Apologies for a longer-than usual silence – I’m waiting to resolve some access problems. In the meantime, and before the backlog gets too awesome, I’ll have to work with mostly just abstracts here.
I’ve been meaning to comment for a long time on a study by David Chandler and his colleagues that extends his notion of fluctuation-driven hydrophobic forces (A. J. Patel et al., J. Phys. Chem. B 114, 1632-1637; 2010 – paper here). Since the original Lum, Chandler & Weeks paper on ‘drying-induced attraction’, David has been developing the idea that what we’re dealing with at a hydrophobic surface is not so much a static gas-like layer but a density depletion due to enhanced density fluctuations. Here he and his coworkers use simulations to show that these fluctuations are similar to those at a water-air interface, and that the resulting depletion does seem to drive the hydrophobic attraction between two such surfaces.
Francesco Mallamace and colleagues have reported experimental evidence of the dynamical crossover in supercooled water that they have previously postulated as an explanation of the glass-like transition in supercooled hydrated proteins (F. Mallamace et al., J. Phys. Chem. B 114, 1870-1878; 2010 – paper here). They have used NMR and neutron scattering to look at water confined in a nanotube, water in the hydration layer of lysozyme and water in a methanol mixture. In all cases they see the predicted change in temperature-dependence of viscosity from Arrhenius to non-Arrhenius form, and say that this seems to coincide with the development of an extended H-bonded network.
Yurina Sekine and Tomoko Ikeda-Fukazawa at Meiji University in Japan appear to be proposing another kind of transition in glassy peptide-like polymers at 37 C. They see a shift in the Raman O-H stretching mode of bound water (to poly-N,N-dimethylacrylamide) at this temperature (J. Phys. Chem. B 114, 3419-3425; 2010 – paper here). I’m not sure that I fully underastand what is going on here without seeing the full paper, but the transition seems to be marking a switch between probing the dynamics of the hydration layer I general below 37 C and the waters bound specifically to polar groups above 37 C.
More on protein denaturation. Angel Garcia and colleagues at RPI have used MD simulations to look at the mechanism of urea-induced unfolding of the Trp-cage peptide (D. R. Canchi et al., JACS 132, 2338-2344; 2010 – paper here). Like earlier studies with urea, they find that the denaturation seems to stem from direct interactions between the denaturant and the peptide chain – via electrostatic and van der Walls interactions rather than hydrogen-bonding.
Nohad Gresh and coworkers in Paris find using molecular mechanics simulations that the energetics of docking of inhibitors to a protein called the focal adhesion kinase depends critically on a group of 5-7 structured water molecules at the binding site (B. de Courcy et al., JACS 132, 3312-3320; 2010 – paper here).
Biman Bagchi and colleagues at the Indian Institute of Science in Bangalore say that the behaviour of bound water within the major groove of DNA is different from that within the minor groove (B. Jana et al., J. Phys. Chem. B 114, 3633-3638; 2010 – paper here). Their MD simulations of hydrated ploy-AT and poly-GC show that the minor-groove water has slower dynamics due to greater tetrahedral ordering.
How cryoprotectants such as poly-sugars work is still not clear. Fabio Bruni and colleagues have looked into this using neutron diffraction to study the hydration of the disaccharide trehalose (S. E. Pagnotta et al., J. Phys. Chem. B 114, 4904-4908; 2010 – paper here). One hypothesis has been that the tetrahedral structure of water is strongly modified in the hydration shell of trehalose. But the experiments show little sign of this; indeed, rather few water molecules are hydrogen-bonded to the disaccharide. Another blow for a ‘modified-water-structure’ view.
How about urea? That question has been much debated, but Abdenacer Idrissi at the Université des Sciences et Technologies de Lille and colleagues consider the issue using MD simulations (A. Idrissi et al., J. Phys. Chem. B 114, 4731-4738; 2010 – paper here). They find that as the concentration of urea in solution is increased, the tetrahedrality of water declines in favour of an ‘unstructured’ arrangement. What this means for ‘water structure’ as such is perhaps quite subtle, given the method used to compute ‘tetrahedrality’ (i.e. a comparison of the mutual orientation of a ‘probe’ water molecule and an adjacent ‘tetrahedral’ group of them). To be continued, I’ve no doubt.
And also on hydration of small organic molecules, Richard Saykally and colleagues have used XAS to look at the hydration shells of alanine and sarcosine (the smallest peptoid or ploy-N-substituted glycine) (J. S. Uejio et al., J. Phys. Chem. B 114, 4702-4709; 2010 – paper here). The two are hydrated in rather different ways: the sarcosine XAS spectrum is much less affected by hydration than is alanine, but much more affected by conformational changes.
You’d have thought that the situation of water confined in slit-like pores or between parallel plates would have been exhaustively studied by now. But Yubo Fan and Yi Qin Gao at Texas A&M report MD studies of this geometry, using either hydrophobic plates or alkane monolayers, for relatively large separations (up to 800 Å) (J. Phys. Chem. B 114, 4246-4251; 2010 – paper here). They say that the effects of confinement are evident in the centre of the pore even for such large separations, with the water in the centre being (surprisingly, I think) of somewhat reduced density and more ice-like. This surprises me very much, to the extent that I am sceptical without seeing the full paper (I don’t know what the temperatures are). I’d not expect to see any significant departure from bulk-like water beyond distances of, say, 2 nm or so from the surfaces.
Daisuke Matsuoka and Masayoshi Nakasako in Japan have developed a program for predicting the hydration structures around the hydrophilic surfaces of proteins, based on their crystal structures (J. Phys. Chem. B 114, 4652-4663; 2010 – paper here). This simply sums the hydration distribution functions for each solvent-exposed polar atom. I’d have expected there to be more cooperativity than this would seem to allow, but it seems that the program works well when tested against known structures, e.g. lysozyme, bacteriorhodopsin, aquaporin.
An unusual approach to the hydration of proteins is taken by Vitaly Kocherbitov and Thomas Arnebrant at Malmö University (Langmuir 26, 3918-3922; 2010 – paper here). They adapt a method commonly used to study adsorption at the solid-gas interface, based on a BET-type analysis but allowing for heterogeneity of the surface. This may apply to the case of ‘dry’ proteins exposed to a humid environment, but presumably not to proteins in solution.
Amit Galande and colleagues at SRI International in Virginia report some designed peptides that will fold in solution via intramolecular hydrogen bonds, regardless of competition from solvating water molecules (B. Song et al., Langmuir 132, 4508-4509; 2010 – paper here). I can’t immediately see if there are generic principles here that get the free-energy balance right.
From time to time, efforts are made to find a computationally cheap way to approximate water structure in complex simulations. Kevin Hadley and Clare McCabe at Vanderbilt University suggest one such (J. Phys. Chem. B 114, 4590-4599; 2010 – paper here). They propose a coarse-graining in which four-molecule water clusters can be represented by single ‘beads’ in a simulation.
Sason Shaik and coworkers have extended their investigations of the role of water in heme catalysis (P. Vidossich et al., J. Phys. Chem. B 114, 5161-5169; 2010 – paper here; and D. Fishelovitch et al., J. Phys. Chem. 10.1021/jp101894k – paper here). They have computed the free-energy landscape for the position of the water molecule that provides a crucial hydrogen-bonded bridge between peroxide (complexed to ferryloxo) and a histidine residue in the active site of peroxidase, showing that the ‘reactive configuration’ corresponds to a minority population, albeit one that is relevant on the timescale of catalysis. And they clarify the roles of a water channel in the active site of cytochrome P450, showing how this facilitates proton transport.
In a related vein, the role of water in the active site of ribonuclease H is studied by C. Satheesan Babu and Carmay Lim in Taiwan (JACS 10.1021/ja101494m; paper here). They find that two different binding modes of magnesium ions, which act as cofactors, are distinguished by having a water-rich and water-depleted environment. This might have implications for the design of inhibitors.
Hydration of the head groups of a phosphatidylcholine film is investigated by Yuki Nagata and Shaul Mukamel at UC Irvine using SFG, revealing three distinct environments for the water molecules at the interface (JACS 10.1021/ja100508n; paper here).
A curious paper by Michele Pavanello at the University of Arizona and coworkers looks at how solvation influences hole transport in DNA, which is relevant to the issue of radiation-induced damage (M. Pavanello et al., J. Phys. Chem. B 114, 4416-4423; 2010 – paper here). The study looks at (theoretical) DNA conductivity of a DNA double strand contacted by an STM tip, and finds that hydration slows hole transport significantly.
I don’t really know what to make of a paper by Dariusz Czapiewski and Jan Zielkiewicz at the Gdansk University of Technology on the structures of hydration shells around peptides (J. Phys. Chem. B 114, 4536-4550; 2010 – paper here). As far as I can tell, they use some approximate analytical method to calculate the degree of ‘water ordering’ in the hydration shells, and conclude that it is not very different from the bulk, but is ‘pseudo-rigid’, with strengthened hydrogen bonds. That would surprise me.
I have a few other bits and pieces to add at some stage, but this brings things relatively up to date for now.
Wednesday, April 28, 2010
Tuesday, February 16, 2010
Denaturants again
Yes, more on denaturants: Shekhar Garde and colleagues at RPI have studied the effects of the common denaturant guanidinium chloride on hydrophobicity using MD simulations (R. Godawat et al., J. Phys. Chem. B jp906976q – paper here). GdmCl acts like simple salts (NaCl and CsCl) in increasing the surface tension of water and decreasing the solubility of small hydrophobic solutes (that is, in this case making it harder to insert a hard sphere into solution). But it also destabilizes the compact state of a hydrophobic polymer. Consistent with earlier studies, it does so via direct (vdW) interaction with the polymer backbone, and not via any indirect effect on ‘water structure’.
Meanwhile, Pannuru Venkatesu at the University of Delhi and colleagues have studied the effect of denaturants (urea, GdnHCl) and osmolytes (TMAO, betaine, sucrose and others) on the activity of an enzyme, specifically alpha-chymotrypsin (P. Attri et al., J. Phys. Chem. B 114, 1471; 2010 – paper here). They measure the stability of the enzyme as reflected in the Gibbs free energy of unfolding changes, and the enthalpy change, on addition of cosolvent. These variables increase with increasing osmolyte concentration, and decrease on addition of denaturant – which is, I guess, what one would anticipate. CD spectroscopy suggests that these effects are manifested via changes in beta-helix stability. The osmolytes do not, however, seem to affect enzyme activity. In contrast, and consistent with the study above, denaturants seem to act by binding to the enzyme surface, and induce sufficient structural disruption to reduce activity virtually to zero.
And Yi Qin Gao and colleagues at Texas A&M have used MD simulations to look at the effects of urea, tetramethyl urea (TMU) and the osmolyte trimethylamine N-oxide (TMAO) on the structure of water and dissolved proteins (H. Wei et al., J. Phys. Chem. B 114, 557; 2010 – paper here). TMAO weakens interactions between amide carbonyls on model peptides and water, while urea and TMU strengthen them. Consistent with previous studies, they find a direct interaction between urea and the peptides (via the carbonyls). But they also find evidence of a role for indirect effects on denaturation, whereby the cosolvents alter the hydrophobic interaction via changes to the structure and dynamics of water. They find that a peptide fragment of a G protein unfolds by step-by-step breaking of its native hydrogen bonds, coupled to the formation of water-carbonyl bonds.
Similar territory is explored by Feng Guo and Joel Friedman at the Albert Einstein College of Medicine, who have used vibronic sideband luminescence spectroscopy of a gadolinium(III) probe ion to explore changes in hydrogen bonding between hydration waters of a protein induced by osmolytes (J. Phys. Chem. B 113, 16632; 2009 – paper here). They say that while urea initially weakens hydrogen bonding in the hydration layer, polyol osmolytes such as trehalose, sucrose and glucose enhance it. But they argue that as the concentration of urea increases, it actually enhances water occupancy within the protein and hydrogen bonding in the hydration layer, and that this is the first step in the urea-induced unfolding process. There is a delicate balance here, they say, between entropic effects that favour water penetration of the protein and enthalpic effects that favour a robust hydrogen-bonded hydration network. If I understand the argument correctly, the latter dominates for osmolytes and accounts for the stabilization of the compact folded structure in that case.
The nature of the hydrated hydrogen ion has been much debated. Christopher Reed and colleagues at UC Riverside have investigated the issue using IR spectroscopy, and argue that the best description is neither an Eigen ion (H9O4+) nor a Zundel ion (H5O2+), but the species H13O6+, containing a delocalized proton in the central O-H-O group (E. S. Stoyanov et al., JACS 10.1021/ja9101826 – paper here).
Greg Voth and Takefumi Yamashita have meanwhile investigated the nature of hydrated protons near lipid membranes, using MS-EVB calculations (J. Phys. Chem. B 114, 592; 2010 – paper here). They are interested in clarifying the proposed proton-antenna effect whereby lipid membranes collect protons and shuttle them by lateral diffusion to membrane proteins such as ATP synthase. They confirm this picture, saying that the effect arises because of the stabilization of the hydrated proton by the lipid phosphate groups: a Zundel-like cation bridges phosphate and carbonyl groups. Diffusion of protons within the interface region is significantly slower than it is in the bulk.
Voth, along with Noam Agmon and Hanning Chen, also has a paper on the kinetics of proton transport in pure water (J. Phys. Chem. B 114, 333; 2010 – paper here). The calculations support the idea that the migration of the proton (in effect, of the centre of excess charge) depends on significant reorganization of (perhaps up to 20!) surrounding water molecules.
Mischa Bonn and colleagues at FOM in the Netherlands have used a microfluidic device to study changes in proton mobility near hydrophobic surface (JACS ja9083094 – paper here). They figured that if water molecule reorientation is, as posited, crucial to rapid proton migration, then the slower reorientation of waters near hydrophobic groups seen previously by Rezus and Bakker (Phys. Rev. Lett. 99, 148301; 2007) should have a significant effect on proton transport in such an environment. It’s a very neat experiment: laminar flow in the device means that fluorescein fluorescence in one half of the microfluidic channel may be quenched by lateral proton transport from the other half down a pH gradient. The proton diffusion decreases by an order of magnitude when the hydrophobe tetramethylurea is added, which is consistent with (if not perhaps definitive support for) the hypothesis.
The diffusion of water molecules at lipid surfaces, meanwhile, has been investigated experimentally by Ravinath Kausik and Songi Han at UCSB, using Overhauser dynamic nuclear polarization of the proton NMR signal (JACS 131, 18254; 2009 – paper here). At this stage this is largely a demonstration of the feasibility of the technique, which they hope will also be applicable to the study of solvent dynamics in the hydration shells of macromolecules.
