Water in Biology

More dynamical transitions?

2012-01-19T01:45:00.000-08:00

Francesco Mallamace at MIT/Messina and colleagues have used proton NMR to follow the rearrangements of water during the thermal (heat and cold) denaturation of lysozyme (F. Mallamace et al., J. Phys. Chem. B 115, 14280; 2011 – paper here). Since the chemical shift is considered to probe hydrogen-bonding interactions in the water network, tracking it as the temperature changes take the protein from the folded to the denatured states reveal some aspects of how changes in protein structure are mirrored by those of the hydration water. The researchers conclude that water plays an active role in the process, and that as denaturation proceeds, the average number of H-bonds with which each water molecule is involved changes correspondingly.

How glycerol acts as a cryoprotectant is the subject of a study by J. Towey and L. Dougan at Leeds (J. Phys. Chem. B jp2093862 - paper here). They use neutron scattering to investigate whether, as one hypothesis has it, dissolved glycerol perturbs water structure to modify the hydrogen bonding ability and suppress ice formation. The solution turns out to be well mixed, with many glycerol monomers, but there is no discernible perturbation of the first coordination shell of water. The second shell, however, is perturbed in a manner similar to that caused by elevated pressure. Quite what this means for “the ability of water molecules to form ice” isn’t clear (indeed, I’m not even too sure what that expression means – displacement of the phase boundary?), but Towey and Dougan conclude that any explanation will need to focus not simply on local perturbations (or changes to water’s ability to form hydrogen bonds) but on changes to the extended hydrogen-bonded network.

More on the mechanisms of osmolytes: Dave Thirumalai and colleagues at Maryland have studied the stabilization of compact peptide conformations by trimethylamine N-oxide (TMAO) (S. S. Cho et al., J. Phys. Chem. B 115, 13401; 2011 – paper here). They attribute it to direct interactions between TMAO and the protein surface, which exclude solvent there. This is then a kind of excluded-volume effect analogous to the stabilization of proteins by molecular crowding (in which there is entropic destabilization of the unfolded state) – making TMAO a ‘nanocrowding’ particle.

In a related vein, M. Paulaitis at Ohio State and colleagues describe an integral-equation approach to deduce preferential interactions between cosolvents, which they say can be used to deduce preferential interactions of cosolvents such as osmolytes, naturants and cryoprotectants locally on the surface of proteins (M. H. Priya et al., J. Chem. Phys. B 115, 13633; 2011 – paper here).

Personally, I find it hard to think about hydration in crowded environments, in which marcomolecules might disturb one another’s hydration shells and sometimes temporarily associate with one another in non-specific ways. Sergio Hassan and Peter Steinbach at NIH have tried to provide a context from framing this question (J. Phys. Chem. B 115, 14668; 2011 – paper here). One issue is how incomplete and anisotropic hydration might create electrostatic effects. Another is how solvation forces due to structured hydration shells (layering, for example) manifest themselves on hydrogen-bonding at solute-water interfaces. Using a continuum solvent model, they say that the electrostatic effects of solvent exclusion can have a strong impact on protein-protein binding. But I think it fair to say that at this point the paper is largely presenting the methodology for investigating the problem, rather than reaching general conclusions about how these aspects of crowding affect the molecular biology.

Confinement will, of course, do other things to water itself. Ivan Brovchenko and Alla Oleinikova have predicted that water in slit-like pores just 2.4 nm wide might undergo the liquid-liquid transition predicted in the metastable bulk at low temperature and high pressure (J. Chem. Phys. 126, 214701; 2007). Limei Xu and Valeria Molinero at Utah have now examined that idea in simulations using their mW model of water held within 1.5-nm diameter cylindrical pores (J. Phys. Chem. B 115, 14210; 2011 – paper here). This system is comparable to the pores of MCM-41 nanoporous silica, as used in recent experiments on confined water (e.g. L. Liu et al., Phys. Rev. Lett. 95, 117802 (2005)). They find no evidence for a first-order liquid-liquid transition, but note that smearing of discontinuous transitions is well known in pores (although not in fact inevitable), and therefore that this doesn’t rule out the existence of such a transition in the bulk. For their simulations of the bulk phase, they do see a possible signature of a L-L critical point – a locus of maximum compressibility – but can’t study this in detail because fast crystallization makes it impossible to equilibrate a metastable water phase in this region.

How do proteins remain dynamic while remaining soluble and resistant to aggregation? Fabrizio Chiti at the University of Florence, Chris Dobson at Cambridge, and their colleagues, have sought to answer this by combining NMR relaxation data, H/D exchange experiments and MD simulations (A. De Simone et al., PNAS 108, 21057; 2011 – paper here). They use the fruitfly acylphosphatase as their model system, and find that the wild-type protein has free-energy barriers that limit access to aggregation-prone conformations except under aggrtegation-prone conditions (addition of small amounts of trifluoroethanol). They sum up the situation nicely: “The sensitivity of the energy surfaces of proteins to minor perturbations supports the view that there is a delicate balance between functionality, stability, and solubility, which is encapsulated by the concept of ‘life on the edge’”.

Hydrogen bonds hydrating hydrophobic regions of a protein or peptide seem to have a greater strength than those in bulk water. It’s been suggested that this might be not so much because the H-bonds are genuinely strengthened but because the orientational preferences of H-bonds in such a situation result in a depletion of weaker, strained H-bonds, i.e. a change in the population (Zichi & Rossky, J. Chem. Phys. 83, 797 (1985)). Peter Rossky and colleagues have now explored this idea further using MD simulations of a 16-residue peptide (J. Phys. Chem. B 115, 14859; 2011 – paper here). They find support for the idea, namely, water is depleted of near neighbours around apolar groups and so samples lower-coordination configurations that are undistorted and unstrained. In other words, the phenomenon is primarly a kind of packing effect.

A new angle on Hofmeister effects is offered by Huib Bakker at FOM Institute for Atomic and Molecular Physics in Amsterdam, who have looked at the orientational dynamics of water around various ions (K. J. Tielrooij et al., J. Chem. Phys. B 115, 12638; 2011 – paper here). When the salt consists of a strongly hydrated ion and a weakly hydrated counterion, the water molecules hydrating the former have impeded orientational dynamics, making it strongly anisotropic. In that case, they say that hydration is ‘semi-rigid’ in the first hydration shell: affected along one vector but not along others. If both ions are strongly hydrated, such perturbations of water dynamics extend well beyond the first hydration shell.

And while we’re there: Daryl Eggers and colleagues at San José State University have taken a thermodynamic line of attack on Hofmeister by determining the molar water volumes in various concentrated electrolyte solutions (A. Y. Payumo et al., J. Phys. Chem. B 115, 14784; 2011 – paper here). They find that the solutions are highly nonideal, presumably because of strong competition under these conditions for hydration water. Moreover, the solubility of the small amide diketopiperazine follows the Hofmeister series for all the anions and cations studied, and the authors explain this on the basis that Hofmeister effects are governed by changes in the average free energy of the bulk aqueous phase – that is, if Hofmeister effects are a bulk phenomenon of water.

The tale of the low-temperature dynamical crossover for hydrated proteins and their hydration shells continues to get more complicated. Using dielectric spectroscopy and MC simulations, Gene Stanley, Giancarlo Franzese and their colleagues now report evidence of two such crossovers for the hydration water of lysozyme: one at about 252 K, the other around 181 K (M. G. Mazza et al., PNAS 108, 19873; 2011 – paper here). Marie-Claire Bellissent-Funel and her colleagues have previously seen something similar – two transitions at 220 and 150 K (J.-M. Zanotti et al., PCCP 10, 4865; 2008). Stanley et al. now ascribe the first of these to maximal fluctuations in the making and breaking of hydrogen bonds, and the second to maximal fluctuations in cooperative reordering of the H-bonded network.

Meanwhile, Sol Gruner and colleagues at Cornell report evidence for another protein dynamical transition right down at 110 K, which they say correlates with the transition of the hydration water from a high- to a low-density amorphous state (C. U. Kim et al., PNAS 108, 20897; 2011 – paper here).

Wilfred van Gunsterden at ETH and colleagues show how solvation free energies, as well as the free energies of protein-ligand binding and protein conformational dynamics, can be calculated using a new software package called GROMOS, which van Gunsterden and colleagues have introduced in a paper in press with Comput. Phys. Commun. (S. Riniker et al., J. Phys. Chem. B 115, 13570; 2011 – paper here).

