Wednesday, November 12, 2014

Hydrophobic 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 et al., Phys. Rev. E 71, 011502, 2005; J. Chem. Phys. 123, 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 et al., Polymer 52, 288; 2011; Ou et al., JPCB 116, 8154; 2012).

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 (J. Chem. Phys., 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.

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, JPC 99, 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.

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.



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.

Martina Havenith has written a nice Perspective for JACS, with Valeria Conti Nibali, on the use of THz spectroscopy to study biomolecular hydration (JACS 136, 12800; 2014 – paper here). 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:



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.”

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 (JPCB 118, 9191; 2014 – paper here). 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.



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 et al., JPCB ASAP jp503914s – paper here). 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.



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 et al., JPCB 118, 9553; 2014 – paper here). 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?

I recently wrote a feature for Chemistry World about the internal structures of quiescent cells and spores (here, 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 (B. subtilis) spores (A. W. Friedline et al., JPCB 118, 8945; 2014 – paper here). 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.



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 et al., JPCB 118, 8750, 2014 – paper here). 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 et al. (Nature 416, 829; 2002), who found that the total number of hydrogen bonds is unchanged in adding the alcohol to water.

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 et al., JPCB 118, 9565; 2014 – paper here). 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.

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 (JPCB 118, 8917; 2014 – paper here). 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 et al., JPCB 118, 8928; 2014 – paper here). 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 et al., JPCB 118, 8700; 2014 – paper here). 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 et al., JPCB 118, 8496; 2014 - paper here).

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 conference on nanobubbles 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.”

Monday, September 1, 2014

Life after Gordon

From 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 New York Times, 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…]

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 deus ex machina 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 et al., JACS 136, 9396; 2014 – paper here). 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.

Had I the presence of mind to have looked at Nuno Galamba’s (University of Lisbon) paper on water around hydrophobic solutes (J. Phys. Chem. B 118, 4169; 2014 – paper here) 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.

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 (J. Chem. Phys. 140, 221102; 2014 – paper here). 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.

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 et al., J. Phys. Chem. B 118, 4490; 2014 – paper here). 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.

More on this topic comes from Tahei Tahara and colleagues at RIKEN’s Molecular Spectroscopy Lab in Saitama (S. Nihonyanagi et al., JACS 136, 6155; 2014 – paper here). 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.

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 et al., J. Phys. Chem B 118, 8744; 2014 – paper here). 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.

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 et al., J. Phys. Chem. B 118, 6604; 2014 – paper here). 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.

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 (J. Phys. Chem. B 118, 4069; 2014 – paper here). It’s a nice illustration of the intimate coupling of protein and solvent.

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 et al., PNAS 111, 11685; 2014 – paper here). 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.

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 (J. Phys. Chem. B 118, 7327; 2014 – paper here). 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”.

Irisbel Guzman and Martin Gruebele at Illinois offer a nice review of methods (especially fast relaxation imaging) for probing protein folding in vivo, where interactions with other proteins, aggregation and macromolecular crowding effects can be important (J. Phys. Chem. B 118, 8459; 2014 – paper here).

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 et al., Chem. Soc. Rev. 43, 4871; 2014 – paper here).

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 et al., J. Phys. Chem. B 118, 8782; 2014 – paper here). They say may explain how it is that RuBP in chloroplasts seems able to significantly enhance the gas solubility, increasing the rate of photosynthesis.

For anyone who wants to check out the full details (and can read French), Guillaume Jeanmairet has made available (http://arxiv.org/abs/1408.7008) his PhD thesis on a computationally inexpensive DFT treatment of water (see G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619; 2013).

Monday, June 23, 2014

Catching up in the Ruhr

The direct-interaction picture of the action of denaturants receives some support from a study by Santosh Kumar Jha and Susan Marqusee of UC Berkeley (PNAS 111, 4856; 2014 – paper here). 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.

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 et al., PNAS 111, 5213; 2014 – paper here). 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.

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 (J. Phys. Chem. B 118, 3018; 2014 – paper here). 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.

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 et al., JACS 136, 5031; 2014 – paper here).


Proof that the RESOLV summer school in Bochum was electrifying...

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 et al., J. Phys. Chem. B 118, 3310; 2014 – paper here). 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.

Ariel Fernández has previously argued (J. Chem. Phys. 139, 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.

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 (J. Phys. Chem. B 118, 2810; 2014 – paper here). 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.

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 et al., PNAS 111, 6988; 2014 – paper here). The results are based on the crystal structure of Complex I from E. coli, 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.

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 et al., J. Phys. Chem. B 118, 2796; 2014 – paper here). 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.

Friday, May 9, 2014

The things internal waters get up to

I’d not previously come across guanine quadruplexes (GQs) before seeing the paper by Van Ngo and colleagues of the University of Southern California (J. Phys. Chem. B 118, 864; 2014 – paper here). 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.

The ion channel and water chain


How sodium ions move down the chain

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 (JACS 130, 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 et al., J. Phys. Chem. B 118, 1574; 2014 - paper here). 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.

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 here). 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.

The water reorientational times mapped onto the surfaces of the respective proteins.

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 et al., J. Phys. Chem. B 118, 1234; 2014 – paper here).