Further along this paper trail, it is the mobility of water molecules in the hydration shells of peptides that is the subject of a simulation study by Charusita Chakravarty at the Indian Institute of Technology in Delhi and colleagues (M. Agarwal et al., J. Phys. Chem. B 114, 651; 2010 – paper here). They consider two small peptides: a 16-residue beta-hairpin structure, and deca-alanine. They see layering structure in the water extending at least 10 Å from the peptide surfaces, and the energetics and dynamics are significantly perturbed relative to the bulk: the discussion is couched mostly in terms of the ‘tagged potential energy’, said to be equivalent to the binding energy of an individual water molecule at a particular location at a given instant in time. This is typically 10-15 percent lower in the innermost hydration layer than in the bulk. But I’m not entirely clear what that implies: does it make diffusion faster or slower? (Surely the latter, but that’s not obvious from this measure.)
In the previous post I mentioned work by Ronen Zangi challenging the notion of ions as structure-makers and structure-breakers. Martina Havenith at Bochum and her colleagues have now raised further problems for this issue, using THz spectroscopy of salt solutions (D. A. Schmidt et al., JACS 131, 18512 (2009) – paper here). They say that the results suggest all ions can be considered simply as defects in the H-bonded network, and so can’t be regarded as either chaotropes or kosmotropes. It turns out that the data can be understood using an appealingly simple model in which the ions undergo damped harmonic oscillations – ‘rattling’ – within the water network. In other words, at least the fast (sub-picosecond) ion motions are essentially decoupled from the dynamics of the network.
One suggested mechanisms of pressure-induced denaturation is the penetration of water into the hydrophobic core. This notion is investigated in simulations by Takashi Imai and Yuji Sugita at RIKEN in Japan (J. Phys. Chem. B jp909701j – paper here). Using ubiquitin as a model case, they look in particular at competing scenarios: does water first penetrate and force the protein to swell, or are the cavities pre-formed by structural fluctuations and then fill with water? They find support for the latter picture: the influx of water stabilizes a pre-existing metastable structure, and drives a distinct transition to a relatively unfolded state.
Harold Sheraga at Cornell and colleagues have probed the nature of hydrophobic interactions as the size of hydrophobic solutes approaches the nanoscale limit (M. Makowski et al., J. Phys. Chem. B jp907794h – paper here). Specifically, they consider the crossover point of around 1 nm at which Lum, Chandler and Weeks (J. Phys. Chem. B 103, 4570; 1999) predicted that the mechanism of the hydrophobic interaction will change from that of small solutes to that of extended surfaces. They calculate the potentials of mean force for large hydrophobes such as adamantine and C60 in water. When two solvation spheres for such large species overlap as they form a dimmer in solution, the water molecules trapped in the concave ‘cleft’ at the edges of the interaction have restricted motion and decreased entropy that offsets any free energy gains from increased solute-particle contact. It seems that fullerenes like this, while too large to be treated as small hydrophobic solutes, are not yet large enough to be considered macroscopic hydrophobic surfaces.
Todd Sformo has sent me a fascinating paper on cold survival strategies of the Alaskan beetle (J. Exp. Biol. 213, 502; 2010 – paper here). He and his coworkers finds that this bug vitrifies at around –76 C, and by that means it can survive cooling of an amazing –150 C. The cryoprotection that supports vitrification is in this case glycerol.
When I was the editor at Nature for Reza Ghadiri’s paper on peptide nanotubes in 1993 (Nature 366; 324), I had to make the decision as something of an act of faith. I remain deeply glad that I did, for the work has stood the test of time. Now Padmanabhan Balaram and colleagues at the Indian Institute of Science have used peptide nanotubes formed from non-cyclic pentamers to study single-file water wires threading through their hydrophobic central channels in molecular crystals (U. S. Raghavender et al., JACS ja9083978 – paper here). This looks like an attractive model system for investigating the relationship between the water structures and the chemical nature of the wall ‘lining’.
Gene Stanley and his coworkers propose a new way of considering the structure of water that involves characterizing the ‘tetrahedral entropy’ associated with the degree of tetrahedral order (P. Kumar et al., PNAS 10.1073/pnas.0911094106 – paper here). They say that this parameter accounts for the specific heat maximum as the Widom line – where there is a cross-over from non-Arrhenius to Arrhenius dynamical behaviour, in general under conditions of supercooling – is crossed.
Meanwhile, Pannuru Venkatesu at the University of Delhi and colleagues have studied the effect of denaturants (urea, GdnHCl) and osmolytes (TMAO, betaine, sucrose and others) on the activity of an enzyme, specifically alpha-chymotrypsin (P. Attri et al., J. Phys. Chem. B 114, 1471; 2010 – paper here). They measure the stability of the enzyme as reflected in the Gibbs free energy of unfolding changes, and the enthalpy change, on addition of cosolvent. These variables increase with increasing osmolyte concentration, and decrease on addition of denaturant – which is, I guess, what one would anticipate. CD spectroscopy suggests that these effects are manifested via changes in beta-helix stability. The osmolytes do not, however, seem to affect enzyme activity. In contrast, and consistent with the study above, denaturants seem to act by binding to the enzyme surface, and induce sufficient structural disruption to reduce activity virtually to zero.
And Yi Qin Gao and colleagues at Texas A&M have used MD simulations to look at the effects of urea, tetramethyl urea (TMU) and the osmolyte trimethylamine N-oxide (TMAO) on the structure of water and dissolved proteins (H. Wei et al., J. Phys. Chem. B 114, 557; 2010 – paper here). TMAO weakens interactions between amide carbonyls on model peptides and water, while urea and TMU strengthen them. Consistent with previous studies, they find a direct interaction between urea and the peptides (via the carbonyls). But they also find evidence of a role for indirect effects on denaturation, whereby the cosolvents alter the hydrophobic interaction via changes to the structure and dynamics of water. They find that a peptide fragment of a G protein unfolds by step-by-step breaking of its native hydrogen bonds, coupled to the formation of water-carbonyl bonds.
Similar territory is explored by Feng Guo and Joel Friedman at the Albert Einstein College of Medicine, who have used vibronic sideband luminescence spectroscopy of a gadolinium(III) probe ion to explore changes in hydrogen bonding between hydration waters of a protein induced by osmolytes (J. Phys. Chem. B 113, 16632; 2009 – paper here). They say that while urea initially weakens hydrogen bonding in the hydration layer, polyol osmolytes such as trehalose, sucrose and glucose enhance it. But they argue that as the concentration of urea increases, it actually enhances water occupancy within the protein and hydrogen bonding in the hydration layer, and that this is the first step in the urea-induced unfolding process. There is a delicate balance here, they say, between entropic effects that favour water penetration of the protein and enthalpic effects that favour a robust hydrogen-bonded hydration network. If I understand the argument correctly, the latter dominates for osmolytes and accounts for the stabilization of the compact folded structure in that case.
The nature of the hydrated hydrogen ion has been much debated. Christopher Reed and colleagues at UC Riverside have investigated the issue using IR spectroscopy, and argue that the best description is neither an Eigen ion (H9O4+) nor a Zundel ion (H5O2+), but the species H13O6+, containing a delocalized proton in the central O-H-O group (E. S. Stoyanov et al., JACS 10.1021/ja9101826 – paper here).
Greg Voth and Takefumi Yamashita have meanwhile investigated the nature of hydrated protons near lipid membranes, using MS-EVB calculations (J. Phys. Chem. B 114, 592; 2010 – paper here). They are interested in clarifying the proposed proton-antenna effect whereby lipid membranes collect protons and shuttle them by lateral diffusion to membrane proteins such as ATP synthase. They confirm this picture, saying that the effect arises because of the stabilization of the hydrated proton by the lipid phosphate groups: a Zundel-like cation bridges phosphate and carbonyl groups. Diffusion of protons within the interface region is significantly slower than it is in the bulk.
Voth, along with Noam Agmon and Hanning Chen, also has a paper on the kinetics of proton transport in pure water (J. Phys. Chem. B 114, 333; 2010 – paper here). The calculations support the idea that the migration of the proton (in effect, of the centre of excess charge) depends on significant reorganization of (perhaps up to 20!) surrounding water molecules.
Mischa Bonn and colleagues at FOM in the Netherlands have used a microfluidic device to study changes in proton mobility near hydrophobic surface (JACS ja9083094 – paper here). They figured that if water molecule reorientation is, as posited, crucial to rapid proton migration, then the slower reorientation of waters near hydrophobic groups seen previously by Rezus and Bakker (Phys. Rev. Lett. 99, 148301; 2007) should have a significant effect on proton transport in such an environment. It’s a very neat experiment: laminar flow in the device means that fluorescein fluorescence in one half of the microfluidic channel may be quenched by lateral proton transport from the other half down a pH gradient. The proton diffusion decreases by an order of magnitude when the hydrophobe tetramethylurea is added, which is consistent with (if not perhaps definitive support for) the hypothesis.
The diffusion of water molecules at lipid surfaces, meanwhile, has been investigated experimentally by Ravinath Kausik and Songi Han at UCSB, using Overhauser dynamic nuclear polarization of the proton NMR signal (JACS 131, 18254; 2009 – paper here). At this stage this is largely a demonstration of the feasibility of the technique, which they hope will also be applicable to the study of solvent dynamics in the hydration shells of macromolecules.
Further along this paper trail, it is the mobility of water molecules in the hydration shells of peptides that is the subject of a simulation study by Charusita Chakravarty at the Indian Institute of Technology in Delhi and colleagues (M. Agarwal et al., J. Phys. Chem. B 114, 651; 2010 – paper here). They consider two small peptides: a 16-residue beta-hairpin structure, and deca-alanine. They see layering structure in the water extending at least 10 Å from the peptide surfaces, and the energetics and dynamics are significantly perturbed relative to the bulk: the discussion is couched mostly in terms of the ‘tagged potential energy’, said to be equivalent to the binding energy of an individual water molecule at a particular location at a given instant in time. This is typically 10-15 percent lower in the innermost hydration layer than in the bulk. But I’m not entirely clear what that implies: does it make diffusion faster or slower? (Surely the latter, but that’s not obvious from this measure.)
In the previous post I mentioned work by Ronen Zangi challenging the notion of ions as structure-makers and structure-breakers. Martina Havenith at Bochum and her colleagues have now raised further problems for this issue, using THz spectroscopy of salt solutions (D. A. Schmidt et al., JACS 131, 18512 (2009) – paper here). They say that the results suggest all ions can be considered simply as defects in the H-bonded network, and so can’t be regarded as either chaotropes or kosmotropes. It turns out that the data can be understood using an appealingly simple model in which the ions undergo damped harmonic oscillations – ‘rattling’ – within the water network. In other words, at least the fast (sub-picosecond) ion motions are essentially decoupled from the dynamics of the network.
One suggested mechanisms of pressure-induced denaturation is the penetration of water into the hydrophobic core. This notion is investigated in simulations by Takashi Imai and Yuji Sugita at RIKEN in Japan (J. Phys. Chem. B jp909701j – paper here). Using ubiquitin as a model case, they look in particular at competing scenarios: does water first penetrate and force the protein to swell, or are the cavities pre-formed by structural fluctuations and then fill with water? They find support for the latter picture: the influx of water stabilizes a pre-existing metastable structure, and drives a distinct transition to a relatively unfolded state.
Harold Sheraga at Cornell and colleagues have probed the nature of hydrophobic interactions as the size of hydrophobic solutes approaches the nanoscale limit (M. Makowski et al., J. Phys. Chem. B jp907794h – paper here). Specifically, they consider the crossover point of around 1 nm at which Lum, Chandler and Weeks (J. Phys. Chem. B 103, 4570; 1999) predicted that the mechanism of the hydrophobic interaction will change from that of small solutes to that of extended surfaces. They calculate the potentials of mean force for large hydrophobes such as adamantine and C60 in water. When two solvation spheres for such large species overlap as they form a dimmer in solution, the water molecules trapped in the concave ‘cleft’ at the edges of the interaction have restricted motion and decreased entropy that offsets any free energy gains from increased solute-particle contact. It seems that fullerenes like this, while too large to be treated as small hydrophobic solutes, are not yet large enough to be considered macroscopic hydrophobic surfaces.
Todd Sformo has sent me a fascinating paper on cold survival strategies of the Alaskan beetle (J. Exp. Biol. 213, 502; 2010 – paper here). He and his coworkers finds that this bug vitrifies at around –76 C, and by that means it can survive cooling of an amazing –150 C. The cryoprotection that supports vitrification is in this case glycerol.
When I was the editor at Nature for Reza Ghadiri’s paper on peptide nanotubes in 1993 (Nature 366; 324), I had to make the decision as something of an act of faith. I remain deeply glad that I did, for the work has stood the test of time. Now Padmanabhan Balaram and colleagues at the Indian Institute of Science have used peptide nanotubes formed from non-cyclic pentamers to study single-file water wires threading through their hydrophobic central channels in molecular crystals (U. S. Raghavender et al., JACS ja9083978 – paper here). This looks like an attractive model system for investigating the relationship between the water structures and the chemical nature of the wall ‘lining’.
Gene Stanley and his coworkers propose a new way of considering the structure of water that involves characterizing the ‘tetrahedral entropy’ associated with the degree of tetrahedral order (P. Kumar et al., PNAS 10.1073/pnas.0911094106 – paper here). They say that this parameter accounts for the specific heat maximum as the Widom line – where there is a cross-over from non-Arrhenius to Arrhenius dynamical behaviour, in general under conditions of supercooling – is crossed.
Tuesday, February 2, 2010
The post-Christmas glut
Well, it was always going to be this way: after several weeks away from the blog there’s now a big stack of papers to catch up on. The list here is incomplete, but more will follow.
One of the most interesting and important papers in this current stack is a MD study by Ronen Zangi of the notion of structure-making and structure-breaking in Hofmeister effects (J. Phys. Chem. B 114, 643; 2010 – paper here). In short, this study offers little succour for that concept, which has long overstayed its welcome. Ronen looks at the correlation between the propensity of various ions to alter the hydrophobic interaction (and thus to salt in/salt out) and changes in structural and dynamical properties they induce in the solvent. While there is a monotonic relationship between the reduction in hydrophobic interaction and the increase in ‘water structure’ as measured by the partial radial distribution factors, Ronen says that he could not identify ‘one property that can predict the change in the strength of the hydrophobic interacitons’. Nor could such properties predict the transition from salting-in to salting-out behaviour. Changes in dynamics, meanwhile, were induced by changes in the ion-water interaction, and not changes that the ions introduce to the ‘structural ordering’ of the water itself. As a result of all this, it seems that predicting whether a particular ion will induce salting-in or salting-out cannot be done on the basis of the properties of the salt solution alone, in the absence of the solute, and the whole notion of kosmotropes and chaotropes seems misleading. It would be nice to think that this paper will serve to banish those terms, but I suspect they will sadly take rather more dislodging than that.