Alan Soper has an intriguing paper in J. Phys. Chem. B (115, 14014; 2011 – paper here) in which he presents a new mixture model of water. This isn’t exactly a two-state model – the two forms are intimately mixed – but it postulates two populations of water molecules, each of which can form hydrogen bonds only with molecules of the other type and not with those of their own type. This is not, as far as I can see, intended as a literal representation of some molecular-scale distinction – both types of water molecule have identical structure – but is imposed as a device for introducing a three-body term into the interactions. The results show good agreement with structural studies using neutron and X-ray scattering, and give rise to a situation where water molecules are H-bonded to some of their neighbours but not others. This, Alan suggests, is perhaps why mixture models of water have been so enduring: not because there really are two distinct populations but because – if I’m understanding this correctly – the three-body terms have the effect of making it appear that way.

Michele Parrinello and colleagues at ETH have investigated the recombination of hydronium and hydroxide ions in water using ab initio MD simulations (A. Hassanali et al., PNAS 108, 20410; 2011 – paper here). They find that the mechanism is rather different from what has traditionally been assumed in terms of a Grotthuss mechanism. The researchers say that the Grotthuss mechanism serves to bring the hydronium and hydroxide to a distance of around 6 Å, when they are bridged by two water molecules as a ‘water wire’. But then there is a collective compression of this water wire that results in a concerted motion of three protons (rather than a series of distinct one-proton hops), converting both ions into water molecules.

Welcome to 2012

2012-01-10T02:15:00.000-08:00

Lots to catch up on here, and while I’m not going to do that exhaustively now, here is an update to let you know that this blog will still be active in 2012.

I’ve recently written a News & Views article for Nature (478, 467; 2011 – here) about, among other things, the recent paper by George Whitesides’ group (PNAS 108, 17889; 2011 – paper here) on the hydrophobic effect in ligand binding – which, as discussed in the previous post, suggests that there is not any single ‘hydrophobic effect’ operating here, but a delicate and case-specific balance of enthalpic and entropic effects. They noted that in the example they studied, the ‘hydrophobic’ aspect of binding was driven largely by the enthalpic effect of displacing/rearranging water around nonpolar contacts. That notion is supported by a paper by Stephen Martin and colleages at the University of Texas at Austin, who find something rather similar for small peptide binding by the SH2 domain of the growth receptor binding protein Grb2 (J. M. Myslinski et al., JACS 133, 18518; 2011 – paper here). They say that increases in the nonpolar contact area don’t necessarily lead to entropic gains due to release of water, but have a primarily enthalpic influence on binding affinity.

How quickly drugs bind to their target molecules can have important pharmacological implications, but these kinetics are generally poorly understood, and thus to design rationally. Xavier Barril from the University of Barcelona and colleagues show using MD simulations that slow kinetics are often a consequence of the presence of buried polar atoms which form hydrogen bonds that are shielded from water, because of the slowness of dehydration/rehydration (P. Schmidtke et al., JACS ja207494u – paper here). In other words, the pace of events in binding can be set by the degree of water accessibility. They show that this effect can be predicted from structural data, and can thus potentially be accessible to design.

Knowing the hydration structure of proteins is important for small-/wide-angle X-ray scattering (SWAXS) studies of proteins not so much for its own sake but because the contribution of the solvent to the scattering must be subtracted in order to extract information about the protein secondary structure. It’s easy enough to extract the contribution of bulk water, but correcting for the scattering of the hydration shell is complicated. Tobin Sosnick and coworkers at the University of Chicago now show two ways to do this (J. J. Virtanen et al., Biophys. J. 101, 2061-2069; 2011 – paper here). One is to deduce the solvation structure by full MD simulations, which they say gives results that match the SWAXS data closely. But they have also developed a much more computationally less intense solvation model called HyPred, which gives a scattering profile that agrees well both with MD and with experiment.

Bernhardt Trout and his coworkers at MIT present an illustration of just how complex the interactons of proteins and ions can be (D. Shukla et al., JACS ja205215t – paper here). Complex ions such as guanidinium create a particularly intricate picture. Gdm+ can destabilize proteins via the formation of hydrogen bonds and electrostatic interactions, but when paired with an anion that is a hydrogen-bonding acceptor it can form clusters with the ions, which suppresses the effect. Molecules (such as arginine) with multiple Gdm+ groups are sometimes used to suppress protein aggregation, and can do so without compromising protein stability. Trout and colleagues investigate the effect of arginine oligomers (n=1-4) on protein aggregation and conformational stability for two different anions, chloride and sulphate. While monomeric arginine chloride is used as an aggregation suppressor, the n-mers only inhibit aggregation at low concentration – they actually accelerate it at moderate to high concentration. Meanwhile, the sulphates inhibit aggregation at all concentrations. And while the chlorides reduce protein stability, the sulphates enhance it. The researchers explain all this in terms of the balance between ion-ion and ion-protein interactions.

All this mirrors an increasing tendency to consider Hofmeister effects of ions on proteins in terms of direct interactions between the two species, rather than as indirect consequences of changes in hydration. Elena Algaer and Nico van der Vegt at the TU Darmstadt provide some support for this notion with a study of the salting-in and –out of small model amides by various sodium salts (J. Phys. Chem. B jp208583w – paper here). They say, for example, that the salting-in if NiPAM by NaI is mediated by interactions of iodide with the nonpolar groups. Such interactions also explain why, of all the salts studied, the iodide alone fails to induce hydrophobic collapse of polyNiPAM.

How does water permeate cell membranes? Its passage through the water-regulating membrane protein aquaporin is fairly well studied, but little is known about other water transporters. The bacterial sodium-galactose transporter vSGLT and its human homologue the sodium-glucose cotransporter hSGLT1 both have the potential to let water through. Jean-Yves Lapointe at the Université de Montréal and colleagues have used MC and MD simulations to show that indeed these protein pores can be filled with water (a pathway of about 100 molecules) which allows passive water permeation (L. J. Sasseville et al., Biophys. J. 101, 1887-1895; 2011 – paper here). This pathway depends on the proteins’ conformation: there is a constriction at one point which reduces the water bridge to a single-molecule chain which then ‘snaps’ at a ‘hydrophobic plug’, creating a 4.3 Å gap of low water density. But the resulting barrier to water permeation is conformation-dependent, and can be altered by varying the membrane potential. The passage of a sugar molecule also can bring water with it, but the mechanism of this is still open to debate.

Jhih-Wei Chu and colleagues at Berkeley conclude from MD simulations that the insolubility of cellulose in water is an entropic effect due primarily to the reduction of solvent entropy if the glucan chains in a fibril unravel (A. S. Gross et al., J. Phys. Chem. B 115, 13433; 2011 – paper here). There are some lessons here for how to solubilize cellulose in other solvents, such as ionic liquids.

Why and how do ions segregate at the air-water interface? This phenomenon seems well attested, with anions, especially large and polarisable ones, tending to accumulate at the interface. But the reason for this is still debated. Yi Qin Gao if the Beijing National Laboratory for Molecular Sciences and coworkers investigate the question with MD simulations, looking in particular at the differences in how anions and cations are solvated (L. Yang et al., J. Phys. Chem. B jp207652h – paper here). They argue that these differences are due to the charge distribution in the water molecules themselves, and that water can approach anions more closely than cations. They suggest that these differences in hydration account for why anions tend to populate the interface more readily.

And on the same topic, Pavel Jungwirth and colleagues have looked at how the hydration of guanidinium ions affects their orientation at the air-water interface (E. Wernersson et al., J. Phys. Chem. B jp207499s – paper here). Guanidinium is depleted at the interface, but the ions that do stay there are preferentially oriented parallel to the surface: in this configuration, it can sit at the surface without needing to break hydrogen bonds. Another way of looking at this is that the ions can take advantage of the deficit of hydrogen bonds between waters at the surface. The authors suggest that similar reasoning might account for the unexpected orientation of some arginine groups (with an analogous structure) in protein side chains.

