differences below 270 K, depending on whether or not the models include explicit lone pairs.
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Shaoyi Jiang and colleagues at the University of Washington in Seattle present a case, from simulations and NMR measurements, that the hydration differences for salt bridges in proteins contribute significantly to their relative stabilities (A. D. White <i>et al., J. Phys. Chem. B</i> <b>117</b>, 7254; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4024469">here</a>).
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More on spectral tuning of photoactive sites by hydration environments. Sivakumar Sekharan and colleagues at Yale say that the chloride-pumping transmembrane retinal protein halorhodopsin in a halophile works by subtle rearrangements of waters and ions in the vicinity of the chromophore as chloride translocation progresses, inducing changes in chromophore bond lengths that affect its absorption wavelength (R. Pal <i>et al., JACS</i> <b>135</b>, 9624; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fja404600z">here</a>). Meanwhile, Hyun Woo Kim and Young Min Rhee at the Pohang University of Science and Technology in Korea say that the pH-dependence of emission from firefly oxyluciferin – a redshift in acidic conditions – seems to be fine-tuned by a water molecule in the active site that can mediate the dynamics of neighbouring groups to the chromophore (<i>J. Phys. Chem. B</i> <b>117</b>, 7260; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4024553">here</a>).
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Valentin Gordeliy of the Université Grenoble Alpes and colleagues describe the mechanism of a different rhodopsin-like pump, an unusual proteorhodopsin from a permafrost bacterium that pumps protons in a different manner to other known rhodopsins (I. Gushchin <i>et al., PNAS</i> <b>110</b>, 12631; 2013 – paper <a href="http://www.pnas.org/content/110/31/12631.abstract">here</a>). Unusually, this structure has a proton release site (a lysine) already connected to the bulk solvent by a water chain in the ground state. There’s a nice graphic that illustrates the similarities and differences in the water-containing cavities of the channel for this structure and other rhodopsins, bacteriorhodopsin and xanthorhodopsin, the closest homologue of this one (ESR):
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg4psJeq1NjRONuaCDkawgJMLyY2Wh7ckRBxyl_lf6NOwD9398XJVy1jkJ4r2TD_OUIi3Z4YhA-woivsHANlwyYgzlcNdY2rrvn_K3I39zWPv8F6kyRw79SpXFeQslqKIdz-OSjHmpSQmQ/s1600/proteorhodopsin.jpg" imageanchor="1" ><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg4psJeq1NjRONuaCDkawgJMLyY2Wh7ckRBxyl_lf6NOwD9398XJVy1jkJ4r2TD_OUIi3Z4YhA-woivsHANlwyYgzlcNdY2rrvn_K3I39zWPv8F6kyRw79SpXFeQslqKIdz-OSjHmpSQmQ/s320/proteorhodopsin.jpg" /></a>
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I guess it is ultimately a cautionary tale that one should extract from the simulation study of reverse micelles by John Straub and colleagues at Boston University: they say that the structure and dynamics of the encapsulated water and the overall micelle assembly depend strongly on the force fields used (A. V. Martinez <i>et al., J. Phys. Chem. B</i> <b>117</b>, 7345; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp402270e">here</a>). In any event, the micelles tend not to be spherical but undergo pronounced shape fluctuations, a point made also by earlier simulations but which tends to be ignored in interpreting experimental data.
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I must confess that I’d not previously come across inhomogeneous fluid solvation theory (IFST) as a general method for calculating the effect of a solute on the solvent structure. But now David Huggins and Mike Payne at Cambridge have assessed how well it does for predicting the hydration free energies of small solutes (<i>J. Phys. Chem. B</i> <b>117</b>, 8232; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021%2Fjp4042233">here</a>). They look at six solutes such as benzene, isobutene and methanol, all in water, and figure that IFST does pretty well in comparison with a more sophisticated theory but that accurate prediction of entropies might suffer from poor sampling of the available configurations unless the simulation times are rather long.
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And here’s a curious one: George Reiter at Houston and colleagues say that water confined on the scale of about 2 nm has a different ground-state configuration of valence electrons than in the bulk (G. F. Reiter <i>et al., Phys. Rev. Lett.</i> <b>111</b>, 036803; 2013 – paper <a href="http://prl.aps.org/abstract/PRL/v111/i3/e036803">here</a>). They explore the issue using X-ray Compton scattering to probe water in the pores of Nafion, but they say, reasonably enough, that “Biological cell function must make use of the properties of this [nanoconfined] state and cannot be expected to be described correctly by empirical models based on the weakly interacting molecules model.”
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com1tag:blogger.com,1999:blog-7540687028464774748.post-48942266025627396802013-07-15T06:07:00.001-07:002013-07-15T06:07:29.825-07:00A role for water in allosteryRearrangement of the water network hydrating a protein can provide a mechanism for allostery, according to a study by Peter Hamm and colleagues (B. Buchli <i>et al., PNAS</i> 10.1073/pnas.1306323110; paper <a href="http://www.pnas.org/content/early/2013/06/26/1306323110.abstract">here</a>). They insert an azobenzene photoswitch in the binding groove of a PDZ domain protein, a common system for studying allostery, such that photo-induced isomerisation induces a conformational change similar to that which occurs on ligand binding. This enables them to use fast IR spectroscopy to look at the opening of the binding groove in a precisely controlled fashion, having first characterized the equilibrium structures using NMR. Their MD simulations show that a change in water density in the vicinity of the photoswitch right after switching propagates slowly through the water network over about 100 ns until it reaches the back of the protein. They suggest that this change in hydration structure could then induce, either dynamically or structurally, a remote allosteric change in protein conformation. In such a case, this would be a particularly dramatic example of how the hydration network is really a part of the functional apparatus of the protein.