Shekhar Garde and his colleagues have extended their earlier work on the conformations of polymers at surfaces (S. N. Jamadagni et al., Langmuir 25, 13092; 2009 – paper here). They have previously shown (J. Phys. Chem. B 113, 4093; 2009) that hydrophobic polymers adsorb preferentially at the interface between water and a hydrophobic surface (or air), and that the polymers here have significantly different structure and dynamics to those in the bulk. The present study looks in more detail at what is going on there, considering surfaces with a range of chemistries from hydrophilic to hydrophobic. The ‘test polymers’ are hydrophobic 35-mers, and the surfaces are SAMs with different terminal groups. The preferential adsorption at hydrophobic surfaces seems to be due to changes in water dynamics: the water has greater density fluctuations here and lower free energy of cavity formation, making it more able to solvate hydrophobes. The polymers have greater translational diffusion and conformational flexibility, typically flattening into pancake-like shapes.
I’ve been looking somewhat into the literature on nanobubbles, and it seems increasingly clear that it is very much in a state of flux and probably in need of some sort of snapshot review. How and when do nanobubbles form in the bulk and at surfaces? How long-lived are they, and how do they survive at all? There are many questions, and the answers so far are diverse. Detlef Lohse and his coworkers have a new contribution on the subject (B. M. Borkent et al., Langmuir 26, 260; 2009 – paper here). They try to clarify the shape of nanobubbles on hydrophobic surfaces (HOPG) using AFM, saying that they seem uniformly to have contact angles of about 119 degrees even for radii as small as 20 nm. It seems that some cantilevers can deposit material on the surfaces, making them rougher and altering the contact angle.
Robert Bryant and coworkers at the University of Virginia have used magnetic relaxation dispersion spectroscopy to characterize the dynamics of protons in a protein (BSA) backbone and its hydration water (G. Diakova et al., Biophys. J. 98, 138; 2010 – paper here). They find remarkably constant relaxation behaviour in the protein over a wide frequency range (0.01-300 MHz). Water dynamics contribute significantly to the relaxation on timescales of tens of ns, thanks to some rare, rather highly constrained, perhaps buried, hydration waters.
There’s a fascinating exploration of the various functional roles that protein hydration waters can have by Matteo Ceccarelli abd colleagues at the University of Cagliari in Italy (M. A. Scorciapino et al., JACS ja909822d – paper here). They have looked at myoglobin as a model system using MD, and observe three distinct ways in which waters modify the intrinsic dynamical behaviour of the protein. They can (1) block access to or escape of ligands from a binding site; (2) change internal dynamics by expanding the distances between residues in the manner of a ‘wedge’; (3) assist ligand transport, in effect by ‘washing it away’.
Another lovely example of water molecules playing an active role in an important biological process is provided by Göran Wallin and Johan Åqvist at Uppsala (PNAS pnas.0914192107 – paper here). They show that a water molecule trapped at the active site of peptide bond formation on the ribosome serves in a proton shuttle, while a second water molecule helps to stabilize the negative charge on the substrate.
Erik Sunde and Bertil Halle at Lund show how water proton magnetic relaxation dispersion measurements can provide information on slow protein dynamics by virtue of the exchange between buried and bulk water molecules (JACS 131, 18214 (2009) – paper here). In effect, the internal water molecules serve as a probe of protein motions with a relaxation timescale comparable to the exchange time (typically 0.1 ns to 10 microseconds).
An intriguing demonstration that the chemistry of hydrated ions can be critically dependent on the geometry of the surrounding water network is provided by Rachael Relph at Yale and colleagues using vibrational spectroscopy of clusters (R. A. Relph et al., Science 327, 308 (2010) – paper here). They find that the extent to which NO+ reacts with water to form HONO varies with different numbers and arrangements of hydration water molecules (1-4). It’s an intriguing demonstration of geometrical effects in hydration, though what it can say in general about hydration in bulk solution is less immediately clear to me. There’s a commentary by Katrin Siefermann and Bernd Abel in the same issue (paper here).
Finally, just for fun, I’ve indulged in a little speculation here about the possibility of quasicrystalline water. There is a lot more behind all this that I was not able to include, following discussions with John Finney and Alan Mackay in particular. The upshot is that Alan gives at least some cause to think it may be possible in theory to construct a plausible H-bonded network with a quasicrystalline geometry. Whether one could make it in practice is, of course, quite another matter.
One of the most interesting and important papers in this current stack is a MD study by Ronen Zangi of the notion of structure-making and structure-breaking in Hofmeister effects (J. Phys. Chem. B 114, 643; 2010 – paper here). In short, this study offers little succour for that concept, which has long overstayed its welcome. Ronen looks at the correlation between the propensity of various ions to alter the hydrophobic interaction (and thus to salt in/salt out) and changes in structural and dynamical properties they induce in the solvent. While there is a monotonic relationship between the reduction in hydrophobic interaction and the increase in ‘water structure’ as measured by the partial radial distribution factors, Ronen says that he could not identify ‘one property that can predict the change in the strength of the hydrophobic interacitons’. Nor could such properties predict the transition from salting-in to salting-out behaviour. Changes in dynamics, meanwhile, were induced by changes in the ion-water interaction, and not changes that the ions introduce to the ‘structural ordering’ of the water itself. As a result of all this, it seems that predicting whether a particular ion will induce salting-in or salting-out cannot be done on the basis of the properties of the salt solution alone, in the absence of the solute, and the whole notion of kosmotropes and chaotropes seems misleading. It would be nice to think that this paper will serve to banish those terms, but I suspect they will sadly take rather more dislodging than that.
Shekhar Garde and his colleagues have extended their earlier work on the conformations of polymers at surfaces (S. N. Jamadagni et al., Langmuir 25, 13092; 2009 – paper here). They have previously shown (J. Phys. Chem. B 113, 4093; 2009) that hydrophobic polymers adsorb preferentially at the interface between water and a hydrophobic surface (or air), and that the polymers here have significantly different structure and dynamics to those in the bulk. The present study looks in more detail at what is going on there, considering surfaces with a range of chemistries from hydrophilic to hydrophobic. The ‘test polymers’ are hydrophobic 35-mers, and the surfaces are SAMs with different terminal groups. The preferential adsorption at hydrophobic surfaces seems to be due to changes in water dynamics: the water has greater density fluctuations here and lower free energy of cavity formation, making it more able to solvate hydrophobes. The polymers have greater translational diffusion and conformational flexibility, typically flattening into pancake-like shapes.
I’ve been looking somewhat into the literature on nanobubbles, and it seems increasingly clear that it is very much in a state of flux and probably in need of some sort of snapshot review. How and when do nanobubbles form in the bulk and at surfaces? How long-lived are they, and how do they survive at all? There are many questions, and the answers so far are diverse. Detlef Lohse and his coworkers have a new contribution on the subject (B. M. Borkent et al., Langmuir 26, 260; 2009 – paper here). They try to clarify the shape of nanobubbles on hydrophobic surfaces (HOPG) using AFM, saying that they seem uniformly to have contact angles of about 119 degrees even for radii as small as 20 nm. It seems that some cantilevers can deposit material on the surfaces, making them rougher and altering the contact angle.
Robert Bryant and coworkers at the University of Virginia have used magnetic relaxation dispersion spectroscopy to characterize the dynamics of protons in a protein (BSA) backbone and its hydration water (G. Diakova et al., Biophys. J. 98, 138; 2010 – paper here). They find remarkably constant relaxation behaviour in the protein over a wide frequency range (0.01-300 MHz). Water dynamics contribute significantly to the relaxation on timescales of tens of ns, thanks to some rare, rather highly constrained, perhaps buried, hydration waters.
There’s a fascinating exploration of the various functional roles that protein hydration waters can have by Matteo Ceccarelli abd colleagues at the University of Cagliari in Italy (M. A. Scorciapino et al., JACS ja909822d – paper here). They have looked at myoglobin as a model system using MD, and observe three distinct ways in which waters modify the intrinsic dynamical behaviour of the protein. They can (1) block access to or escape of ligands from a binding site; (2) change internal dynamics by expanding the distances between residues in the manner of a ‘wedge’; (3) assist ligand transport, in effect by ‘washing it away’.
Another lovely example of water molecules playing an active role in an important biological process is provided by Göran Wallin and Johan Åqvist at Uppsala (PNAS pnas.0914192107 – paper here). They show that a water molecule trapped at the active site of peptide bond formation on the ribosome serves in a proton shuttle, while a second water molecule helps to stabilize the negative charge on the substrate.
Erik Sunde and Bertil Halle at Lund show how water proton magnetic relaxation dispersion measurements can provide information on slow protein dynamics by virtue of the exchange between buried and bulk water molecules (JACS 131, 18214 (2009) – paper here). In effect, the internal water molecules serve as a probe of protein motions with a relaxation timescale comparable to the exchange time (typically 0.1 ns to 10 microseconds).
An intriguing demonstration that the chemistry of hydrated ions can be critically dependent on the geometry of the surrounding water network is provided by Rachael Relph at Yale and colleagues using vibrational spectroscopy of clusters (R. A. Relph et al., Science 327, 308 (2010) – paper here). They find that the extent to which NO+ reacts with water to form HONO varies with different numbers and arrangements of hydration water molecules (1-4). It’s an intriguing demonstration of geometrical effects in hydration, though what it can say in general about hydration in bulk solution is less immediately clear to me. There’s a commentary by Katrin Siefermann and Bernd Abel in the same issue (paper here).
Finally, just for fun, I’ve indulged in a little speculation here about the possibility of quasicrystalline water. There is a lot more behind all this that I was not able to include, following discussions with John Finney and Alan Mackay in particular. The upshot is that Alan gives at least some cause to think it may be possible in theory to construct a plausible H-bonded network with a quasicrystalline geometry. Whether one could make it in practice is, of course, quite another matter.
Friday, November 6, 2009
How do spores survive?
How do bacterial spores survive in a dormant state for years, perhaps in the face of high temperatures or toxic substances? It has been long suspected that the state of water in the cell compartments plays a role. Bertil Halle and his coworkers at Lund have now looked that the state of water in Bacillus subtilis spores using deuterium and oxygen-17 spin relaxation, and they find that the water is not glassy, contrary to some earlier suggestions (E. P. Sunde et al., PNAS 10.1073/pnas.0908712106; paper here). However, the water permeability of the inner membrane is unusually low, providing a barrier to the transport of toxic substances. And some of the key enzymes in the core of the spore seem to be in a relatively dehydrated state, their rotational mobility severely reduced, which might be expected to reduce the tendency of the denatured proteins to aggregate – in other words, the changes in hydration may not provide stabilization against heat-denaturation in itself, but will avoid this becoming an irreversible process.
While most studies of hydration forces between surfaces have tended to focus on hydrophobic surfaces, the nature of the interaction between hydrophilic surfaces is also controversial. It is repulsive, but the reason for this remains debated. There is some suggestion that several mechanisms might act at different length scales – for example, genuine ‘hydration’ effects due to water orientation at moderate separations (between about 0.4 and 0.8 nm), and undulation effects at larger separations. Max Berkowitz at UNC has studied this phenomenon previously using simulations of lipid bilayers (Lu & Berkowitz, J. Chem. Phys. 124, 101101 (2006) and Mol. Phys. 104, 3607 (2006)), but now he and Changsun Eun return to the problem with more accurate simulations in which the lipid head groups are allowed to be mobile (Eun & Berkowitz, J. Phys. Chem. B 113, 13222-13228; 2009 – paper here). They do indeed find three regimes. At short range (<1 nm), the repulsion is dominated by steric van der Waals interactions between the lipid headgroups. They focus mainly on the intermediate-range (1-1.6 nm) interaction, which they argue is due to the free-energy cost of removing waters hydrating the head groups. William Jorgensen has continued his examination of water in protein binding sites, an earlier instance of which was mentioned in the previous post. With Julien Michel and Julian Tirado-Rives, he reports a MD method for determining how water molecules will be situated in binding sites with or without the ligand (J. Phys. Chem. B 113, 13337-13346; 2009 – paper here). The accuracy of the method is shown by comparison with five cases where the crystal structures are known.
Another extension of earlier work: Nicolas Giovambattista, Peter Rossky and Pablo Debenedetti look at how temperature affects the behaviour of water confined between hydrophobic, hydrophilic and heterogeneous nanoscale plates (J. Phys. Chem. B 113, 13723-13734; 2009 - paper here) – the system they considered earlier in Phys. Rev. E 73, 041604 (2006), J. Phys. Chem. C 11, 1323 (2007) and PNAS 105, 2274 (2008). Cooling enables the water to approach the hydrophobic plates more closely, consistent with the expected suppression of the vapour phase. It also blurs the differences in water density between hydrophobic and hydrophilic regions of a heterogeneous surface. This would be consistent with invasion of hydrophobic cavities by water in cold denaturation.
Somewhat related is a study by Ateeque Malani at the Indian Institute of Science in Bangalore and coworkers on the differences in water structure when confined between pairs of two types of hydrophilic surface: hydroxylated silca and mica (J. Phys. Chem. B 113, 13825-13839; 2009 – paper here). While an oscillatory solvation force and a bulk-like H-bond network near the interface are found for silica (these are simulations), the network is disrupted near mica, where there are potassium ions at the surface which are themselves hydrated.
Water diffusion on the surfaces of lipid vesicles has been studied by Ravinath Kausik and Songi Han at UCSB using Overhauser dynamic nuclear polarization of hydrogen-1 NMR (JACS ASAP; paper here). They find diffusion coefficients about half those of bulk water; the key result here is a demonstrating of the feasibility of the technique for obtaining this sort of information. And James Skinner and colleagues at Wisconsin use MD and IR spectroscopy to study water inside reverse micelles (P. A. Pieniazek et al., J. Phys. Chem. B ASAP; paper here). They say that the distance from the surfactant headgroups over which the water becomes bulk-like increases with decreasing micelle size (increasing curvature), eventually becoming larger than the micelle radius. In the smallest micelle (containing 52 water molecules), the water seems to be near-glassy, with very slow rotational relaxation.