Lum-Chandler-Weeks under the microscope

2011-10-13T10:41:00.000-07:00

Shekhar Garde and his colleagues have shown in several recent publications how hydration of solutes and its consequences, such as conformational changes in polymers, can be significantly altered near the air-water interface. The more general effect of interfaces on hydrophobic phenomena is now probed by Garde along with David Chandler, Amish Patel and others (A. Patel et al., PNAS doi 10.1073/pnas.1110703108 – paper here). They look at how interactions between hydrophobic solutes of various sizes from sub-nm to several nm are altered close to the interface of water with self-assembled monolayers of various surface chemistries, from hydrophobic to hydrophilic. They find that the driving force for the assembly of hydrophobic particles is smaller near a hydrophobic surface than it is in bulk, and decreases with increasing temperature, in contrast to the bulk (and to hydrophilic surfaces). This implies that hydrophobic surfaces should act as catalysts for the unfolding of proteins. It might also account for how chaperonins work: their initially hydrophobic surfaces help misfolded proteins to unfold, and then ATP-driven conversion of the walls to hydrophilic release the unfolded protein from the wall so that it might fold again in bulk.

Misfolding in the context of Lum-Chandler-Weeks theory is also the subject of a paper by Ruhong Zhou and colleagues (Z. Yang et al., J. Phys. Chem. B 115, 11137 (2011) – paper here). They have looked at whether dewetting transtions play a role in the assembly of two amyloidogenic beta-sheets. For the peptides considered there are two conformations that lead to stacking of beta-sheet pairs: one containing water between the sheets in a 2D slab-like geometry, the other with the water in a 1D tube-like geometry. In both cases the sheets are brought together by a drying transition, but surprisingly this is stronger for the slab-like than the tube-like case. This is attributed here to the different surface roughness of the two packing modes: the ‘staggered’ packing in the slab-like case, which is rougher, disrupts the H-bonding network of the intervening water to a greater extent.

Some further new insights into the Lum-Chandler-Weeks dewetting mechanism for hydrophobic interactions are offered by two recent papers. Li and Walker appear to see the cross-over region between the mechanisms of hydrophobic hydration at small (<1 nm) and large (>1 nm) scales that this theory predicts, by measuring the free energy of hydration of individual monomers of various size in hydrophobic polymers, using an AFM to pull the chains out from a collapsed conformation (Li, I. T. S. & Walker, G. C. PNAS 108, 16527-16532; 2011 – paper here). At a monomer size of around 1 nm in the temperature region of 50 C or so, they find a switch in the hydration entropy from negative to positive (this crossover size reduces to just 3.5 Å at 150 C). Shekhar Garde and Amish Patel have published a commentary on it (10.1073/pnas.1113256108).

And Garde and Patel have joined forces with David Chandler and others in a preprint (arxiv.org/1109.4431 – paper here) that attempts to unravel the issue of why some protein subunits (such as melittin) seem to aggregate via dewetting while others (such as BphC) do not. They find that at model (SAM) hydrophobic surfaces, simulations show that the statistics of large-amplitude fluctuations in the density of interfacial water are altered relative to the Gaussian stats of both bulk water and water at a hydrophilic surface. In other words, despite similar average interfacial water densities, the fluctuations reveal the proximity of the hydrophobic interface to a dewetting transition. This tuning of the interfacial water is, they argue, common to biological systems, where it induces a strong sensitivity to small changes in conformation, allowing the system to take advantage of the phase transition in engineering biomolecular function (in a manner analogous to the finely balanced wetting or drying of ion channels for ‘vapour-lock’ gating). Although melittin and BphC lie on opposite sides of this transition, small modifications to both can tip the balance one way or the other. This offers what seems to me to be a persuasive argument that dewetting is relevant to hydrophobic aggregation even if it does not exactly provide the mechanism for it in all (or even in most) cases: the transition is, if you like, ‘there’ even if it doesn’t manifest itself.

Alenka Luzar and her colleagues have considered this issue from the perspective of whether or not cavitation can take place at the protein-protein interface (J. Wang et al., PCCP 10.1039/c1cp22082a – paper here). They present a lattice model which offers a fast method for predicting if cavitation can happen, and find that part of the surface of melittin is sufficiently hydrophobic to permit this on a timescale that is consistent with that seen in the earlier simulations.

Alenka and her colleagues have also examined how this putative crossover length-scale for hydration behaviour is influenced by charge on the solute (J. Stat. Phys. 10.1007/s10955-011-0337-1 – paper here). They conclude that, for moderate charge, the electrostatic contribution to the solvation free energy is in fact essentially independent of solute curvature, because of a compensation between counterion shielding and the dielectric screening of water – the solvation free energy remains more or less a function only of solute surface area.

To what extent protein-ligand binding requires an atomistic description of changes in hydration is a crucial question, not least for attempts to design synthetic ligands in drug development. Ulf Ryde at Lund University and colleagues have looked at this issue by comparing the ability of continuum methods to predict binding free energies for four different protein-ligand pairs with quite different degrees of solvent exposure at the binding site (S. Genheden et al., JACS ja202972m – paper here). They find that the continuum methods often perform badly, particularly for cases with a greater degree of solvent exposure. We need to know precisely where the waters are and where they go.

And that is somewhat elucidated by Nan-jie Deng at Rutgers University and colleagues for the case of two synthetic inhibitors of HIV-1 protease, Nelfinavir and Amprenavir (N.-j. Deng et al., J. Phys. Chem. B jp204047b – paper here). The binding of these drugs is apparently entropically driven, but the question is where that entropic contribution comes from. A classical view would be inclined to attribute it to the release of water from the binding cleft, but it seems that this isn’t so: these MD simulations suggest that any entropy gain there is more than offset by the restriction of ligand rotation and vibration on binding. Instead, the favourable entropic contribution seems to come from desolvation of the ligand.

A different view of water’s influence on bimolecular recognition is provided by Stacey Wetmore and colleagues at the University of Lethbridge in Alberta (F. M. V. Leavens et al., J. Phys. Chem. B jp205424z – paper here). They have looked at how water molecules can affect the pi-pi interactions between DNA and DNA-binding proteins. Solvating water molecules seem to have essentially no influence on the strength of pi-pi stacking for histidine and adenine, but do weaken the interaction if the histidine is protonated. The latter interaction, however, remains in all cases stronger than the former.

Protons seem to be delivered to membrane proteins such as the proton pump cytochrome c oxidase via some kind of surface-enhanced, two-dimensional transport at the membrane surface. This has been previously postulated as a series of jumps between ionisable groups (phosphate and carbonyl) at the membrane surface. But that notion is challenged by Peter Pohl at the Johannes Kepler University in Linz and colleagues, whose fluorescence measurements of proton transfer at membranes show that proton transport can be equally fast in the absence of ionisable groups (A. Springer et al., PNAS 108, 14461-14466; 2011 – paper here). They conclude that it is probably the network of interfacial water molecules that is responsible instead for the rapid proton motion: as they say, “water structuring at the interface seems to be mandatory for providing the pathway”.

It has of course been long thought that protons may be delivered to the interior of an enzyme via chains of water molecules. That process is studied by heme peroxidase by Emma Lloyd Raven and coworkers at the University of Leicester (I. Efimov et al., JACS ja2007017 – paper here). Kinetic isotope effects reveal that the proton pathway utilizes a Grotthus-like shuttling of protons along a pathway towards the ferryl oxygen that involves three bound waters and two arginine residues.

A model system for studying such proton transfer in confined geometry is reported by Bradley Habenicht and Stephen Paddison at the University of Tennessee in Knoxville (J. Phys. Chem. B jp205787f – paper here). They use MD simulations to look at how protons are transported within carbon nanotubes whose inner walls are functionalized with perfluoro sulphonic acid groups. If these groups are spaced far apart (~8 Å), they tend to be individually hydrated by clusters of water molecules with little interaction between them, and correspondingly reduced acidic proton dissociation. But there is also a pronounced effect of confinement at small nanotube diameters: in the smaller tubes there are stronger interactions between the walls and the water molecules, which can lead to break-up of the hydrogen-bonded network of waters linking the sulphonic acid groups. That network may be restored by polarized charges of fluorine atoms attached to the nanotube walls.

ATP hydrolysis in the active cleft of actin plays an important role in the state of its filamentous form F-actin, affecting its rigidity and its binding of regulatory proteins. There is water in this active site, but it hasn’t previously been clear what, if anything, it does. Marissa Saunders and Greg Voth at Chicago have clarified this through MS simulations based on the crystal structure (J. Mol. Biol. 413, 279-291; 2011 – paper here). They say that the ordered waters help the protein to flatten and brings about a conformational change that promotes ATP hydrolysis. These changes also stabilize the charge on the phosphate and accelerate the deprotonation of the catalytic water involved in hydrolysis. In short, the bound water helps to organize the active-site geometry.