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 et al., Biophys. J. 106, 548; 2014 – paper here). 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.

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 et al., J. Phys. Chem. B 118, 1309; 2014 – paper here). 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.

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 et al., PNAS 111, 3413; 2014 – paper here). 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.

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 et al., J. Phys. Chem. B 118, 3026; 2014 – paper here).

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 et al., JACS 136, 3475; 2014 – paper here). 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).


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 et al., J. Phys. Chem. B 118, 2306; 2014 – paper here). They have studied one of these enzymes, Cel48A from Thermobifida fusca, 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.


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.

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 (J. Phys. Chem. B 118, 1564; 2014 – paper here). 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.

Hydrophobicity map for hydrophobin II, from two directions

A different approach to the same end is described by Jürgen Hubbuch at the Karlsruhe Institute of Technology and coworkers (S. Amrhein et al., J. Phys. Chem. B 118, 1707; 2014 – paper here). 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.

Water self-diffusion in salt solutions is anomalous with respect to the pure bulk (e.g. J. S. Kim et al., J. Phys. Chem. B 116, 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” (PNAS 111, 3310; 2014 – paper here). 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.

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 reported some while back, has now been extended by these authors with a comparison to the network geometry in hexagonal ice (JACS 136, 3395; 2014 – paper here). 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”.

Wednesday, March 12, 2014

Weird antifreeze


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 et al., Science 343, 795; 2014 – paper here). 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 news story for Chemistry World.

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 et al., JACS 136, 2000; 2014 – paper here). 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 et al. 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.

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 et al., J. Phys. Chem. B 117, 14589; 2013 – paper here). 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.

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 (J. Phys. Chem. B 118, 771; 2014 – paper here). 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.”

Similar issues are also explored by Abani Bhuyan and coworkers at the University of Hyderabad (P. Sashi et al., J. Phys. Chem. B 118, 717; 2014 – paper here). 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.

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 et al., JACS 136, 2642; 2014 – paper here). 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.”

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 http://www.arxiv.org/abs/1401.7776. 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.

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 et al., JACS 136, 1170; 2014 – paper here). These chains can bridge two ions of opposite charge, and remain locked in place even at room temperature.

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 (Phys. Rev. Lett. 112, 044501; 2014 – paper here). The solitons are composed of defects in the single-file water chain that convect mass.

Thursday, January 23, 2014

Does 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 et al., J. Phys. Chem. B 117, 16486; 2013 – paper here). 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.

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 et al., J. Phys. Chem. B 117, 16428; 2013 – paper here). 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.

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 et al., J. Phys. Chem. B 117, 15958; 2013 – paper here). 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.

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 et al., Phys. Rev. Lett. 112, 028101; 2014 – paper here). 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.

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 et al., JACS 138, 188; 2014 – paper here) 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.

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 (Phys. Rev. Lett. 112, 020603; 2014 – paper here). 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.

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 (J. R. Soc. Interface 11, 20130799; 2014 – paper here). 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.

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 et al., PNAS 108, 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 et al., J. Phys. Chem. B jp4115139; 2014 – paper here).

Thursday, December 12, 2013

Enthalpy/entropy compensation

The 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 et al., J. Phys. Chem. B 117, 12360; 2013 – paper here). They use the model to examine the barnase-barstar complex, and say that it could be extended to multi-protein systems.

A rather exquisite water-mediated mechanism of enzymatic activity is reported by Qiang Cui at Wisconsin-Madison and colleagues (P. Goyal et al., PNAS 110, 18886 – paper here). 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.

Enthalpy/entropy compensation in protein-ligand binding is the topic of a nice study by George Whitesides’ group in a special issue of the European Physical Journal (doi:10.1140/epjst/e2013-01818-y – paper here). The group examines this issue further in a paper in JACS (B. Breiten et al., JACS 135, 15579; 2013 – paper here), where they look at the human carbonic anhydrase system that they have also studied earlier (see P. W. Snyder et al., PNAS 108, 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.”

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 (J. Phys. Chem. B 117, 14676; 2013 – paper here). 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.

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 et al., J. Phys. Chem. B 117, 14589; 2013 – paper here). 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.

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 (JACS 135, 17200; 2013 – paper here). Their calculations suggest that the hexacoordinated magnesium ions polarize the bound water more strongly, resulting in stronger ion-water-protein interactions.

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 et al., J. Phys. Chem. B 117, 12475; 2013 – paper here). 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.

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 et al., J. Phys. Chem. B 117, 12007; 2013 – paper here). 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.”

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 (J. Mol. Biol. 10.1016/j.jmb.2013.09.039 – paper here). 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.

Another computational challenge is addressed by Sergio Pantano of the Institut Pasteur de Montevideo in Uruguay and coworkers (H. C. Gonzalez et al., J. Phys. Chem. B 117, 14438; 2013 – paper here). 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.

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 et al., JACS 135, 15033; 2013 – paper here). 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.

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 et al., PNAS 10.1073/pnas.1312458110 – paper here). This shows what an improved theory will have to shoot at.

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 et al. (J. Savolainen et al., PNAS 10.1073/pnas.1317459110 – paper here). 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.

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 et al., Phys. Rev. Lett. 111, 238001; 2013 – paper here). 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.