Vincent Craig at ANU, now working with Christine Henry, has extended his long-standing studies of the effects of solutes on bubble coalescence. They have looked at the effect on this phenomenon of osmolytes: sucrose and other sugars, and urea (Langmuir 25, 11406-11412; 2009 – paper here). Urea seems to have little effect, but sucrose and other sugars show an inhibiting influence on coalescence. This suggests that, contrary to what one might have been tempted to infer from previous studies on electrolytes, the inhibitory effect does not stem from solute charge. They speculate that concentration gradients close to the bubble-water interface may instead be responsible.
The influence of urea and another osmolyte, trimethylamine-N-oxide on the structure of water and hen egg-white lysozyme are studied using FTIR by Janusz Stangret and colleagues at the Gdansk University of Technology in Poland (A. Panuszko et al., J. Phys. Chem. B ASAP; paper here). Water structure is barely affected by urea, they say, but more strongly perturbed by TMAO, forming stronger and more ‘ordered’ H-bonds. They monitor the protein via the amide I band and suggest that the changes seen there are consistent with changes in water structure, resembling in the case of TMAO changes that are evident on dehydration. This all seems to be presented within the framework of osmolytes exerting indirect effects via their influence on water structure – but I guess one would want to know precisely how the osmolytes interact with the protein itself.
Haiping Fang at Shanghai and colleagues have continued their investigation of water transport through nanochannels. They show how symmetry-breaking of water orientation in a one-dimensional H-bonded chain threading through a carbon nanotube can give rise to spontaneous unidirectional net flux in the absence of any external pressure gradient (R. Wan et al., Phys. Chem. Chem. Phys. 11, 9898-9902; 2009 – paper here doi:10.1039/b907926m). And Haiping also has a paper in PNAS (10.1073/pnas.0902676106; paper here) reporting simulations in which the presence of a single-electron charge in one arm of a Y-shaped carbon nanotube junction can, by flipping the orientation of a water molecule in a single-file chain within the nanotube, reorient the dipoles of the water chains in the other two branches, thus multiplying the single-electron signal. With a suitable arrangement of junctions, it can be multiplied more than twofold.
On a similar topic, Padmanabhan Balaram and colleagues at the Indian Institute of Science use MD simulations to look at the structure of one-dimensional water chains inside the hydrophobic core of a tubular synthetic protein (U. S. Raghavender et al., JACS 131, 15130-15132; 2009 – paper here). They find two distinct states in different peptides: one in which the water molecules are disordered over two possible positions in the chain, the other in which the molecules are perfectly ordered along a sixfold screw axis.
There’s a very neat demonstration of how water in binding sites can be engineered to improve function in a paper on a catalytic antibody by Ian Wilson at Scripps and colleagues (E. W. Debler et al., PNAS 10.1073/pnas.0902700106; paper here). They find that an oriented water molecule in the hydrophobic pocket of the antibody 13G5, which catalyses the cleavage of benzisoxazoles, stabilizies the developing charge on the leaving group. And in a single-residue Glu-to-Ala mutant, a hydrogen-bonded complex involving four water molecules is restructured in a way that enhances still further the rate of the proton transfer involved in the process. A key role for water in another catalytic antibody is reported by Orlando Acevedo at Auburn University in Alabama (J. Phys. Chem. B ASAP; paper here). He looks at the antibody 4B2, which catalyses both a Kemp elimination and an allylic isomerization of an unsatuated ketone. For the former, water molecules in the active site help stabilize the transition state during proton abstraction, while in the latter case the water takes an active role as a proton source. Acevedo suggests that water might be usefully engaged in other designed catalysts to perform this function as a proton donor.
A paper on the behaviour of water and proteins confined in nanoporous (c. 5 nm) silica by Eduardo Reátegui and Alptekin Aksan at Minnesota (J. Phys. Chem. B 113, 13048-13060; 2009 – paper here) contains rather more information than I can easily digest yet. They use FTIR to characterize what is happening to the water, which is of course a slightly blunt tool on its own – certainly, the claim to see liquid-liquid transitions analogous to the putative HDL-LDL transition seems a big one to make on these grounds alone. Changes in the encapsulated proteins, monitored by amide IR bands, seem to mirror those seen in water OH bands, but it’s again not too clear what these actually correspond to in terms of structure or function.
Sotiris Xantheas and Greg Voth, working with Francesc Paesani, have developed an ab initio force field for water that, in MD simulations, provides a good fit for the experimental IR spectra probing H-bond dynamics (J. Phys. Chem. B ASAP; paper here).
The hydrodynamics of water at surfaces has been a controversial topic, and one with some important practical implications. It seems clear that the common no-slip assumption for fluids at solid interfaces doesn’t necessarily hold at the nanoscale. Roland Netz and his coworkers have investigated this for hydrophilic and hydrophobic surfaces using MD simulations (C. Sendner et al., Langmuir 25, 10768-10781; 2009 – paper here). They find something like an inverse square dependence of slip length on contact angle for hydrophobic surfaces, but slip lengths of typically only a few nm for realistic contact angles. This is little affected by dissolved gas at the interface, and the viscosity of the interfacial water is only a few times higher than that of the bulk, with molecular motions being purely diffusive. In contrast, on hydrophilic surface water molecules may become trapped, there is no slip, and the interfacial water viscosity may be enhanced significantly. In the same vein (and consistent with these results), Bharat Bushan and colleagues report measurement of the hydrodynamic forces acting on a glass sphere glued to an AFM tip as it approaches a mica surface (A. Maali et al., Langmuir 25, 12002-12005; 2009 – paper here). They say that the measurements are consistent with a no-slip assumption at both glass and mica surfaces.
Xavier Tadeo and colleagues at the Centro de Investigación Cooperativa bioGUNE in Derio, Spain, have looked at how the anions of the Hofmeister series affect protein stability, using as their test case the IGg binding domain of protein L from Streptoccocal magnus (ProtL) (Biophys. J. 97, 2595-2603; 2009 – paper here). They look at changes in thermostability of a lysine-to-glutamine mutant in the presence sodium salts of sulfate, phosphate, fluoride, nitrate, perchlorate and thiocyanate, and say that the results are consistent with stabilization of the native state by an increase in solution surface tension due to the anions. I’ve not seen the full paper, but I do wonder whether such bulk effects on surface tension can be a reliable guide to what is going on here, without knowing how the ions are partitioned at the protein-solvent interface.
More on Hofmeister effects: Xin Wen and colleagues at CSU at Los Angeles look at the effects of monovalent salts on the activity of the antifreeze protein DAFP-1 from the beetle Dendroides canadensis (S. Wang et al., J. Phys. Chem. B ASAP; paper here). Specifically, they use DSC to monitor how the difference in melting and freezing point of water due to the antifreeze protein is altered by the salts: salting-out seems, as might be expected, to enhance the adsorption of DAFP-1 on the ice surface, thereby boosting its activity.
Henry Ashbaugh at Tulane University has a nice paper on how different sequences of hydrophobic and hydrophilic monomers in a heteropolymer will affect its conformation in aqueous solution (J. Phys. Chem. B 113, 14043-14046; 2009 – paper here). Intermediate segregation of monomer types favours a collapsed conformation, while more strictly alternating monomers favours a random coil.
James Beattie and his coworkers in France and Australia have another paper making the case that the interface of water with air or oil is basic rather than acidic, due to specific adsorption of hydroxide (P. Creux et al., J. Phys. Chem. B ASAP; paper here). This claim is made on the basis of measurements of the zeta potential. I suspect the debate will continue.
There may not be another post from me here for a couple of months, owing to an imminent new arrival in the family. No doubt this means I’ll miss some interesting papers in the interim. But do feel free to send me or tell me of interesting ones (p.ball@btinternet.com). Hope to be back up and running after Christmas – have a good one.
While most studies of hydration forces between surfaces have tended to focus on hydrophobic surfaces, the nature of the interaction between hydrophilic surfaces is also controversial. It is repulsive, but the reason for this remains debated. There is some suggestion that several mechanisms might act at different length scales – for example, genuine ‘hydration’ effects due to water orientation at moderate separations (between about 0.4 and 0.8 nm), and undulation effects at larger separations. Max Berkowitz at UNC has studied this phenomenon previously using simulations of lipid bilayers (Lu & Berkowitz, J. Chem. Phys. 124, 101101 (2006) and Mol. Phys. 104, 3607 (2006)), but now he and Changsun Eun return to the problem with more accurate simulations in which the lipid head groups are allowed to be mobile (Eun & Berkowitz, J. Phys. Chem. B 113, 13222-13228; 2009 – paper here). They do indeed find three regimes. At short range (<1 nm), the repulsion is dominated by steric van der Waals interactions between the lipid headgroups. They focus mainly on the intermediate-range (1-1.6 nm) interaction, which they argue is due to the free-energy cost of removing waters hydrating the head groups. William Jorgensen has continued his examination of water in protein binding sites, an earlier instance of which was mentioned in the previous post. With Julien Michel and Julian Tirado-Rives, he reports a MD method for determining how water molecules will be situated in binding sites with or without the ligand (J. Phys. Chem. B 113, 13337-13346; 2009 – paper here). The accuracy of the method is shown by comparison with five cases where the crystal structures are known.
Another extension of earlier work: Nicolas Giovambattista, Peter Rossky and Pablo Debenedetti look at how temperature affects the behaviour of water confined between hydrophobic, hydrophilic and heterogeneous nanoscale plates (J. Phys. Chem. B 113, 13723-13734; 2009 - paper here) – the system they considered earlier in Phys. Rev. E 73, 041604 (2006), J. Phys. Chem. C 11, 1323 (2007) and PNAS 105, 2274 (2008). Cooling enables the water to approach the hydrophobic plates more closely, consistent with the expected suppression of the vapour phase. It also blurs the differences in water density between hydrophobic and hydrophilic regions of a heterogeneous surface. This would be consistent with invasion of hydrophobic cavities by water in cold denaturation.
Somewhat related is a study by Ateeque Malani at the Indian Institute of Science in Bangalore and coworkers on the differences in water structure when confined between pairs of two types of hydrophilic surface: hydroxylated silca and mica (J. Phys. Chem. B 113, 13825-13839; 2009 – paper here). While an oscillatory solvation force and a bulk-like H-bond network near the interface are found for silica (these are simulations), the network is disrupted near mica, where there are potassium ions at the surface which are themselves hydrated.
Water diffusion on the surfaces of lipid vesicles has been studied by Ravinath Kausik and Songi Han at UCSB using Overhauser dynamic nuclear polarization of hydrogen-1 NMR (JACS ASAP; paper here). They find diffusion coefficients about half those of bulk water; the key result here is a demonstrating of the feasibility of the technique for obtaining this sort of information. And James Skinner and colleagues at Wisconsin use MD and IR spectroscopy to study water inside reverse micelles (P. A. Pieniazek et al., J. Phys. Chem. B ASAP; paper here). They say that the distance from the surfactant headgroups over which the water becomes bulk-like increases with decreasing micelle size (increasing curvature), eventually becoming larger than the micelle radius. In the smallest micelle (containing 52 water molecules), the water seems to be near-glassy, with very slow rotational relaxation.
Vincent Craig at ANU, now working with Christine Henry, has extended his long-standing studies of the effects of solutes on bubble coalescence. They have looked at the effect on this phenomenon of osmolytes: sucrose and other sugars, and urea (Langmuir 25, 11406-11412; 2009 – paper here). Urea seems to have little effect, but sucrose and other sugars show an inhibiting influence on coalescence. This suggests that, contrary to what one might have been tempted to infer from previous studies on electrolytes, the inhibitory effect does not stem from solute charge. They speculate that concentration gradients close to the bubble-water interface may instead be responsible.
The influence of urea and another osmolyte, trimethylamine-N-oxide on the structure of water and hen egg-white lysozyme are studied using FTIR by Janusz Stangret and colleagues at the Gdansk University of Technology in Poland (A. Panuszko et al., J. Phys. Chem. B ASAP; paper here). Water structure is barely affected by urea, they say, but more strongly perturbed by TMAO, forming stronger and more ‘ordered’ H-bonds. They monitor the protein via the amide I band and suggest that the changes seen there are consistent with changes in water structure, resembling in the case of TMAO changes that are evident on dehydration. This all seems to be presented within the framework of osmolytes exerting indirect effects via their influence on water structure – but I guess one would want to know precisely how the osmolytes interact with the protein itself.
Haiping Fang at Shanghai and colleagues have continued their investigation of water transport through nanochannels. They show how symmetry-breaking of water orientation in a one-dimensional H-bonded chain threading through a carbon nanotube can give rise to spontaneous unidirectional net flux in the absence of any external pressure gradient (R. Wan et al., Phys. Chem. Chem. Phys. 11, 9898-9902; 2009 – paper here doi:10.1039/b907926m). And Haiping also has a paper in PNAS (10.1073/pnas.0902676106; paper here) reporting simulations in which the presence of a single-electron charge in one arm of a Y-shaped carbon nanotube junction can, by flipping the orientation of a water molecule in a single-file chain within the nanotube, reorient the dipoles of the water chains in the other two branches, thus multiplying the single-electron signal. With a suitable arrangement of junctions, it can be multiplied more than twofold.
On a similar topic, Padmanabhan Balaram and colleagues at the Indian Institute of Science use MD simulations to look at the structure of one-dimensional water chains inside the hydrophobic core of a tubular synthetic protein (U. S. Raghavender et al., JACS 131, 15130-15132; 2009 – paper here). They find two distinct states in different peptides: one in which the water molecules are disordered over two possible positions in the chain, the other in which the molecules are perfectly ordered along a sixfold screw axis.
There’s a very neat demonstration of how water in binding sites can be engineered to improve function in a paper on a catalytic antibody by Ian Wilson at Scripps and colleagues (E. W. Debler et al., PNAS 10.1073/pnas.0902700106; paper here). They find that an oriented water molecule in the hydrophobic pocket of the antibody 13G5, which catalyses the cleavage of benzisoxazoles, stabilizies the developing charge on the leaving group. And in a single-residue Glu-to-Ala mutant, a hydrogen-bonded complex involving four water molecules is restructured in a way that enhances still further the rate of the proton transfer involved in the process. A key role for water in another catalytic antibody is reported by Orlando Acevedo at Auburn University in Alabama (J. Phys. Chem. B ASAP; paper here). He looks at the antibody 4B2, which catalyses both a Kemp elimination and an allylic isomerization of an unsatuated ketone. For the former, water molecules in the active site help stabilize the transition state during proton abstraction, while in the latter case the water takes an active role as a proton source. Acevedo suggests that water might be usefully engaged in other designed catalysts to perform this function as a proton donor.