Another nail in the coffin of ‘structure-making and –breaking’: Fabio Bruni and colleagues in Rome have looked at how local solvent structure around ions affects their influence on viscosity – specifically, on how changes in ionic concentration affect the viscosity of the solution (T. Corridoni et al., J. Phys. Chem. B jp202755u – paper here). Classically, the viscosity is found to be (almost) linearly related to the concentration. It has been asserted that the magnitude of the coefficient of proportionality, denoted B, depends on how the ions perturb the water structure. Fabio et al. use neutron scattering and simulations to look for some structural parameter that can be correlated with B. They find that the nature of the (univalent) ions is all but irrelevant to the size of the percolating water clusters in solution. The change in viscosity seems to be unrelated to any structural changes in the bulk liquid, but instead pertain to changes in the local hydration shells of the ions. As a result, they say, “the particular effect of solutes ranked in the Hofmeister series must be looked at in terms of specific ion interactions with hydrophilic or hydrophobic surfaces”, and not in terms of any generalized propensity for structure-making or –breaking.

In an intriguing preprint, Jampa Maruthi Pradeep Kanth and Ramesh Anishetty at the Institute of Mathematical Sciences in Chennai propose that the hydrophobic interaction should be understood as an effect analogous to the Casimir effect (the attraction of two surfaces separated by a vacuum due to the suppression of long-wavelength electromagnetic fluctuations of the vacuum in the gap) (preprint here). Their molecular mean-field analytical method suggests that confinement alters the allowed fluctuations of the hydrogen-bond network, specifically the long-ranged correlations between water molecular orientations. Now what I’d like to know is whether an explicit connection can be made to the alleged role of fluctuations in the Lum-Chandler-Weeks model. But that seems to argue in the opposite direction, namely that fluctuations are actually enhanced in the gap owing to the destabilizing influence of the hydrophobic surfaces on the intervening water layer. It’s not clear to me whether in Kanth and Anishetty the water in the gap is, aside from the suppression of fluctuations, any different from bulk water, except perhaps for the monolayer adjacent to the surfaces…? And why would this not work for hydrophilic confinement too?

Alenka Luzar and her colleagues Christopher Daub and Dusan Bratko have just published a review of how electric fields at interfaces can modify their wettability (Top. Curr. Chem. 10.1007/128_2011_188; 2011 – paper here). Effects of this nature may play a role in the behaviour of voltage-sensitive ion channels.

Still more on denaturants. Thomas Record and colleagues at Wisconsin ask why urea is a denaturant while glycine betaine is a protein stabilizer (E. J. Guinn et al., PNAS 108, 16932-16937; 2011 – paper here). They use osmomentry and solubility measurements to look at the interactions of these molecules with 45 model proteins, and conclude that the explanation for the different behaviours lies with the details of how and where the molecules interact with the peptide surfaces. For example, urea accumulates at amide O groups, and to a lesser extent at aliphatic carbon atoms, whereas glycine betaine is excluded from them. This adds further weight to the notion that such osmolytes exert their effects via direct interactions with proteins rather than any generalized influence on ‘water structure’.

Phosphate groups turn out to be a sensitive probe of electric fields, including those that can be induced by hydration. As Steven Boxer and colleagues at Stanford show (N. M. Levinson et al., JACS 133, 13236; 2011 – paper here), electric fields perturb the vibrational spectra of organophosphates in a way that can reveal changes in hydration within partially hydrated environments, such as the active sites of enzymes.

Is there a liquid-liquid transition in confined water? That question is investigated via MD simulations by Limei Xu and Valeria Molinero at Utah (J. Phys. Chem. B jp205045k – paper here). The possibility has been raised by simulations of water in slit-like pores 2.4 nm wide (Brovchenko & Oleinikova, J. Chem. Phys. 126, 214701; 2007). Valeria and Limei use the mW water model to look at water’s behaviour in 1.5-nm hydrophilic pores at a range of temperatures and pressures up to 4000 atm. They find that at high pressures there is a signature of a somewhat abrupt but nonetheless continuous phase transition in the supercooled regime which could be interpreted as a ‘shadow’ of a L-L transition in the bulk phase which cannot itself be accessed.

A new and unusual view of the protein dynamical transition at c.200-220 K is presented in a preprint by Andrei Krokhotin and Antti Niemi at Uppsala University (paper here). They say that it this transition can be regarded as an analogue of the transition of a high-temperature superconductor to a non-superconducting pseudo-gap state. In other words, proteins can be assigned an order parameter formally equivalent to the quasiparticle wave function of superconductors. It’s not clear to me how/if this description modifies what is known already about the transition (on which, and on the role that hydration plays, there seems still to be no real consensus), but it is an original idea.

How hydration forces assemble protein aggregates

2011-08-17T05:55:00.000-07:00

Dielectric spectroscopy has been widely used to study the dynamics of proteins and their hydration shells, but is somewhat hampered by ambiguities about the origin of the atomistic motions that contribute to the signals. Sheila Khodadadi at NIST and colleagues have now shown just how fraught a business this is. The dielectric response of hydrated proteins typically contains two components – a fast (20-50 ps) relaxation, thought to be due to hydration water (which is slowed down relative to the bulk), and a slow (0.5-10 ns) relaxation ascribed to ‘tightly bound water’. Khodadadi and colleagues have previously questioned the former assignment (J. Phys. Chem. B 112, 14273; 2008), and now they question the latter too (J. Phys. Chem. B 115, 6222; 2011 – paper here). They say that comparisons of MD simulations to dielectric spectroscopic data suggest that the nanosecond relaxation is in fact due to motions of the protein atoms themselves, while the hydration water relaxes much more quickly.

Cytochrome c oxidase (CcO) is one of the classic examples of an enzyme that uses embedded water wires for proton transport. But how does it avoid back transport of protons along the same route? One proposal is that the water wire becomes reoriented to prevent this. Another is that a side-chain element of the hydrogen-bonded network, Glu-286, rotates to break the chain. Shuo Yang and Qiang Cui of the University of Wisconsin now show that neither process seems to be a viable gating mechanism (Biophys. J. 101, 61; 2011 – paper here). They suspect that the vectorial proton transport is probably achieved instead in a more subtle way, by stabilization of the proton-transfer transition state by the charge distribution around the active site, to explore which will require sophisticated quantum-chemical modelling.

Bacteriorhodopsin is of course another archetype for the functional water wire. It has been claimed by Klaus Gerwert at Bochum and others that the proton pumped through the protein by light absorption is stored in a water cluster inside the channel. This idea is challenged in another paper by Cui and coworkers, soon to appear in JACS (P. Goyal et al., JACS ja201568s – paper here). They say that for the proton to be stored on water requires an implausibly high increase in the pKa of a hydronium, and argue that the stored proton is instead shared between Glu194 and Glu204. One can be sure this is not going to be the last word on the matter…

I missed an interesting paper last year by Ariel Fernández and colleagues on how proteins can ‘seal’ backbone hydrogen bonds (BHBs) at their surface against competition from hydration water by a close control of the local curvature: if the BHBs are in a sufficiently highly curved location, water cannot penetrate without compromising its own H-bonded network for purely geometric reasons (E. Schultz et al., PLoS ONE 5, e12844; 2010 – paper here). Misfolded proteins fail adequately to protect their BHBs this way. This work is rather closely related to the recent paper by Fernández and Michael Lynch at Indiana on how BHBs that are ‘poorly wrapped’ by hydrophobic groups can become sites of protein-protein aggregation, which lead to complexification of the ‘interactome’ due to the degradation of wrapping created by genetic random drift (Nature 474, 502; 2011 - paper here). I have discussed that work in the August issue of Chemistry World (here – requires a subscription).

Somewhat relevant to this work is a study of protein ‘hot spots’ where preferential binding of organic small-molecule probes bind, by Frank Guarnieri of Virginia Commonwealth University in Richmond and colleagues (J. L. Kulp III et al., JACS 133, 10740; 2011 – paper here). They use simulated annealing to look at the interactions of eight probe molecules, and water, with hen egg lysozyme, and find that all the probes bind in the known binding site, which is evidently the ‘hot spot’. This implies that ligand binding isn’t simply a case of molecular recognition – the ligand is already guided towards that site by the fact that other potential binding spots are ‘guarded’ by tightly bound water. The researchers say that these hot spots can therefore also act as sites for potential protein-protein binding.