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How aquaporins transport water across membranes – and specifically how they do so without also transporting protons – has been a topic of much debate. The consensus has come to focus on the so-called NPA motif in the centre of the channel, a bottleneck through which water kolecules pass in single file, which seems to prohibit proton transport via electrostatic repulsion. Urszula Kosinska Eriksson at the University of Gothenburg and colleagues have recently reported a new high-resolution crystal structure of yeast aquaporin 1 which sheds new light on the issue (<i>Science</i> <b>340</b>, 1346; 2013 – paper <a href="https://www.sciencemag.org/content/340/6138/1346.abstract">here</a>). As Jeff Abramson and Armand Vartanian of ULCA explain in an accompanying perspective (<i>Science</i> <b>340</b>, 1294 – paper <a href="https://www.sciencemag.org/content/340/6138/1294.summary">here</a>), the structure shows that proton transport isn’t (as some have suggested) blocked by hydrogen-bonding of a single water molecule in the NPA region to two asparagines. Rather, there are two independent waters here, but the interactions with the asparagines constrain their dynamics in such a way as to effectively break the ‘water wire’ threading through the channel. The authors say that water transport then seems to happen in pairwise fashion, similar to the ion transport in potassium channels – a possible example of convergent evolution to solve related problems.
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A carefully structured water cluster also seems to play an important role in oxygen evolution during the photocycle of photosystem II, as Brandon Polander and Bridgette Barry of Georgia Tech deduce using laser flashes to induce the process and following it by FTIR spectroscopy (<i>PNAS</i> 10.1073/pnas1306532110 – paper <a href="http://www.pnas.org/content/early/2013/06/11/1306532110.abstract">here</a>). The hydrogen-bonded cluster of five water molecules, bound to the catalytic Mn4CaO5 cluster, seems to become protonated during the S1→S2 part of the cycle, and it stores the proton until a later stage of the reaction. Ammonia can poison the reaction by disrupting the water cluster.
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Water molecules that gain access to the interiors of globular proteins can act as probes of the intrinsic conformational dynamics that enable proteins to function. These waters in the ‘dry’ protein interior have been studied by magnetic relaxation dispersion spectroscopy, but atomistic models are needed to interpret those results. The problem is that such deep water penetration tends to be a rare event, demanding very long (millisecond) run times for simulations. A technique has recently been developed that enables this (D. E. Shaw <i>et al., Science</i> <b>330</b>, 341; 2010), and now Filip Persson and Bertil Halle at Lund have used the method to compare MD with the MRD experiments for bovine pancreatic trypsin inhibitor (<i>JACS</i> <b>135</b>, 8735; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/ja403405d">here</a>). They find that some of these internal hydration sites have water residence times of several microseconds, and that the water molecules gain access along single-file hydrogen-bonded chains.
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Dewetting transtions are known to be important for at least some instances of hydrophobic assembly, and Bruce Berne and colleagues at Columbia now extend their earlier studies of dewetting-induced protein collapse to look at the potential role of such transitions in the docking of hydrophobic ligands in their binding pockets (J. Mondal <i>et al.</i>, preprint <a href="http://www.arxiv.org/abs/1305.7505">http://www.arxiv.org/abs/1305.7505</a>). In this way the solvent dynamics, which are retarded in the concave cavity, are explicitly included in the kinetics of the binding process – the process can be parametrized through a state variable that describes whether the pocket is ‘wet’ or ‘dry’, while the ligand diffuses across a potential-energy surface that can switch between these two states.
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Daniel Sindhikara and Fumio Hirata of the Ritsumeikan University in Japan present a fast algorithm, based on the three-dimensional reference interaction site model (3D-RISM), for calculating the solvent distribution around solutes (<i>J. Phys. Chem. B</i> <b>117</b>, 6718; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp4046116">here</a>). This is a wholly theoretical approach derived from the Ornstein-Zernicke equation. They say that it gives water positions and orientations that agree well with available experimental data, and demonstrate its use on HIV-1 protease.
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Paul Ben Ishai at the Hebrew University of Jerusalem and colleagues have used quasielastic neutron scattering to look at salt effects on water dynamics (<i>J. Phys. Chem. B</i> <b>117</b>, 7724; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp4030415">here</a>). They find that water diffusion is slower than in pure water, on average, in NaCl solution, but faster in KCl. They interpret the result in terms of structure-making and –breaking, saying that the disruption of the hydrogen-bonding network by potassium ions accounts for its apparent ‘lubricating’ effect.
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The hydration state of arginine side chains can be deduced from its UV resonance-enhanced Raman spectrum, according to Sanford Asher at Pittsburgh and colleagues (Z. Hong <i>et al., J. Phys. Chem. B</i> <b>117</b>, 7145; 2013 – paper <a href="http://pubs.acs.org/doi/abs/10.1021/jp404030u">here</a>). Their density-functional calculations show that a particular vibration of this residue is sensitive to hydration. They use this signal to characterize differing degrees of hydration of Arg in two polyAla model peptides.
Philip Ballhttp://www.blogger.com/profile/09986655706443117158noreply@blogger.com6