A paper on the behaviour of water and proteins confined in nanoporous (c. 5 nm) silica by Eduardo Reátegui and Alptekin Aksan at Minnesota (J. Phys. Chem. B 113, 13048-13060; 2009 – paper here) contains rather more information than I can easily digest yet. They use FTIR to characterize what is happening to the water, which is of course a slightly blunt tool on its own – certainly, the claim to see liquid-liquid transitions analogous to the putative HDL-LDL transition seems a big one to make on these grounds alone. Changes in the encapsulated proteins, monitored by amide IR bands, seem to mirror those seen in water OH bands, but it’s again not too clear what these actually correspond to in terms of structure or function.
Sotiris Xantheas and Greg Voth, working with Francesc Paesani, have developed an ab initio force field for water that, in MD simulations, provides a good fit for the experimental IR spectra probing H-bond dynamics (J. Phys. Chem. B ASAP; paper here).
The hydrodynamics of water at surfaces has been a controversial topic, and one with some important practical implications. It seems clear that the common no-slip assumption for fluids at solid interfaces doesn’t necessarily hold at the nanoscale. Roland Netz and his coworkers have investigated this for hydrophilic and hydrophobic surfaces using MD simulations (C. Sendner et al., Langmuir 25, 10768-10781; 2009 – paper here). They find something like an inverse square dependence of slip length on contact angle for hydrophobic surfaces, but slip lengths of typically only a few nm for realistic contact angles. This is little affected by dissolved gas at the interface, and the viscosity of the interfacial water is only a few times higher than that of the bulk, with molecular motions being purely diffusive. In contrast, on hydrophilic surface water molecules may become trapped, there is no slip, and the interfacial water viscosity may be enhanced significantly. In the same vein (and consistent with these results), Bharat Bushan and colleagues report measurement of the hydrodynamic forces acting on a glass sphere glued to an AFM tip as it approaches a mica surface (A. Maali et al., Langmuir 25, 12002-12005; 2009 – paper here). They say that the measurements are consistent with a no-slip assumption at both glass and mica surfaces.
Xavier Tadeo and colleagues at the Centro de Investigación Cooperativa bioGUNE in Derio, Spain, have looked at how the anions of the Hofmeister series affect protein stability, using as their test case the IGg binding domain of protein L from Streptoccocal magnus (ProtL) (Biophys. J. 97, 2595-2603; 2009 – paper here). They look at changes in thermostability of a lysine-to-glutamine mutant in the presence sodium salts of sulfate, phosphate, fluoride, nitrate, perchlorate and thiocyanate, and say that the results are consistent with stabilization of the native state by an increase in solution surface tension due to the anions. I’ve not seen the full paper, but I do wonder whether such bulk effects on surface tension can be a reliable guide to what is going on here, without knowing how the ions are partitioned at the protein-solvent interface.
More on Hofmeister effects: Xin Wen and colleagues at CSU at Los Angeles look at the effects of monovalent salts on the activity of the antifreeze protein DAFP-1 from the beetle Dendroides canadensis (S. Wang et al., J. Phys. Chem. B ASAP; paper here). Specifically, they use DSC to monitor how the difference in melting and freezing point of water due to the antifreeze protein is altered by the salts: salting-out seems, as might be expected, to enhance the adsorption of DAFP-1 on the ice surface, thereby boosting its activity.
Henry Ashbaugh at Tulane University has a nice paper on how different sequences of hydrophobic and hydrophilic monomers in a heteropolymer will affect its conformation in aqueous solution (J. Phys. Chem. B 113, 14043-14046; 2009 – paper here). Intermediate segregation of monomer types favours a collapsed conformation, while more strictly alternating monomers favours a random coil.
James Beattie and his coworkers in France and Australia have another paper making the case that the interface of water with air or oil is basic rather than acidic, due to specific adsorption of hydroxide (P. Creux et al., J. Phys. Chem. B ASAP; paper here). This claim is made on the basis of measurements of the zeta potential. I suspect the debate will continue.
There may not be another post from me here for a couple of months, owing to an imminent new arrival in the family. No doubt this means I’ll miss some interesting papers in the interim. But do feel free to send me or tell me of interesting ones (p.ball@btinternet.com). Hope to be back up and running after Christmas – have a good one.
Tuesday, September 29, 2009
Water in drug design... and why green tea keeps you young?
Can the displacement of water from binding sites be used as a tool for drug design? John Ladbury has written a fair amount on this question in the past (e.g. Chem. Biol. 3, 973; 1996), but it remains hard to deduce any general principles. In principle both the enthalpy and the entropy of ligand binding can be enhanced by displacing water molecules, but the balance is subtle and not obviously generic. Julien Michel, Julian Tirado-Rives and William Jorgensen at Yale have now looked at what can be learnt from some specific cases, namely ligands designed to bind to three proteins: scytalone dehydratase, p38-aMAP kinase and EGFR kinase (JACS ja906058w – paper here). They find for a series of ligands that in general the binding affinity correlates with ease of water displacement, but also that it can be important to ensure that it can be important to compensate for the free-energy increase of water displacement by building in additional favourable interactions between the binding site and the displacing group – that is, it’s not necessarily enough to expel the water; one has to put something amenable in its place. My reading of this paper is that there are no wholly reliable short-cuts or rules of thumb – the details matter.
Nicolas Giovambattista, Pablo Debenedetti and Peter Rossky continue their investigations of how surface topography affects hydrophobicity (PNAS 106, 15181; 2009 – paper here). They have used simulations to look at the hydration of a silica surface on which they vary the surface polarity and topography (atomic- to micrometre-scale roughness), and find that the two can couple in such a way as make a somewhat polar surface more hydrophobic than an apolar one. This suggests that surface patterning could be a powerful tool for altering hydrophobicity.
Feng Guo and Joel Friedman at the Albert Einstein College of Medicine have probed Hofmeister effects by looking at the effect of adding anions and cations to a solution of gadolinium (III) ions, both free and coordinated to organic and biological molecules (JACS 131, 11010; 2009 – paper here). The idea is that changes in the OH stretching mode of waters in the Gd hydration shell offer a sign of what is happening elsewhere in the solution. It’s not entirely clear how the former changes relate to the latter, but Guo and Friedman suggest two possibilities. For example, the tight hydration clusters of high-charge-density cations might both alter water structure quite generally, and might sequester water molecules in a way that frees up anions to interact with the Gd hydration shell. In the first of these cases, the interpretation is predicated on a notion of inhomogeneous bulk water structure composed of a mixture of high- and low-density water clusters, based on Wilse Robinson’s model. Frankly, I’m not persuaded that this is a persuasive way to interpret the findings – the two-state water model is of course controversial. But the overall conclusion – that Hofmeister ordering of salts can be best explained by disruption of hydrogen bonding in hydration-shell water rather than bulk water – has a ring of truth to it.
But the Hofmeister plot thickens further. Yanjie Zhang and Paul Cremer at Texas A&M have also been investigating these effects, and they find that for lysozyme, aggregation in salt solution (followed by looking at cloudiness of the solution and eventual phase separation) seems to follow two different Hofmeister series depending on salt concentration (PNAS 106, 15249; 2009 – paper here). At low concentration, the usual series for anions (which dominate aggregation effects in this case) is reversed, and is correlated with size and hydration thermodynamics of the ions. At high concentrations, there is a normal Hofmeister series correlated with the ionic polarizability.
Daisuke Matsuoka and Masayoshi Nakasako at Keio University in Japan have conducted a massive study of the probability distributions of water molecules hydrating proteins, using nearly 18,000 crystal structures from the Protein Data Bank (J. Phys. Chem. B 113, 11274; 2009 – paper here). They find that the angular distributions are narrowest in the direction of N-H and O-H bonds, and that pairs of polar atoms are often arranged to satisfy the tetrahedral H-bonding geometry, suggesting that – if one may put it like this – the protein’s secondary structure is arranged to ‘suit’ the solvent rather than vice versa.
Is the hydrophobic core of a protein rigid or fluid? In reality neither extreme seems terribly likely, but Liliya Vugmeyster at the University of Alaska-Anchorage and colleagues have probed its dynamics using deuteron solid-state NMR (JACS ja902977u – paper here). Specifically, they look at the chicken villin headpiece subdomain protein HP36 labelled with deuterons at either of the two methyl groups of a leucine residue. They find that there is restricted diffusion along an arc, and larger jumps between rotameric conformers.
Eduard Schreiner and colleagues at Bochum have used ab initio MD simulations to look at the reaction kinetics and mechanisms of peptide bond formation and hydrolysis among activated amino acids (alpha-amino acid N-carboxyanhydrides, NCAs). These are used in the synthesis of large polypeptides, and may also have prebiotic relevance. The team compares the processes in water under ambient conditions and in hot pressurized water, such as might be found at hydrothermal vents (JACS ja9032742 – paper here). The hydrolysis mechanisms are different in the two cases, but in both the barrier to hydrolysis is greater than that to peptide bond formation, showing that peptide production is feasible in either case.
Ali Eftekhari-Bafrooei and Eric Borguet at Temple University use IR pump-probe spectroscopy to look at how the vibrational dynamics of O-H stretching of interfacial water groups is altered by surface charge at the interface with silica (JACS 131, 12035; 2009 – paper here). They say that, while the vibrational dynamics are retarded at the neutral surface (at low pH), surface charging at higher pH causes polarization of the water molecules that leads to more bulk-like behaviour.
Changes in water dynamics are also the subject of a paper by Matías Pomata in the National Commission for Atomic Energy of Argentina and colleagues, who consider this issue for carbohydrate (fructose) solutions (J. Phys. Chem. B jp904019c – paper here). They say that for sugar concentrations above about 45%, the sugar molecules form a percolating H-bonded network encompassing patches of solvent, resulting in a slowing of translational, rotational and H-bonding dynamics (especially for water-solute) that is comparable to what is seen for the hydration layers of proteins (e.g. Pizzitutti et al., J. Phys. Chem. B 111, 7584; 2007).
Most of the work on the pseudo-glass transition of proteins around 200 K has been based on globular proteins. How do extended structural proteins such as elastin and collagen compare? That question is probed by Catalin Gainaru and colleagues at TU Dortmund (J. Phys. Chem. B jp9065899 – paper here). Elastin exhibits something like a glass transition at temperatures only slightly below physiological, but not collagen. Yet the dielectric relaxation appears to be the same for both molecules between about 140 and 220 K, showing that relaxation is Arrhenius-like (thermally activated) over the entire temperature range: there seems in this case nothing ‘anomalous’ about the dynamics in this regime.
Some time ago Haiping Fang at the Shanghai Institute of Applied Physics sent me a preprint describing MD simulations of the wetting properties of water films on polar, neutral surfaces. This has now been published (C. Wang et al., Phys. Rev. Lett. 103, 137801 (2009) – paper here). The paper looks at the behaviour of a water monolayer on a surface designed to resemble a semiconductor such as InSb(110). On some such surfaces (including metals), a monolayer at low temperatures is found to adopt a 2D ice-like structure with no dangling bonds, making it somewhat hydrophobic. But one would expect thermal fluctuations to create some dangling OH bonds at room temperature, increasing the hydrophilicity. That does happen here, but surprisingly the monolayer nevertheless remains significantly hydrophobic even at room temperature, so that a water droplet does not wet it.
On the same theme of interfacial water at solid surfaces, Andrei Sommer at Ulm and colleagues have continued their investigations of thin water films on diamond (Crystal Growth and Design 9, 3852; 2009 – paper here). They have studied the nature of water fimls on hydrogenated and non-hydrogenated nanocrystalline diamond at room temperature with atomic force acoustic microscopy. For the hydrogenated (hydrophobic) surfaces, water monolayers seem to be securely anchored and crystalline, promoting lubrication. The authors suggest that similar water layers might exist at the surfaces of biological fibrous tissues such as elastin, promoting easy sliding – an idea proposed in 1971 by Albert Szent-Györgyi (Perspect. Biol. Med. 14, 239; 1971).
Andrei and colleagues also found that red laser light can influence the structure of the water films, from which they think they may be able to develop new skin treatments. This is what Andrei has just sent to me:
“From what we learned about the interaction of red light with interfacial water layers on hydrophobic and hydrophilic surfaces, we designed a model of physiological aging and applied it in a real skin rejuvenation study. The good news is that the paper dealing with the model and its results (Facial Rejuvenation in the Triangle of ROS, Crystal Growth & Design, October 7 issue) produced an extraordinary impact in Google (Key words: green tea, light, wrinkles.)
“The bad news is that the journalists who wrote about the work overlooked the point in the study, whose implications are more interesting: we put forward the first physicochemical explanation of the shortening of the telomeres, and thereby of cellular aging. In a nutshell: we postulated that the shortening of telomeres is due to the coincidence of mechanical pulling during cell division and the build-up of a glue-like interfacial water in the space between the nuclear matrix and telomeres. The latter is modulated by an increase in interfacial pH, triggered by the emergence of reactive oxygen species (ROS) in the cell. The increase of intracellular ROS is induced by oxidative stress, which can have two different causes: external (e.g., UV radiation, air pollution), or internal (e.g., replicative stress). In both scenarios the principal actors involved in the production of ROS are mitochondria in the cell. This part of the process is known and comprehensively described in the literature.
“The exciting thing in all this is that, according to our research, it is possible to liquidify the glue-like interfacial water layers (to reduce the viscosity) by shining moderately intense red light on them. (Albert Szent Györgyi would like to read this, because it relates interfacial water with the the biological clock underlying the limited division potential of somatic cells, which is the length of the telomeres.)
“In our study we used to rejuvenate the skin a combination of topically applied green tea and red light (670 nm). We just discovered a recent paper (R. Chan et al., Brit. J. Nutr., August 12, 2009) in which the authors report that green tea is instrumental in preventing the shortening of the telomeres, and they extrapolate that drinking green tea might extend our life by 5 years.
“Interestingly the cells of turtles - the methuselahs in our world - present no or only very limited shortening of their telomeres. Their shells provide them a perfect protection from destructive environmental impacts, including UV, and air pollution (i.e. volcanic ashes on a primitive Earth). In addition, their oxygen turnover rate is very low.”
This is fascinating stuff, and I must explore it some more. In the meantime, I think I will put the kettle on.