Coming back to the previous paper, Ariel also believes that poor wrapping of BHBs is implicated in the aggregation of proteins in amyloid diseases – and that these are thus potentially an alarming result of evolution’s failure to deal with random drift in anything more than an ad hoc manner. The question of how hydration is related to amyloid aggregation is also considered in a preprint by Dave Thirumalai and colleagues (arxiv 1107.4820 – paper here). They argue that “water controls the self-assembly of higher-order structures”, just as the expulsion of water is a key stage in the interaction between peptides forming beta-sheet protofilaments. Specifically, water accelerates the formation of fibrils from mainly hydrophobic peptides, but slows down the aggregation of hydrophobic sequences by stabilizing them. In the higher-order hydrophobic structures, trapped water can be considered to be analogous to water confined within carbon nanotubes – in which it seems that there is a sensitive dependence of the water structure on the width of the confining region. Thus the work nicely connects studies of confined water to an important biological problem.

A different picture – I’ve not quite figured out if it competes with or complements the above picture – of self-assembly of protein fibrils is presented by Krishnakumar Ravikumar and Wonmuk Hwang at Texas A&M (JACS 133, 11766; 2011 – paper here). They compare the role of hydration forces in the self-assembly of hydrated, dry nonpolar and dry polar surfaces, represented by collagen and two amyloidic peptides, the former a ‘steric zipper’ with interdigitating hydrophobic side-chain groups. In all cases the surfaces have hydration shells, and an oscillating hydration force as the surfaces come together due to coalescence and depletion of the hydration shells. What differs is the magnitude of these. Thus the interactions have a common origin, being water-mediated in all cases. I can’t improve on what the authors say here about the role of the hydration shells: “Thus, designating a protein surface as either “hydrophobic” or “hydrophilic” may be too simplistic of a dichotomy, as surfaces in reality lie between these idealized limits. There should be no fundamental difference in the way hydration forces arise among different types of protein surfaces, even with varying affinity for water.”

The idea that water can support two liquid states in the high-pressure supercooled regime has not been directly verified experimentally, but has received enough indirect support from both experiments and simulations to have gained wide acceptance. So a preprint from David Limmer and David Chandler at Berkeley making strong claims for the non-existence of the two liquid states is bound to cause waves (arxiv 1107.0337 – paper here). On the basis of calculations using Valeria Molinero’s recently reported mW model of water, they assert that the signatures of a phase transition seen by others relate to a solid-liquid transition, or artifacts due to imperfect equilibration (which is extremely slow in this region for, e.g. ST2 water), and that there is no sign of two liquid basins anywhere in this part of the free-energy landscape. This work, and the topic in general, will be debated in a water mini-session at the Mini Stat Mech meeting at Berkeley in January (see here), which promises to be lively.

Majed Chergui at EPFL in Lausanne and colleagues have described a nice study of the time-resolved ultrafast changes in hydration of an iodide ion as it is transformed to neutral iodine by electron abstraction, probed using XAS (V.-T. Pham et al., JACS ja203882y – paper here). This transformation changes the solute from hydrophilic to hydrophobic, and so entails a considerable reorganization of the hydration shell. The hydrogens are reoriented from pointing towards the solute to pointing away from it, forming a hydrogen-bonded ‘hydrophobic cavity’. This reorganization process takes about 3-4 ps.

Achim Müller at Bielefeld and colleagues have developed a new way to study hydrophobic species encapsulated in genuinely hydrophobic cavities. They make hollow capsules from molybdenum-based polyoxometalates, with hydrophobic interior surfaces due to ligands coordinated there (C. Schäffer et al., Chem. Eur. J. 10.1002/chem.201101454 – paper here). Much less water is found inside these shells than in those with hydrophilic interior surfaces. And hydrophobic entities such as n-hexanol are spontaneously taken up into the porous shells.

Gaurav Chopra and Michael Levitt at Stanford have used state-of-the-art quantum chemical methods to map out the hydration shell of C60 (PNAS 10.1073/pnas.1110626108 – paper here). These reveal dramatic ordering of the surrounding water, evident in the time-averaged azimuthal distribution function, which is not seen when empirical force fields are used for the calculation. Moreover, ordering of the water molecules is evident as far out as about 1 nm from the C60’s centre (as I recall, the molecule is itself about 4 Å in radius). Significantly, the azimuthal water ordering around the buckyball is not due to some kind of ice-like clathration of a non-polar species but to strong dispersion attractions between the solute and solvent molecules themselves. I guess one thing this study illustrates is the sensitivity of the important details of the hydration structure of hydrophobes to the interaction potentials used.

I think I somehow failed previously to comment on an important and provocative paper by Roy Daniel and colleagues published towards the end of last year (M. Lopez et al., Biophys. J. 99, L62; 2010 – paper here). They report significant catalytic activity of pig liver esterase in near-anhydrous conditions – not merely in a non-aqueous medium, but in a ‘dry’ powder with just 3±2 water molecules per enzyme molecule. Let me quote from the abstract: “This indicates that neither hydration water nor fast anharmonic dynamics are required for catalysis by this enzyme, implying that one of the biological requirements of water may lie with its role as a diffusion medium rather than any of its more specific properties.” They admit, naturally, that it remains an open question whether this result can be generalized to all enzymes – this one might just happen to be particularly rigid. All the same, this is most definitely a finding to chew on.

Jeremy England’s paper on allostery and hydrophobic burial, mentioned in an earlier post, has now been published in Structure (paper here). To save you a click, here’s what I said before:
The paper shows that it is possible to estimate low-energy conformational changes in a protein, such as those involved in allosteric effects, on the basis simply of residue-by-residue hydrophobic effects. Specifically, he develops a method for determining the most energetically favourable way of burying hydrophobic residues, given a particular amino-acid sequence. This amounts to identifying the particular ‘burial modes’ of any given sequence. Thus, although the stabilities of conformations are doubtless multifactorial, hydrophobicity seems to be the major governing factor.

Stabilizing and destabilizing proteins

2011-07-07T06:32:00.000-07:00

How do osmolytes stabilize proteins against denaturation? Using mechanically induced unfolding by means of atomic-force microscopy of protein I27 (in fact 8 repeat units in a polyprotein), Julio Fernández and colleagues at Chicago find that osmolytes can act as ‘solvent bridges’ during the unfolding transition, pinning together hydrogen-bonding sites on the polypeptide backbone (L. Dougan et al., PNAS 108, 9759; 2011 – paper here). They found in earlier studies that water molecules generally act in this capacity. They now investigate this process in the presence of glycerol, which is known to enhance protein stability, and related solutes. They find that while glycerol, ethylene glycol and propylene glycol all enhance the mechanical stability, larger hydrogen-bondong osmolytes such as sucrose and sorbitol do so to a far lesser extent – MD simulations suggest that the latter are unable to penetrate the folded structure and act as stabilizing bridges, and any stabilizing influence they exert must be indirect.

The effects of methanol on protein conformational stability are even more complex, to judge from the NMR and MD results of Christian Hilty of Texas A&M and coworkers (S. Hwang et al., J. Phys. Chem. B 115, 6653; 2011 – paper here). They report that the alcohol stabilizes the secondary structure by strengthening hydrogen-bonding interactions in the backbone (a consequence of partially eliminating the water molecules that compete with these interactions), while also weakening hydrophobic interactions and thus swelling and loosening the folded structure overall. So whether methanol tightens or loosens the structure overall is a complex balance that depends on the sequence and initial structure of the protein.

Urea and guanidinium both help to denature the model protein the Trp-cage, according to the experiments and simulations of Pavel Jungwirth in Prague and colleagues (J. Heyda et al., J. Phys. Chem. B 10.1021/jp200790h – paper here). Although these two small molecules are chemically quite different, it appears that their denaturing mechanisms here are essentially the same, involving first the destabilizing displacement (positional exchange) of two proline residues within the hydrophobic core, followed by a gradual unravelling of secondary structural elements.

The conformational stability of proteins is also influenced by ions: Hofmeister ‘salting out’ agents such as the strongly solvated, high-charge carbonate and sulphate ions also stabilize the folded state, whereas weakly solvated low-charge ions such as bromide and iodide promote denaturation. This tendency overlaps with the classical denaturation properties of complex ions such as guanidinium (Gdm+). Christopher Dempsey at Bristol and colleagues have studied these effects for the cases of the sulphates and chlorides of guanidinium and tetrapropylammonium (TPA+) (C. Dempsey et al., JACS 133, 7300; 2011 – paper here). They find that the question of conformational stabilization is subtle. TPA+, like Gdm+, perturbs the stability of some proteins (specifically the tryptophan zipper trizip, a beta-hairpin peptide), but stabilizes the alpha-helices of alahel peptides, apparently because TPA+ cannot compete effectively for hydrogen bonds in H-bond-stabilized conformations. Moreover, the cation effects may be modified by the anion: sulphate counteracts the denaturing effects of Gdm+ on trizip, but has no effect on the influence of TPA+ in that case, because Gdm+ but not TPA+ forms ion pairs with sulphate. The emerging picture is thus one in which the Hofmeister-like effects of ions must be understood in the light of a detailed consideration of (i) ion hydration; (ii) anion-cation interactions; and (iii) direct ion-protein interactions.

More on Hofmeister from Corinne Gibb and Bruce Gibb of the University of New Orleans, who offer a new perspective: namely, that so-called chaotropic anions in fact display bind preferentially to concave hydrophobic surfaces, thus effectively weakening hydrophobic attraction and promoting ‘salting in’ (JACS 133, 7344; 2011 – paper here). They reach this conclusion by looking at the thermodynamics of ion effects in the binding of adamantane carboxylic acid within the deep hydrophobic cavity of a cavitand – an interaction perturbed by anions binding to the cavity. Sure, the extension to proteins is purely by analogy, but it’s an intriguing take on the old problem. Meanwhile, Oleg Krasilnikov and colleague at the Federal University of Pernambuco in Brazil have considered how ions affect molecular interactions in nanopores, and find that these too seem to display a Hofmeister-like sequence of activities (C. G. Rodrigues et al., Biophys. J. 100, 2929; 2011 – paper here). They look at how simple ions alter the rate constant for the interaction of poly(ethylene glycol) with the protein pore alpha-hemolysin, and see a change consistent with the Hofmeister series for halide anions. They suggest that this results from a competition for hydration water between the ions and other solutes within the pore.

Protein aggregation is commonly suppressed by the addition of surfactants and sugars or polyols. But arginine hydrochloride has also been found to possess this capability, and unlike some conventional aggregation-suppressors it does so by reducing protein-protein interactions without seeming to affect the stability of the folded conformation. This behaviour hasn’t been fully explained, although Bernhardt Trout and colleagues at MIT have proposed that at least part of the mechanism might be non-specific entropic effects due to the exclusion of arginine from the gap between two proteins as they come together (B. M. Baynes et al., Biochemistry 44, 4919; 2005). They now refine this picture by looking at the influence of the anionic counterion, showing that these display the usual Hofmeister progression for aggregation suppression (C. P. Schneider et al., J. Phys. Chem. B 10.1021/jp111920y – paper here). The protonated arginine contains a guanidinium group, again potentially making the connection to denaturant activity – but the relevant behaviour here seems in fact to be the ability of the arginine ions to self-associate in stacks. Thus, while arginine can, like Gdm+, bind directly to the protein surface, the self-association weakens this interaction so that it does not cause denaturation yet still weakens protein-protein interactions. Schneider et al. elucidate this process further by looking, both experimentally and computationally, at the anion effects. Some anions, such as sulphate, phosphate and citrate, can enhance the cationic clustering by forming multiple hydrogen bonds, creating larger clusters and thus stronger exclusion effects on aggregation – and perhaps also slowing protein diffusion via an enhancement of solvent viscosity.

Understanding how bacteria void toxic substances from the cell interior could have a profound impact on our ability to combat antibiotic resistance. E. coli have a multi-drug efflux pump called AcrAB-TolC, in which the AcrB protein in the inner membrane binds drugs non-specifically and pumps them to the TolC exit duct. Attilio Vargiu of the University of Cagliari and colleagues have taken a close look at how this pump works, with a particular focus on the role of water molecules in carrying the extruded substrate along (R. Schulz et al., J. Phys. Chem. B 10.1021/jp200996x – paper here). The protein has several small holes that allow water molecules to enter and flow in a directional manner. This water acts as a lubricant and transport medium for the drug, but also flattens out the electrostatic profile in the channel that might otherwise cause the drugs to get stuck (perhaps by hydrogen bonding), and thus it contributes to the polyspecificity of the mechanism.

The role of water-mediated interactions in protein-substrate binding and associated drug design has been given a fair bit of attention, but W. David Wilson of Georgia State University and colleagues show that such things may be relevant to small-molecule DNA-binding agents too. They look at the binding of the synthetic molecule DB921 into the AT-rich minor groove of DNA, an interaction that might be useful for the disruption of parasite mitochondria (Y. Liu et al., JACS 10.1021/ja202006u – paper here). The binding is mediated by a water molecule, and to better understand how this works the researchers look at the effect on the structure, kinetics and thermodynamics of binding of introducing a host of modifications to DB291. This information, in particular the characteristics responsible for the water-mediated interaction, could be valuable for designing new agents that bind strongly in the minor groove in a sequence-specific manner.

Combining vibrational sum-frequency measurements with simulations containing three-body terms, James Skinner and colleagues at the University of Wisconsin say that the liquid-vapour interface of water shows no evidence of ‘enhanced’ molecular structuring such as ice-like ordering (P. A. Pieniazak et al., JACS 10.1021/ja2026695 – paper here).

The charge and pH of this interface have recently become contentious issues. Sylvie Roke at the MPI for Metals Research in Stuttgart and colleagues now offer a profile of the oil-water interface, using zeta-potential and sum-frequency scattering measurements alongside MD simulations (R. Vácha et al., JACS 10.1021/ja202081x – paper here). They say that the water orientations at the surface are like those at a negatively charged surface, even though there is no hydroxide absorption to make it so. There is nonetheless a surface charge, which comes instead from a disturbance in the balance of hydrogen-bond donors and acceptors at the interface.

The notion that the hydration water of proteins is dynamically coupled to the protein itself receives more support from a study by Nguyen Quang Vinh and colleagues at UCSB, who have used terahertz spectroscopy to look at the large-scale collective vibrations of lysozyme (N. Q. Vinh et al., JACS 133, 8942; 2011 – paper here). They find that the protein is surrounded by 150-180 water molecules (a sub-monolayer) that, in the authors’ words, ‘in terms of their picosecond dynamics behave as if they are an integral part of the protein’. THz spectroscopy seems to be emerging as a nigh-incomparable technique for probing these long-ranged collective motions.

The dynamics of hydration water are also studied by Cesare Cametti at the University of Rome ‘La Sapienza’ and colleagues, using dielectic spectroscopy (C. Cametti et al., J. Phys. Chem. B 10.1021/jp2019389 – paper here). They find that the dielectric relaxation of the lysozyme hydration sphere is bimodal at high concentrations, corresponding to tightly and loosely bound waters, although monomodal in dilute solution.

The nature of the protein dynamical transition at 200-220 K shows no sign of being resolved. Salvatore Magazù and colleagues at the University of Messina now throw a cat among the pigeons by suggesting that there is no such transition at all: it is an artefact caused by the coincidence of the system’s relaxation time with the instrumental resolution (S. Magazù et al., J. Phys. Chem. B 115, 7736; 2011 – paper here). Nonetheless, they say – can life really be this complicated? – there is a crossover of some sort at 220 K, at least for the case of lysozyme considered here, for this marks a change from Arrhenius to super-Arrhenius behaviour in the coupled hydration-water/protein motions. I think what this implies – it is a little unclear – is that there is no intrinsic, qualitative change in the protein dynamics at the ‘dynamical transition’, but rather, a change due to the coupling of these to the hydration water dynamics. I could be wrong.

Water rotational dynamics are slowed down around many small solutes, both hydrophilic and hydrophobic. So it stands to reason that the same should happen for larger solutes, such as proteins. And it does – but Ana Vila Verde and R. Kramer Campen at the FOM Institute in Amsterdam suggest that the latter is not necessarily just a straightforward extension of the former (J. Phys. Chem. B 10.1021/jp112178c – paper here). Their simulations of water dynamics around the disaccharides kojibiose and trehalose show that the sheer size of these solutes, relative to smaller ones, induces additional mechanisms of water retardation as a result of topological constraints on water motions. Thus, one can’t for example imagine that the hydration of a free amino acid is the same as that when the amino acid represents a peptide residue.

Bear that in mind, perhaps, in considering the hydration structure of glycine as deduced from ab initio calculations by Bo Liu at Henan University and colleagues. They build up the hydration shell molecule by molecule from a gas-phase picture (Y. Yao et al., J. Phys. Chem. B 115, 6213; 2011 – paper here).