Nicolas Giovambattista, Pablo Debenedetti and Peter Rossky continue their investigations of how surface topography affects hydrophobicity (PNAS 106, 15181; 2009 – paper here). They have used simulations to look at the hydration of a silica surface on which they vary the surface polarity and topography (atomic- to micrometre-scale roughness), and find that the two can couple in such a way as make a somewhat polar surface more hydrophobic than an apolar one. This suggests that surface patterning could be a powerful tool for altering hydrophobicity.
Feng Guo and Joel Friedman at the Albert Einstein College of Medicine have probed Hofmeister effects by looking at the effect of adding anions and cations to a solution of gadolinium (III) ions, both free and coordinated to organic and biological molecules (JACS 131, 11010; 2009 – paper here). The idea is that changes in the OH stretching mode of waters in the Gd hydration shell offer a sign of what is happening elsewhere in the solution. It’s not entirely clear how the former changes relate to the latter, but Guo and Friedman suggest two possibilities. For example, the tight hydration clusters of high-charge-density cations might both alter water structure quite generally, and might sequester water molecules in a way that frees up anions to interact with the Gd hydration shell. In the first of these cases, the interpretation is predicated on a notion of inhomogeneous bulk water structure composed of a mixture of high- and low-density water clusters, based on Wilse Robinson’s model. Frankly, I’m not persuaded that this is a persuasive way to interpret the findings – the two-state water model is of course controversial. But the overall conclusion – that Hofmeister ordering of salts can be best explained by disruption of hydrogen bonding in hydration-shell water rather than bulk water – has a ring of truth to it.
But the Hofmeister plot thickens further. Yanjie Zhang and Paul Cremer at Texas A&M have also been investigating these effects, and they find that for lysozyme, aggregation in salt solution (followed by looking at cloudiness of the solution and eventual phase separation) seems to follow two different Hofmeister series depending on salt concentration (PNAS 106, 15249; 2009 – paper here). At low concentration, the usual series for anions (which dominate aggregation effects in this case) is reversed, and is correlated with size and hydration thermodynamics of the ions. At high concentrations, there is a normal Hofmeister series correlated with the ionic polarizability.
Daisuke Matsuoka and Masayoshi Nakasako at Keio University in Japan have conducted a massive study of the probability distributions of water molecules hydrating proteins, using nearly 18,000 crystal structures from the Protein Data Bank (J. Phys. Chem. B 113, 11274; 2009 – paper here). They find that the angular distributions are narrowest in the direction of N-H and O-H bonds, and that pairs of polar atoms are often arranged to satisfy the tetrahedral H-bonding geometry, suggesting that – if one may put it like this – the protein’s secondary structure is arranged to ‘suit’ the solvent rather than vice versa.
Is the hydrophobic core of a protein rigid or fluid? In reality neither extreme seems terribly likely, but Liliya Vugmeyster at the University of Alaska-Anchorage and colleagues have probed its dynamics using deuteron solid-state NMR (JACS ja902977u – paper here). Specifically, they look at the chicken villin headpiece subdomain protein HP36 labelled with deuterons at either of the two methyl groups of a leucine residue. They find that there is restricted diffusion along an arc, and larger jumps between rotameric conformers.
Eduard Schreiner and colleagues at Bochum have used ab initio MD simulations to look at the reaction kinetics and mechanisms of peptide bond formation and hydrolysis among activated amino acids (alpha-amino acid N-carboxyanhydrides, NCAs). These are used in the synthesis of large polypeptides, and may also have prebiotic relevance. The team compares the processes in water under ambient conditions and in hot pressurized water, such as might be found at hydrothermal vents (JACS ja9032742 – paper here). The hydrolysis mechanisms are different in the two cases, but in both the barrier to hydrolysis is greater than that to peptide bond formation, showing that peptide production is feasible in either case.
Ali Eftekhari-Bafrooei and Eric Borguet at Temple University use IR pump-probe spectroscopy to look at how the vibrational dynamics of O-H stretching of interfacial water groups is altered by surface charge at the interface with silica (JACS 131, 12035; 2009 – paper here). They say that, while the vibrational dynamics are retarded at the neutral surface (at low pH), surface charging at higher pH causes polarization of the water molecules that leads to more bulk-like behaviour.
Changes in water dynamics are also the subject of a paper by Matías Pomata in the National Commission for Atomic Energy of Argentina and colleagues, who consider this issue for carbohydrate (fructose) solutions (J. Phys. Chem. B jp904019c – paper here). They say that for sugar concentrations above about 45%, the sugar molecules form a percolating H-bonded network encompassing patches of solvent, resulting in a slowing of translational, rotational and H-bonding dynamics (especially for water-solute) that is comparable to what is seen for the hydration layers of proteins (e.g. Pizzitutti et al., J. Phys. Chem. B 111, 7584; 2007).
Most of the work on the pseudo-glass transition of proteins around 200 K has been based on globular proteins. How do extended structural proteins such as elastin and collagen compare? That question is probed by Catalin Gainaru and colleagues at TU Dortmund (J. Phys. Chem. B jp9065899 – paper here). Elastin exhibits something like a glass transition at temperatures only slightly below physiological, but not collagen. Yet the dielectric relaxation appears to be the same for both molecules between about 140 and 220 K, showing that relaxation is Arrhenius-like (thermally activated) over the entire temperature range: there seems in this case nothing ‘anomalous’ about the dynamics in this regime.
Some time ago Haiping Fang at the Shanghai Institute of Applied Physics sent me a preprint describing MD simulations of the wetting properties of water films on polar, neutral surfaces. This has now been published (C. Wang et al., Phys. Rev. Lett. 103, 137801 (2009) – paper here). The paper looks at the behaviour of a water monolayer on a surface designed to resemble a semiconductor such as InSb(110). On some such surfaces (including metals), a monolayer at low temperatures is found to adopt a 2D ice-like structure with no dangling bonds, making it somewhat hydrophobic. But one would expect thermal fluctuations to create some dangling OH bonds at room temperature, increasing the hydrophilicity. That does happen here, but surprisingly the monolayer nevertheless remains significantly hydrophobic even at room temperature, so that a water droplet does not wet it.
On the same theme of interfacial water at solid surfaces, Andrei Sommer at Ulm and colleagues have continued their investigations of thin water films on diamond (Crystal Growth and Design 9, 3852; 2009 – paper here). They have studied the nature of water fimls on hydrogenated and non-hydrogenated nanocrystalline diamond at room temperature with atomic force acoustic microscopy. For the hydrogenated (hydrophobic) surfaces, water monolayers seem to be securely anchored and crystalline, promoting lubrication. The authors suggest that similar water layers might exist at the surfaces of biological fibrous tissues such as elastin, promoting easy sliding – an idea proposed in 1971 by Albert Szent-Györgyi (Perspect. Biol. Med. 14, 239; 1971).
Andrei and colleagues also found that red laser light can influence the structure of the water films, from which they think they may be able to develop new skin treatments. This is what Andrei has just sent to me:
“From what we learned about the interaction of red light with interfacial water layers on hydrophobic and hydrophilic surfaces, we designed a model of physiological aging and applied it in a real skin rejuvenation study. The good news is that the paper dealing with the model and its results (Facial Rejuvenation in the Triangle of ROS, Crystal Growth & Design, October 7 issue) produced an extraordinary impact in Google (Key words: green tea, light, wrinkles.)
“The bad news is that the journalists who wrote about the work overlooked the point in the study, whose implications are more interesting: we put forward the first physicochemical explanation of the shortening of the telomeres, and thereby of cellular aging. In a nutshell: we postulated that the shortening of telomeres is due to the coincidence of mechanical pulling during cell division and the build-up of a glue-like interfacial water in the space between the nuclear matrix and telomeres. The latter is modulated by an increase in interfacial pH, triggered by the emergence of reactive oxygen species (ROS) in the cell. The increase of intracellular ROS is induced by oxidative stress, which can have two different causes: external (e.g., UV radiation, air pollution), or internal (e.g., replicative stress). In both scenarios the principal actors involved in the production of ROS are mitochondria in the cell. This part of the process is known and comprehensively described in the literature.
“The exciting thing in all this is that, according to our research, it is possible to liquidify the glue-like interfacial water layers (to reduce the viscosity) by shining moderately intense red light on them. (Albert Szent Györgyi would like to read this, because it relates interfacial water with the the biological clock underlying the limited division potential of somatic cells, which is the length of the telomeres.)
“In our study we used to rejuvenate the skin a combination of topically applied green tea and red light (670 nm). We just discovered a recent paper (R. Chan et al., Brit. J. Nutr., August 12, 2009) in which the authors report that green tea is instrumental in preventing the shortening of the telomeres, and they extrapolate that drinking green tea might extend our life by 5 years.
“Interestingly the cells of turtles - the methuselahs in our world - present no or only very limited shortening of their telomeres. Their shells provide them a perfect protection from destructive environmental impacts, including UV, and air pollution (i.e. volcanic ashes on a primitive Earth). In addition, their oxygen turnover rate is very low.”
This is fascinating stuff, and I must explore it some more. In the meantime, I think I will put the kettle on.
Tuesday, August 25, 2009
Nanobubbles: birth, motion, and consequences
The role of bridging bubbles in the so-called ‘long-range hydrophobic force’ seems now fairly well established. In a study of this effect, Viveca Wallqvist and colleagues argue that in cases where this is the identified mechanism of attraction, it would be preferable to call it a ‘capillary force’ rather than a ‘hydrophobic interaction’. Their study looks at the effect of surface roughness on such forces between hydrophobic surfaces (V. Wallqvist et al., Langmuir 25, 9197 (2009) – paper here). They find that the range and magnitude of the force can vary significantly at different points on nanostructured surfaces due to local variations in contact angle. A high density of nanoscale crevices leads to accumulation of air bubbles that coalesce and weaken the capillary attraction.
William Ducker offers an explanation of the low contact angle and the unusual stability of these nanobubbles, in terms of a thin film of surface-active contaminant at the air-water interface (Langmuir 25, 8907 (2009) – paper here). This, he says, will both decrease the surface tension (and thus the contact angle) and hinder gas diffusion out of the bubble. It’s an alternative to Michael Brenner and Detlef Lohse’s suggestion of a dynamic stabilization of the nanobubbles (Phys. Rev. Lett. 101, 214505 (2008)).
Yi Zhang and colleagues at the Shanghai Institute of Applied Sciences suggest that a precursor to these nanobubbles may be a multilayer (bilayer or trilayer) of adsorbed gas at the hydrophobic interface (L. Zhang et al., Langmuir 25, 8860 (2009) – paper here). They have imaged such bi- and trilayer islands of gas, of up to micron-sized lateral dimensions, at the surface of HOPG, and have watched them evolve into nanobubbles, sometimes under the influence of the AFM tip used for imaging.
And in the same vein, Bharat Bhushan and coworkers look at how the mobility of nanobubbles at hydrophobic surfaces is affected by surface heterogeneity (Y. Wang et al., Langmuir 25, 9328 (2009) – paper here). They find that surfaces partly and totally covered with polystyrene films, which form small islands or can become indented at the nanoscale by the presence of bubbles, tend to have relatively immobile nanobubbles compared with bare, smooth hydrophobic surfaces. Bubble immobility reduces the frictional drag force between such surfaces in motion, and so is sometimes desired in mechanical contexts.
How do you measure hydrophobicity? Macroscopically, that is of course done using contact angles. But what are the microscopic signatures? This question is examined by Shekhar Garde and colleagues at RPI using an extensive range of simulation studies of water at various surfaces ranging from very hydrophobic to very hydrophilic (R. Godawat et al., PNAS advance online publication - paper here). They say that water density is a poor measure of hydrophobicity, but that both the probability of cavity formation and the free energy of binding of hydrophobic solutes to the surface correlates much better with the macroscopic wetting properties. This paper adds weight to the notion that it is in the dynamic rather than the structural characteristics of water that the true nature of hydrophobicity is located.
Gerhard Hummer and colleagues have developed a rather comprehensive model of gated proton pumping in cytochrome c oxidase (Y. C. Kim et al., PNAS advance online publication - paper here). This reveals show the electrostatic interaction between the proton loading site and the electron source for reduction of oxygen at the heme site is central to the pumping efficiency, and also how gating is accomplished.
Water in protein cavities is hard to detect with diffraction methods if it is disordered. Robert Goldbeck at UC Santa Cruz, Raymond Esquerra at San Franscisco State University and their colleagues have shown that non-specific hydration of the cavities of myoglobin mutants can be detected optically via its perturbing effect on the optical spectrum of the pentcoordinate heme group (R. Goldbeck et al., JACS ASAP ja903409j - paper here).
How do membrane proteins compensate, within the hydrocarbon core of a membrane, for loss of hydrophobic interactions? One possibility is that they enhance packing efficiency and thus van der Waals interactions between the hydrophobic residues. Or they might have stronger hydrogen-bonding interactions between hydrophilic regions. But James Bowie and colleagues at UCLA report structural and thermodynamic arguments for why neither plays a strong role (JACS 131, 10846 (2009) – paper here). Rather, they suspect that the reduced entropy cost of folding in membrane proteins might be responsible for their stability.
There is a small clutch of papers on the structure of the air-water interface and other species located there. Yi Qin Gao and colleagues at Texas A&M use vibrational sum frequency spectroscopy and MD simulations to investigate orientational ordering of water molecules, and suggest that this occurs to any significant degree only in the first two layers at the surface (Y. Fan et al., J. Phys. Chem. B ASAP jp900117t - paper here). Joyce Noah-Vanhoucke and Phillip Geissler argue that the preferential segregation of some ions at the air-water interface is due primarily to the way the ions induce deformations of the interfacial geometry, causing electrostatic fluctuations that are not accounted for in the conventional picture (PNAS advance online publication - paper here).
In water confined to nanoscale dimensions (as in the crowded environment of a cell), hydration effects can be quite different from those of the bulk. Margaret Cheung and colleagues at Houston provide an illustration of this by using MD to look at the conformations of hexane in nanoscale water droplets (D. Homouz et al., J. Phys. Chem. B ASAP jp907318d - paper here). They find that the hexane molecules are situated at the droplet surface, where disruption of the H-bonding favours the all-trans conformation.
Meanwhile, Michael Fayer and colleagues at Stanford use ultrafast IR spectroscopy to look at water dynamics close to the neutral and ionic surfaces of reverse micelles (E. E. Fenn et al., PNAS advance online publication - paper here). They find that the orientational relaxations times are rather similar in both cases, both being significantly slower than in the bulk, and conclude that it is the mere presence of an interface, rather than its chemical nature, which exerts the dominant effect.
Nanoscopic water films on metals and other simple surfaces are known often to adopt ordered structures in the first one or two monolayers that may or may not be like bulk ice. On Pt(111), for example, it seems to form a monolayer that is flat rather than having the puckering expected of a ‘slice of ice’. Now Greg Kimmel, Bruce Kay and colleagues find that water on graphene (supported on Pt(111) also forms a flat film, here two monolayers thick (G. A. Kimmel et al., JACS ASAP ja904708f - paper here). This structure has been predicted previously for confined bilayers between hydrophobic walls, but it seems that confinement is not needed to induce it. The bilayer has no dangling bonds or lone pairs on either face, and so one might anticipate that it will itself be somewhat hydrophobic, as indeed Greg Kimmel and others found previously for the flat monolayer on Pt(111) (G. A. Kimmel et al., Phys. Rev. Lett. 95, 166102 (2005).).
Jürgen Köfinger and Christoph Dellago have used MD calculations to probe the dynamics and dielectric response of single-file water chains in narrow pores (Phys. Rev. Lett. 103, 080601; paper here). This supplies a baseline for using dielectric spectroscopy to investigate the properties of such highly confined water, for example enabling the diffusion of defects in the H-bonded chain to be studied.
Kafui Tay and Anne Boutin at the Université Paris-Sud XI have studied the dynamics of hydrated electrons using MD, and say that their diffusion is dictated by fluctuations in the H-bonded network: in the temperature region where the diffusion is Arrhenius-like, the activation energy is determined by H-bond breaking (J. Phys. Chem. B ASAP jp810538f - paper here).
Lars Pettersson, Anders Nilsson and their colleagues at Stanford, Stockholm and in Japan have published a controversial paper claiming to see inhomogeneities in water structure on length scales of around 1 nm (C. Huang et al., PNAS advance online publication - paper here). They say that they see these using SAXS, and argue that the density contrast is due to the coexistence of two water structures: one tetrahedral, the other with distorted H-bonds, related respectively to low- and high-density liquid water. This is, needless to say, a revival of the very old two-state picture of water structure, which in various forms goes right back to Roentgen. It will be disputed, no doubt, but demonstrates again how remarkably tenacious this two-state notion is.
William Ducker offers an explanation of the low contact angle and the unusual stability of these nanobubbles, in terms of a thin film of surface-active contaminant at the air-water interface (Langmuir 25, 8907 (2009) – paper here). This, he says, will both decrease the surface tension (and thus the contact angle) and hinder gas diffusion out of the bubble. It’s an alternative to Michael Brenner and Detlef Lohse’s suggestion of a dynamic stabilization of the nanobubbles (Phys. Rev. Lett. 101, 214505 (2008)).
Yi Zhang and colleagues at the Shanghai Institute of Applied Sciences suggest that a precursor to these nanobubbles may be a multilayer (bilayer or trilayer) of adsorbed gas at the hydrophobic interface (L. Zhang et al., Langmuir 25, 8860 (2009) – paper here). They have imaged such bi- and trilayer islands of gas, of up to micron-sized lateral dimensions, at the surface of HOPG, and have watched them evolve into nanobubbles, sometimes under the influence of the AFM tip used for imaging.
And in the same vein, Bharat Bhushan and coworkers look at how the mobility of nanobubbles at hydrophobic surfaces is affected by surface heterogeneity (Y. Wang et al., Langmuir 25, 9328 (2009) – paper here). They find that surfaces partly and totally covered with polystyrene films, which form small islands or can become indented at the nanoscale by the presence of bubbles, tend to have relatively immobile nanobubbles compared with bare, smooth hydrophobic surfaces. Bubble immobility reduces the frictional drag force between such surfaces in motion, and so is sometimes desired in mechanical contexts.
How do you measure hydrophobicity? Macroscopically, that is of course done using contact angles. But what are the microscopic signatures? This question is examined by Shekhar Garde and colleagues at RPI using an extensive range of simulation studies of water at various surfaces ranging from very hydrophobic to very hydrophilic (R. Godawat et al., PNAS advance online publication - paper here). They say that water density is a poor measure of hydrophobicity, but that both the probability of cavity formation and the free energy of binding of hydrophobic solutes to the surface correlates much better with the macroscopic wetting properties. This paper adds weight to the notion that it is in the dynamic rather than the structural characteristics of water that the true nature of hydrophobicity is located.
Gerhard Hummer and colleagues have developed a rather comprehensive model of gated proton pumping in cytochrome c oxidase (Y. C. Kim et al., PNAS advance online publication - paper here). This reveals show the electrostatic interaction between the proton loading site and the electron source for reduction of oxygen at the heme site is central to the pumping efficiency, and also how gating is accomplished.
Water in protein cavities is hard to detect with diffraction methods if it is disordered. Robert Goldbeck at UC Santa Cruz, Raymond Esquerra at San Franscisco State University and their colleagues have shown that non-specific hydration of the cavities of myoglobin mutants can be detected optically via its perturbing effect on the optical spectrum of the pentcoordinate heme group (R. Goldbeck et al., JACS ASAP ja903409j - paper here).
How do membrane proteins compensate, within the hydrocarbon core of a membrane, for loss of hydrophobic interactions? One possibility is that they enhance packing efficiency and thus van der Waals interactions between the hydrophobic residues. Or they might have stronger hydrogen-bonding interactions between hydrophilic regions. But James Bowie and colleagues at UCLA report structural and thermodynamic arguments for why neither plays a strong role (JACS 131, 10846 (2009) – paper here). Rather, they suspect that the reduced entropy cost of folding in membrane proteins might be responsible for their stability.
There is a small clutch of papers on the structure of the air-water interface and other species located there. Yi Qin Gao and colleagues at Texas A&M use vibrational sum frequency spectroscopy and MD simulations to investigate orientational ordering of water molecules, and suggest that this occurs to any significant degree only in the first two layers at the surface (Y. Fan et al., J. Phys. Chem. B ASAP jp900117t - paper here). Joyce Noah-Vanhoucke and Phillip Geissler argue that the preferential segregation of some ions at the air-water interface is due primarily to the way the ions induce deformations of the interfacial geometry, causing electrostatic fluctuations that are not accounted for in the conventional picture (PNAS advance online publication - paper here).
In water confined to nanoscale dimensions (as in the crowded environment of a cell), hydration effects can be quite different from those of the bulk. Margaret Cheung and colleagues at Houston provide an illustration of this by using MD to look at the conformations of hexane in nanoscale water droplets (D. Homouz et al., J. Phys. Chem. B ASAP jp907318d - paper here). They find that the hexane molecules are situated at the droplet surface, where disruption of the H-bonding favours the all-trans conformation.
Meanwhile, Michael Fayer and colleagues at Stanford use ultrafast IR spectroscopy to look at water dynamics close to the neutral and ionic surfaces of reverse micelles (E. E. Fenn et al., PNAS advance online publication - paper here). They find that the orientational relaxations times are rather similar in both cases, both being significantly slower than in the bulk, and conclude that it is the mere presence of an interface, rather than its chemical nature, which exerts the dominant effect.
Nanoscopic water films on metals and other simple surfaces are known often to adopt ordered structures in the first one or two monolayers that may or may not be like bulk ice. On Pt(111), for example, it seems to form a monolayer that is flat rather than having the puckering expected of a ‘slice of ice’. Now Greg Kimmel, Bruce Kay and colleagues find that water on graphene (supported on Pt(111) also forms a flat film, here two monolayers thick (G. A. Kimmel et al., JACS ASAP ja904708f - paper here). This structure has been predicted previously for confined bilayers between hydrophobic walls, but it seems that confinement is not needed to induce it. The bilayer has no dangling bonds or lone pairs on either face, and so one might anticipate that it will itself be somewhat hydrophobic, as indeed Greg Kimmel and others found previously for the flat monolayer on Pt(111) (G. A. Kimmel et al., Phys. Rev. Lett. 95, 166102 (2005).).
Jürgen Köfinger and Christoph Dellago have used MD calculations to probe the dynamics and dielectric response of single-file water chains in narrow pores (Phys. Rev. Lett. 103, 080601; paper here). This supplies a baseline for using dielectric spectroscopy to investigate the properties of such highly confined water, for example enabling the diffusion of defects in the H-bonded chain to be studied.
Kafui Tay and Anne Boutin at the Université Paris-Sud XI have studied the dynamics of hydrated electrons using MD, and say that their diffusion is dictated by fluctuations in the H-bonded network: in the temperature region where the diffusion is Arrhenius-like, the activation energy is determined by H-bond breaking (J. Phys. Chem. B ASAP jp810538f - paper here).
Lars Pettersson, Anders Nilsson and their colleagues at Stanford, Stockholm and in Japan have published a controversial paper claiming to see inhomogeneities in water structure on length scales of around 1 nm (C. Huang et al., PNAS advance online publication - paper here). They say that they see these using SAXS, and argue that the density contrast is due to the coexistence of two water structures: one tetrahedral, the other with distorted H-bonds, related respectively to low- and high-density liquid water. This is, needless to say, a revival of the very old two-state picture of water structure, which in various forms goes right back to Roentgen. It will be disputed, no doubt, but demonstrates again how remarkably tenacious this two-state notion is.
Monday, July 27, 2009
How proteins loosen up
What happens during protein denaturation? One emerging view is that at least some forms of denaturation (such as pressure-induced) involve penetration of water into the hydrophobic interior. But that picture is challenged in a paper by Santosh Kumar Jha and Jayant Udgaonkar at the Tara Institute of Fundamental Research in Bangalore, at least for the case of denaturant-induced (GdnHCl) unfolding (PNAS 10.1073/pnas.0905744106; paper here). They have used UV circular dichroism measurements on the small plant protein monellin to show that here unfolding seems to involve a dry molten-globule intermediate, reached from the native state in a rather sharp configurational transition.
Also on this topic, Paul Cremer and colleagues at Texas A&M have used FTIR and thermodynamic measurements to probe the notion that urea denatures via direct hydrogen-bonding to the protein surface (L. B. Sagle et al., JACS 131, 9304 (2009); paper here). They challenge that idea, saying that hydrogen-bonding of urea seems to actually promote hydrophobic collapse of a polyamide (PNIPAM, here used as a protein analogue).
Ahmed Zewail and his colleagues have looked at how solvent motion couples to the unfolding of a model protein (melittin) in the presence of a denaturant (trifluoroethanol) (C. M. Othon et al., PNAS 10.1073/pnas.0905967106; paper here). Using time-resolved fluorescence spectroscopy, they see an abrupt change in solvent dynamics at a critical TFE concentration associated with a change in protein structure, in which the tetramers dissociate into loosely bound monomers owing to penetration of TFE into the hydrophobic core. The dissociation of the monomers happens in a distinct second step.
Sapna Sarupria and Shekhar Garde at RPI have studied the compressibility and fluctuations of hydration shells of hydrophobic solutes and proteins using MD simulations (Phys. Rev. Lett. 103, 037803; 2009 – paper here). They say that the compressibility is non-monotonic as a function of solute size, and that it is greater near hydrophobic solutes, relative to the bulk. The latter implies that hydrophobic interactions get weaker as pressure is increased, which may be important for pressure-induced denaturation. This pressure sensitivity is also dependent on the curvature of the solute, being greater for low-curvature surfaces. That might have a role in the pressure dissociation of multi-subunit proteins.
Incidentally, I am preparing a feature article on denaturation for Chemistry World, and would welcome any papers that might be relevant to this.
Padmanabhan Balaram and colleagues at the Indian Institute of Science in Bangalore report a very nice crystal structure of a model peptide containing a hydrophobic channel containing a linear water wire of nine molecules (U. S. Raghavender et al., JACS 10.1021/ja9038906; paper here). Looks like a good model system for studying such structures.
There is a clutch of papers on hydration dynamics of proteins. A painstaking study of femtosecond dynamics in the hydration network of apomyoglobin by Dongping Zhong and colleagues at Ohio State has revealed two distinct classes of water-network relaxation (L. Zhang et al., JACS 10.1021/ja902918p; paper here). One comes from collective hydrogen-bond rearrangements in the water shell, while the other is considerably slower and results from coupled water-protein motions. They are also able to follow changes in these motions in the transition from the native to the molten-globule state. This looks like the kind of careful study that is needed to really figure out what the intimate coupling of protein and water motions entails.
M. Vogel at the Technical University of Darmstadt has used MD simulations to look at how the dynamics of the hydration shells of peptide analogues of structural proteins (elastic and collagen) change with temperature (J. Phys. Chem. B 113, 9386 (2009); paper here). He finds that there is a change from diffusive motion at higher temperatures to jump-like motion on cooling, corresponding to a weak fragile-to-strong crossover of the water dynamics.
And Giorgio Schirò and colleagues at the University of Rome III use dielectric spectroscopy to study the dynamics of myoglobin confined in porous silica at low hydration levels, with only one or two layers of water around the protein (G. Schirò et al., J. Phys. Chem. B 113, 9606 (2009); paper here). They find that confinement has a big effect relative to hydrated myoglobin powder, suppressing the cooperativity of the water motions and the strong coupling to the protein dynamics. All the same, there still seems to be some slaving of protein relaxation in the porous medium to one mode of solvent relaxation.
Dor Ben-Amotz and colleagues at Purdue have seen the spectroscopic signature of dangling OH bonds in the hydration shells of small dissolved nonpolar molecules, similar to those seen at macroscopic water-oil interfaces (P. N. Perera et al., PNAS 10.1073/pnas.0903675106; paper here). And Pier Luigi Silvestrelli at the University of Padova offers further evidence, from first-principles calculations, that hydrophobic groups (here the methyl of methanol) don’t immobilize water molecules, iceberg-like, in the immediate hydration shell, but rather, merely slow down many surrounding molecules (J. Phys. Chem. B 10.1021/jp9044447; paper here).
It’s occasionally and justifiably said that too little attention has been given to polysaccharide hydration, in contrast to proteins. As a result, we know relatively little about glycoprotein hydration. Claudio Margulis and colleagues at Iowa State attempt to redress that imbalance somewhat with a paper looking at the hydration shells of a diverse range of carbohydrates (S. K. Ramadugu et al., J. Phys. Chem. B 10.1021/jp904981v; paper here). I’m not sure I can easily summarize the results, but there looks to be a lot of valuable information here, for example in terms of how water structure and dynamics are affected by branching, size and type of linkage in the polysaccharides.
The behaviour of water in carbon nanotubes continues to intrigue as a model for hydrophobic protein pores. MD simulations by Biswaroop Mukherjee of the Indian Institute of Science and coworkers suggest that jump reorientation of water molecules inside narrow nanotubes involves a switch of which of the two hydrogens are H-bonded to a neighbour, in contrast to such jumps in the bulk which involve H-bonding to a different neighbour (B. Mukherjee et al., J. Phys. Chem. B 10.1021/jp904099f; paper here).