Salt bridges play a role in stabilizing the glycosyl hydrolase (an enzyme with potentially important industrial applications) of the hyperthermophile Rhodothermus marinus (L. Bleicher et al., J. Phys. Chem. B 115, 7940; 2011 – paper here). But perhaps surprisingly, the enzyme also contains salt bridges that seem to be destabilizing: located in the hydrophobic core, where they might facilitate the permeation of water.

C. Preston Moon and Karen Fleming at Johns Hopkins have a neat idea for developing a hydrophobicity scale for amino acids based on their energy of transfer from water to within a phospholipid bilayer, thus relating the measure directly to the driving forces for the assembly and stabilization of membrane proteins (PNAS 108, 10174; 2011 – paper here). Their thermodynamics measurements show some differences from the predictions of simulations, especially for the translocation of arginines – which makes the results relevant to voltage-sensitive ion channel gating mechanisms, since these involve the movement of arginines into the hydrophobic interior of the membrane.

How homogeneous are concentrated aqueous solutions? This question has been studied for methanol, which seems to aggregate to some extent in water; now Lorna Dougan at the University of Leeds and colleagues study the case of glycerol using neutron scattering, motivated by the relevance to cryoprotection (J. J. Towey et al., J. Phys. Chem. B 115, 7799; 2011 – paper here). They find that glycerol-glycerol hydrogen-bonding in the pure liquid is scarcely affected by the addition of water, while the water-water bonding is highly disrupted. In effect, the waters become isolated from one another, binding preferentially to glycerols. Thus, it seems likely that glycerol could act as a cryoprotectant by keeping water molecules apart and preventing for the formation of an ice network.

Water can penetrate the hydrophobic interior of carbon nanotubes, a fact that is being investigated for potential desalination technologies among other things. William Goddard at Caltech and colleagues take a look at what drives the filling process for different tube diameters (T. A. Pascal et al., PNAS pnas.1108073108 – paper here). For CNTs between 0.8 and 2.7 nm, the interior water phase is always more stable than the bulk, but for several different reasons. For nanotubes thinner than 1 nm, the water phase is gas-like, with an entropic driving force. For nanotubes of 1.1-1.2 nm the encapsulated phase is ice-like and enthalpy-stabilized. For nanotubes wider than 1.4 nm the interior phase is liquid-like, but stabilized by increased translational energy. The overall message is sobering in showing how very fine adjustments to the hydrogen-bonded network and the balance of interactions with the surrounding environment can create quite different phase behaviour and thermodynamic driving forces in confined situations even for very small differences in dimensions.

A new method for rapidly calculating solvation energies in water is presented by Jianzhong Wu and coworkers at the University of California at Riverside (S. Zhao et al., J. Phys. Chem. B 10.1021/jp201949k – paper here), which combines DFT with MD simulations. The researchers have so far tested it for simple ions, for which it works well. Meanwhile, Merchant and Dilip Asthagiri at JHU have a preprint (arxiv 1106.0448 – paper here) in which they examine the range of ion-specific effects in water and conclude that, at least for sodium, potassium, chloride and fluoride, these extend no more than about 4 Å, so not much more than the size of a single water molecule.

This hasn’t yet exhausted my list of papers: still to come (soon) are developments on the putative liquid-liquid transition of water and on proton transport in bacteriorhodopsin…

Hydration of PSII

2011-05-24T10:13:00.000-07:00

What a beautiful crystal structure is reported by Yasufumi Umena of Osaka City University and colleagues in Nature (473, 55; 2011 – paper here). They have revealed the entire photosystem II complex at 1.9 Å resolution, showing the hydration structure of the core Mn4CaO5 cluster along with the locations of 1,300 water molecules in a hydration shell that seems to offer several hydrogen-bonded channels for protons, water molecules for photolysis, or oxygen molecules. The latter are probably formed by oxidation of some of the four waters bound to the Mn cluster. I don’t recall ever seeing before such a complex, orchestrated and carefully rationalized example of a multifunctional hydration structure.

Collagen is generally considered a structural protein, but particular collagen motifs are also recognized as substrates by collagen binding proteins such as adhesins in some human pathogens. On the basis of MD simulations and comparison with crystal structures, Luigi Vitagliano at the Consiglio Nazionale delle Ricerce in Naples and colleagues say that the regions of collagen-binding adhesin CNA involved in binding to hydrophobic parts of the collagen triple helix are inherently prone to dewetting, making them primed to bind their target by reducing the desolvation penalty (Vitagliano et al., Biophys. J. 100, 2253-2261; 2011 – paper here). Moreover, besides these hydrophobic contacts the interaction between CNA and collagen is mediated by an intricate network of 13 water molecules.

Local water densities around biological systems can be calculated fairly accurately with a computationally cheap interaction-site model (based on the Ornstein-Zernicke integral equation), rather than with a full MD simulation, according to a new study by Vijay Pande at Stanford and colleagues, who compare the two for the hydration of GroEL (M. C. Stumpe et al., J. Phys. Chem. B 115, 319; 2011 – paper here).

In drug design, the surfaces of target proteins are often mapped out to look for ‘hot spots’ where it is particularly advantageous to place functional groups in the ligand complementary to those on the protein. This process often identifies many such local minima in a rugged potential-energy surface. But that’s in vacuo for a rigid surface. One might expect that including the protein’s conformational flexibility and interactions with water will smooth out this rugged landscape. But Katrina Lexa and Heather Carlson at the University of Michigan say that it doesn’t, unless the protein is allowed its full flexibility (JACS 133, 200; 2011 – paper here). In other words, there are no short cuts: if the molecule is semi-rigid, spurious hot spots remain.

Structured water molecules bound within cytochrome c have been suspected for some time of participating in the enzyme’s electron-transfer and oxygen reduction reactions, but it hasn’t been clear exactly how. Amandine Maréchal and Peter Rich at University College London have used FTIR spectroscopy to investigate the issue (PNAS pnas.1019419108 – paper here). They find that rearrangements of up to 8 water molecules are associated with the photolysis reaction, probably forming transient hydrogen-bonded pathways for proton conduction and gating.

More roles for water in protein-ligand binding are revealed by Michelle Sahai and Philip Biggin at Oxford (J. Phys. Chem. B 10.1021/jp200776t – paper here). They consider how the GluA2 ionotropic glutamate receptor binds both glutamate and the related compound AMPA, and find two quite distinct modes of binding. The difference seems to be in the location of a single water molecule in the binding cleft. They use density functional theory to figure out why it is more favourable for the water to sit in different positions in the two different cases. That they don’t seem yet to have fully settled that question (they cannot consider entropic contributions) seems to underline how tricky it might be to use bound waters in rational drug design.

Joe Dzubiella in Berlin has an interesting preprint on the thermodynamics of hydrophobic association which claims that the curvature of the interface is important. He points out how there seems to be a crossover at small size scales (about 1 nm) between enthalpy-driven hydrophobic association at larger scales and entropy-driven at smaller scales. But for concave binding cavities this does not seem to apply: enthalpy continues to dominate even at very small scales. Joe explains this on the basis that the surface-area-based models used to describe large-scale interactions on the basis of solvent-accessible area and surface tension remain applicable at small scales so long as “the antagonistic effects on concave vs. convex bending on water interface thermodynamics are properly taken into account”. The paper will appear in a forthcoming special issue of J. Stat. Phys. dedicated to water.

There’s a nice potted summary of current understanding of antifreeze protein ice-binding mechanisms by Kim Sharp of the University of Pennsylvania in PNAS (pnas.1104618108 – paper here). It is a commentary on a new study by Garnham et al. (PNAS pnas.1100429108), which I haven’t yet got hold of. They report the crystal structure of the AFP of an Antarctic bacterium, Marinomonas primoryensis, which has a new binding motif, a parallel beta-helix. This structure has the ice-binding surface fully solvent-exposed in the crystalline state, and so is likely to be “free from crystal-packing artifacts.” Much of this surface is hydrophobic (although anchored at the edges by H-bonds), and the claim is that this induces a clathrate-like structure in the first hydration layer that is close to the structure of ice – in other words, the AFP “brings its own ‘ice’ with it”.