Francesco Mallamace, Gene Stanley and their collaborators have a paper in Nature Physics that describes the appearance of a fractional Stokes-Einstein relation (which provides information about viscosity, connecting the self-diffusion coefficient to temperature and relaxation time) below 290 K in water confined within silica nanopores (2 nm diameter) (Nature Physics 10.1038/nphys1328; paper here). They suggest that this switch marks a crossover to a water structure that is locally more similar to LDA ice – a point at which the proportions of HDA-like and LDA-like configurations starts to change rapidly. It’s an intriguing idea, and there is apparently some indication (I can say no more yet) that the dynamical crossover might be a more general phenomenon for liquids. Some, though, will reasonably wonder whether water within 2-nm silica pores can really be considered representative of the bulk.
Perhaps relevant in this respect, Patrick Huber at Saarland University in Germany and colleagues have studied the dynamics of capillary rise in silica pores 3-5-5 nm across (S. Gruener et al., Phys. Rev. E 79, 067301 (2009); paper here). They find that they can account for the timescales of pore filling according to macroscopic hydrodynamics, so long as they assume the presence of a ‘sticky preadsorbed boundary layer of about two monolayers of water molecules’. In other words, there is dynamical partitioning of the water ‘filling’ into two components.
Masakazu Matsumoto at Nagoya University offers a new picture of the density maximum of water cooled towards freezing (Phys. Rev. Lett. 103, 017801 (2009); paper here). He challenges the common, somewhat arm-waving idea that the decrease in density below 4 C is due to a dominance of LDA-like local configurations. Rather, he says, a proper description of the associated structural changes needs to be broken down in more detail: the anomaly seems to stem from a combination of the change in average hydrogen bond length as a function of temperature (which is monotonic) and the contraction of the HB network due to bond-angle distortion. I’m imagining (it is not made explicit) that this differs from a decline in H-bond-breaking caused by a switch from HDA-like to LDA-like.
Yizhak Marcus at the Hebrew University of Jerusalem uses standard partial molar volumes to calculate the hydration numbers of a range of univalent and divalent ions under ambient conditions (J. Phys. Chem. B 10.1021/jp9027244; paper here). And László Pusztai at the Hungarian Academy of Sciences and colleagues use simulations and neutron/X-ray diffraction to find the hydration numbers of CsCl over a range of concentrations (V. Mile et al., J. Phys. Chem. B 10.1021/jp900092g; paper here). But the numbers don’t agree: Marcus calculates hydration numbers of 1.5-2.5 (depending on the definition) for Cs and 1.4-2.0 for Cl (at 25 C), whereas Pusztai et al. find respective figures of 8-6.5 (for increasing salt concentration) and 5-7. I’m not clear why the numbers are so different. Thanks to Jan Engberts for pointing me to these two papers.
How do specific ions bind to protein surfaces? The answer to this question promises to shed light on the much debated Hofmeister effects on protein aggregation, but there is still no consensus. One common rule of thumb talks of the law of ‘matching water affinities’, whereby cations and anions form ion pairs if they are more or less matched in size. Berk Hess and Nico van der Vegt present simulations which suggest that this simple relationship breaks down for alkali metal cations binding to carboxylate groups on protein surfaces (PNAS 10.1073/pnas.0902904106 – paper here). They argue that the picture is more complicated than such as simple physico-chemical law can express, involving the nature of the hydrated ion complex and the possibility of water-bridged interactions.
The mechanism of fast proton transport in water has been long debated, with the traditional view of Grotthus-like proton hopping along water chains now refined to a picture that tends to invoke intermediates of either the Eigen or Zundel ions (H3O+.3H2O or H5O2+). Rather similar considerations have been applied to the transport on hydroxide ions – are they just a mirror image of proton transport, or do they involve other ionic species such as H3O2-? Andrei Tokmakoff at MIT and his coworkers now present femtosecond pump-probe IR spectroscopic results that they say points to the significant involvement of a Zundel-like transition state in proton transfer in hydroxide solutions, in which a proton is delocalized between a hydroxide ion and a water molecule (S. T. Roberts et al., PNAS 10.1073/pnas.0901571106 – paper here).
Shuxun Cui at Southwest Jiaotong University in Chengdu has published a paper in which he speculates about the prebiotic implications of his recent single-molecule force spectroscopy work (some with Herman Gaub) on the structures of DNA in water and non-aqueous media (see for example JACS 128, 6636 (2006) and JACS 129, 14710 (2007)). He argues that double-stranded DNA can be seen as an adaptation to an aqueous environment (S. Cui, IUBMB Life 61, 860 (2009) – paper here). I have the strong sense that this, rather than Lawrence Henderson’s ‘fitness of the environment’, is the right way round to be examining this question.
Also on this topic, Paul Cremer and colleagues at Texas A&M have used FTIR and thermodynamic measurements to probe the notion that urea denatures via direct hydrogen-bonding to the protein surface (L. B. Sagle et al., JACS 131, 9304 (2009); paper here). They challenge that idea, saying that hydrogen-bonding of urea seems to actually promote hydrophobic collapse of a polyamide (PNIPAM, here used as a protein analogue).
Ahmed Zewail and his colleagues have looked at how solvent motion couples to the unfolding of a model protein (melittin) in the presence of a denaturant (trifluoroethanol) (C. M. Othon et al., PNAS 10.1073/pnas.0905967106; paper here). Using time-resolved fluorescence spectroscopy, they see an abrupt change in solvent dynamics at a critical TFE concentration associated with a change in protein structure, in which the tetramers dissociate into loosely bound monomers owing to penetration of TFE into the hydrophobic core. The dissociation of the monomers happens in a distinct second step.
Sapna Sarupria and Shekhar Garde at RPI have studied the compressibility and fluctuations of hydration shells of hydrophobic solutes and proteins using MD simulations (Phys. Rev. Lett. 103, 037803; 2009 – paper here). They say that the compressibility is non-monotonic as a function of solute size, and that it is greater near hydrophobic solutes, relative to the bulk. The latter implies that hydrophobic interactions get weaker as pressure is increased, which may be important for pressure-induced denaturation. This pressure sensitivity is also dependent on the curvature of the solute, being greater for low-curvature surfaces. That might have a role in the pressure dissociation of multi-subunit proteins.
Incidentally, I am preparing a feature article on denaturation for Chemistry World, and would welcome any papers that might be relevant to this.
Padmanabhan Balaram and colleagues at the Indian Institute of Science in Bangalore report a very nice crystal structure of a model peptide containing a hydrophobic channel containing a linear water wire of nine molecules (U. S. Raghavender et al., JACS 10.1021/ja9038906; paper here). Looks like a good model system for studying such structures.
There is a clutch of papers on hydration dynamics of proteins. A painstaking study of femtosecond dynamics in the hydration network of apomyoglobin by Dongping Zhong and colleagues at Ohio State has revealed two distinct classes of water-network relaxation (L. Zhang et al., JACS 10.1021/ja902918p; paper here). One comes from collective hydrogen-bond rearrangements in the water shell, while the other is considerably slower and results from coupled water-protein motions. They are also able to follow changes in these motions in the transition from the native to the molten-globule state. This looks like the kind of careful study that is needed to really figure out what the intimate coupling of protein and water motions entails.
M. Vogel at the Technical University of Darmstadt has used MD simulations to look at how the dynamics of the hydration shells of peptide analogues of structural proteins (elastic and collagen) change with temperature (J. Phys. Chem. B 113, 9386 (2009); paper here). He finds that there is a change from diffusive motion at higher temperatures to jump-like motion on cooling, corresponding to a weak fragile-to-strong crossover of the water dynamics.
And Giorgio Schirò and colleagues at the University of Rome III use dielectric spectroscopy to study the dynamics of myoglobin confined in porous silica at low hydration levels, with only one or two layers of water around the protein (G. Schirò et al., J. Phys. Chem. B 113, 9606 (2009); paper here). They find that confinement has a big effect relative to hydrated myoglobin powder, suppressing the cooperativity of the water motions and the strong coupling to the protein dynamics. All the same, there still seems to be some slaving of protein relaxation in the porous medium to one mode of solvent relaxation.
Dor Ben-Amotz and colleagues at Purdue have seen the spectroscopic signature of dangling OH bonds in the hydration shells of small dissolved nonpolar molecules, similar to those seen at macroscopic water-oil interfaces (P. N. Perera et al., PNAS 10.1073/pnas.0903675106; paper here). And Pier Luigi Silvestrelli at the University of Padova offers further evidence, from first-principles calculations, that hydrophobic groups (here the methyl of methanol) don’t immobilize water molecules, iceberg-like, in the immediate hydration shell, but rather, merely slow down many surrounding molecules (J. Phys. Chem. B 10.1021/jp9044447; paper here).
It’s occasionally and justifiably said that too little attention has been given to polysaccharide hydration, in contrast to proteins. As a result, we know relatively little about glycoprotein hydration. Claudio Margulis and colleagues at Iowa State attempt to redress that imbalance somewhat with a paper looking at the hydration shells of a diverse range of carbohydrates (S. K. Ramadugu et al., J. Phys. Chem. B 10.1021/jp904981v; paper here). I’m not sure I can easily summarize the results, but there looks to be a lot of valuable information here, for example in terms of how water structure and dynamics are affected by branching, size and type of linkage in the polysaccharides.
The behaviour of water in carbon nanotubes continues to intrigue as a model for hydrophobic protein pores. MD simulations by Biswaroop Mukherjee of the Indian Institute of Science and coworkers suggest that jump reorientation of water molecules inside narrow nanotubes involves a switch of which of the two hydrogens are H-bonded to a neighbour, in contrast to such jumps in the bulk which involve H-bonding to a different neighbour (B. Mukherjee et al., J. Phys. Chem. B 10.1021/jp904099f; paper here).
Francesco Mallamace, Gene Stanley and their collaborators have a paper in Nature Physics that describes the appearance of a fractional Stokes-Einstein relation (which provides information about viscosity, connecting the self-diffusion coefficient to temperature and relaxation time) below 290 K in water confined within silica nanopores (2 nm diameter) (Nature Physics 10.1038/nphys1328; paper here). They suggest that this switch marks a crossover to a water structure that is locally more similar to LDA ice – a point at which the proportions of HDA-like and LDA-like configurations starts to change rapidly. It’s an intriguing idea, and there is apparently some indication (I can say no more yet) that the dynamical crossover might be a more general phenomenon for liquids. Some, though, will reasonably wonder whether water within 2-nm silica pores can really be considered representative of the bulk.
Perhaps relevant in this respect, Patrick Huber at Saarland University in Germany and colleagues have studied the dynamics of capillary rise in silica pores 3-5-5 nm across (S. Gruener et al., Phys. Rev. E 79, 067301 (2009); paper here). They find that they can account for the timescales of pore filling according to macroscopic hydrodynamics, so long as they assume the presence of a ‘sticky preadsorbed boundary layer of about two monolayers of water molecules’. In other words, there is dynamical partitioning of the water ‘filling’ into two components.
Masakazu Matsumoto at Nagoya University offers a new picture of the density maximum of water cooled towards freezing (Phys. Rev. Lett. 103, 017801 (2009); paper here). He challenges the common, somewhat arm-waving idea that the decrease in density below 4 C is due to a dominance of LDA-like local configurations. Rather, he says, a proper description of the associated structural changes needs to be broken down in more detail: the anomaly seems to stem from a combination of the change in average hydrogen bond length as a function of temperature (which is monotonic) and the contraction of the HB network due to bond-angle distortion. I’m imagining (it is not made explicit) that this differs from a decline in H-bond-breaking caused by a switch from HDA-like to LDA-like.
Yizhak Marcus at the Hebrew University of Jerusalem uses standard partial molar volumes to calculate the hydration numbers of a range of univalent and divalent ions under ambient conditions (J. Phys. Chem. B 10.1021/jp9027244; paper here). And László Pusztai at the Hungarian Academy of Sciences and colleagues use simulations and neutron/X-ray diffraction to find the hydration numbers of CsCl over a range of concentrations (V. Mile et al., J. Phys. Chem. B 10.1021/jp900092g; paper here). But the numbers don’t agree: Marcus calculates hydration numbers of 1.5-2.5 (depending on the definition) for Cs and 1.4-2.0 for Cl (at 25 C), whereas Pusztai et al. find respective figures of 8-6.5 (for increasing salt concentration) and 5-7. I’m not clear why the numbers are so different. Thanks to Jan Engberts for pointing me to these two papers.
How do specific ions bind to protein surfaces? The answer to this question promises to shed light on the much debated Hofmeister effects on protein aggregation, but there is still no consensus. One common rule of thumb talks of the law of ‘matching water affinities’, whereby cations and anions form ion pairs if they are more or less matched in size. Berk Hess and Nico van der Vegt present simulations which suggest that this simple relationship breaks down for alkali metal cations binding to carboxylate groups on protein surfaces (PNAS 10.1073/pnas.0902904106 – paper here). They argue that the picture is more complicated than such as simple physico-chemical law can express, involving the nature of the hydrated ion complex and the possibility of water-bridged interactions.
The mechanism of fast proton transport in water has been long debated, with the traditional view of Grotthus-like proton hopping along water chains now refined to a picture that tends to invoke intermediates of either the Eigen or Zundel ions (H3O+.3H2O or H5O2+). Rather similar considerations have been applied to the transport on hydroxide ions – are they just a mirror image of proton transport, or do they involve other ionic species such as H3O2-? Andrei Tokmakoff at MIT and his coworkers now present femtosecond pump-probe IR spectroscopic results that they say points to the significant involvement of a Zundel-like transition state in proton transfer in hydroxide solutions, in which a proton is delocalized between a hydroxide ion and a water molecule (S. T. Roberts et al., PNAS 10.1073/pnas.0901571106 – paper here).
Shuxun Cui at Southwest Jiaotong University in Chengdu has published a paper in which he speculates about the prebiotic implications of his recent single-molecule force spectroscopy work (some with Herman Gaub) on the structures of DNA in water and non-aqueous media (see for example JACS 128, 6636 (2006) and JACS 129, 14710 (2007)). He argues that double-stranded DNA can be seen as an adaptation to an aqueous environment (S. Cui, IUBMB Life 61, 860 (2009) – paper here). I have the strong sense that this, rather than Lawrence Henderson’s ‘fitness of the environment’, is the right way round to be examining this question.
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