With an eye on the Lum/Chandler/Weeks model of hydrophobic attraction, Pablo Debenedetti and colleagues have calculated the evaporation length scale – the separation of solvophobic plates at which capillary evaporation occurs – for water and a range of organic liquids (C. A. Cerdeiriña et al., J. Phys. Chem. Lett. 2, 1000; 2011 – paper here). There’s nothing conceptually new here, but the numbers are somewhat surprising: for water they find a length scale of about 1.5 microns at atmospheric pressure, which is much larger than I’d have expected. However, this applies for purely repulsive surfaces (contact angle of 180 degrees), which is of course rarely found, and never for protein surfaces. The length is also large for the organics, such as benzene, heptane and cyclohexane, but about a factor of 3 less so – water is (somewhat) anomalous here because of its large surface tension.

Hydration seems to respond to the flexibility of alicyclic systems, according to Annalisa Boscaino and Kevin Naidoo of the University of Cape Town in South Africa (J. Phys. Chem. B 10.1021/jp110248j – paper here). They find from MD simulations that molecules with a cyclopyranose framework, such as glucose, have a significantly higher hydration number than those based on a cyclohexane framework with hydroxyls, such as cyclohexanol. This seems to result from the greater rigidity of the former, enabling the formation of longer-lived hydrogen bonds to the surrounding water.

It’s generally thought that rearrangements of the hydrogen-bond network in bulk water must have a collective character. Andrei Tokmakoff at MIT and colleagues now provide evidence of that (R. A. Nicodemus et al., J. Phys. Chem. B 115, 5604; 2011 – paper here). They have used ultrafast IR spectroscopy of HOD in pure water to measure the energy barriers to spectral diffusion and reorientational relaxation, and find that the slow-decay component is consistent with collective reorganization.

Marcus Weinwurm and Christoph Dellago have calculated the vibrational spectra of single-file water molecules in narrow pores, enabling them to distinguish it from the stacked-ring structure in wider pores (J. Phys. Chem. B 115, 5268; 2011 – paper here).

Water as glue

2011-04-28T09:43:00.000-07:00

There is a very nice crop of papers to draw on for this post, many of which speak to very central questions in this field. First up is a paper in Nature Communications from Volkhard Helms and colleagues at Saarbrücken, which looks at the detailed role of interfacial water in the association of hydrophilic protein surfaces (M. Ahmad et al., Nat. Commun. 2, 261; 2011 – paper here). Whereas hydrophobic association has been the focus of a lot of recent attention, especially with a view to the possibility of a dewetting-induced process, hydrophilic surfaces have received less attention. That’s an important lacuna, since as the authors point out, around 70% of interfacial residues are hydrophilic. The common approach is to assume direct electrostatic interaction mediated by a continuum solvent. But the water network has a more complex role. As shown in these MD simulations of the barnase-barstar complex, water molecules mediate and stabilize the interactions between native contacts. Moreover, for electrostatic interactions to be important, the interfacial water’s dielectric constant needs to be reduced to reduce screening. This happens as a consequence of changes in the structure of the interfacial layers (the dielectric permittivity is less than 50% of the bulk value for interfacial separations of less than 1.2 nm), and it preferentially promotes electrostatic interactions normal to the surfaces. In other words, you could say that (once again, though arguably to put the cart before the horse) water does exactly what is required of it.

Jeremy England, now at Princeton, has a paper in press with Structure which shows that it is possible to estimate low-energy conformational changes in a protein, such as those involved in allosteric effects, on the basis simply of residue-by-residue hydrophobic effects. Specifically, he develops a method for determining the most energetically favourable way of burying hydrophobic residues, given a particular amino-acid sequence. This amounts to identifying the particular ‘burial modes’ of any given sequence. Thus, although the stabilities of conformations are doubtless multifactorial, hydrophobicity seems to be the major governing factor.

Calculating the surface free energies of heterogeneous surfaces exposed to water (such as protein surfaces) is tough. The approach of the Cassie equation is additive, but as Alenka Luzar and colleagues point out, that doesn’t always work (J. Wang et al., PNAS 108, 6374-6379; 2011 – paper here). They show that deviations from linear additivity result when parts of a surface are unevenly exposed to solvent. In particular, it seems that polar patches exert an inordinately strong influence, being able to ‘pin’ a droplet so that it might remain closely attached to adjacent hydrophobic patches. They examine these effects with reference to water droplets first on a functionalized graphene surface and then on the surface of melittin.

Daryl Eggers at San José State University presents an interesting approach to the energetics of reactions in aqueous solution, geared especially to biochemical equilibria, that treats the water as a reactant and product, thereby subsuming the local changes in water structure that inevitably accompany the reaction (Biochemistry 50, 2004-2012; 2011 – paper here). Here the free energy of bulk water is treated as a variable, allowing for the effects of all solutes including those that may not participate directly in the reaction (such as dissolved salts). As I understand it, this offers a means of accommodating the effects of such solutes (for example, in salting in/out) that does not make any assumptions about global changes in ‘water structure’, but represents only the global average of localized changes. Also jettisoned in that process is any insistence on putative structure-makers and structure-breakers; rather, solvation effects need be discussed only in what seems like relatively uncontentious terms of subpopulations of water with differing free energies. I haven’t yet quite figured out how one gets at these free energies in experimental terms, but I like the principle, not least because it explicitly acknowledges the role of water as a participant.

Yingkai Zhang at New York University and coworkers have used ab initio MD simulations to study the mechanism of action of histone deacetylase (HDAC) enzymes, which remove acetyl groups from histone residues and have been identified as a target for anti-cancer drugs (R. Wu et al., JACS 133, 6110-6113; 2011 – paper here). They suggest that some HDACs function via a mechanism involving a modulation of water access (a hydrogen-bonded chain of waters) to the binding pocket, in which a zinc ion in the metalloenzyme binds to its substrate. The presence or absence of water alters the dielectric constant in the binding pocket and thereby affects the strength of zinc binding.

Transitions of DNA between A, B and Z forms are thought to be associated with and perhaps driven by transitions in the nature of hydration. Karim Fahmy and colleagues at the Institute of Radiochemistry in Dresden now suggest that the same applies to the more subtle sub-transitions between the BI and BII states of the B-form (H. Khesbak et al., JACS 133, 5834-5842; 2011 – paper here). Specifically, there are two sub-populations of water molecules – one bound to phosphates, the other not – that contribute to stabilizing the two conformations via entropic effects. These water rearrangements can also be involved in interactions with DNA-binding ligands, such as the antimicrobial peptide indolicidin, by a water-mediated induced fit.

The structures of amyloid fibrillar assemblies are still far from well understood. The hydration state of the peptides is a particularly important issue in determining their stability and perhaps their mode of formation. Beat Meier at ETH and colleagues report some tricks that enable this question to be probed by NMR (Van Melckebeke et al., J. Mol. Biol. 405, 765; 2011 – paper here). For a particular prion domain called HET-s(218-289) they show that, although these protofibrils have a hydrophobic core and a semi-hydrophobic pocket, they do not engage in ‘dry’ interfibril contacts but are each surrounded by water.

The behaviour of water close to and between lipid bilayers has been much studied, but there doesn’t seem to have been much consideration of how that behaviour might feature in biological membrane processes such as fusion. This issue is investigated by Vijay Pande at Stanford and colleagues using simulations (P. M. Kasson, E. Lindahl & V. S. Pande, JACS 133, 3812-3815; 2011 – paper here). They look at the water trapped between the faces of two approaching membranes – that is, in hydrophilic confinement – and find that the dynamics are altered significantly. Specifically, the trapped water has reduced rotational entropy, and it helps the two membranes to adhere. However, the slower dynamics also retards the process of fusion itself – the formation of the ‘stalk’ that bridges the lipid membranes.

Mafumi Hishida and Koichiro Tanaka at Kyoto have also looked at the hydration of phospholipid bilayers, here experimentally using terahertz spectroscopy and SAXS (Phys. Rev. Lett. 106, 158102; 2011 – paper here). They conclude that water structure is perturbed up to 4-5 layers from the surface, over a distance of at least 1 nm, and that the average density in this hydration layer is slightly greater than that in the bulk.

Meanwhile, Joshua Layfield and Diego Troya at Virginia Tech have considered a water droplet confined between hydrophobic surfaces of self-assembled monolayers (J. Phys. Chem. B 115, 4662-4670; 2011 – paper here). Here the water motions (lateral translational diffusion) are accelerated by confinement, and this effect seems to operate over distances of more than 1 nm from the surfaces. Structural effects (preferential orientation of the water molecules) aren’t evident beyond 1 nm, however – but while the authors consider this to be a relatively short-ranged effect, I’d have been surprised to see anything structural with a longer reach.

Daniela Russo at the ILL and colleagues have used inelastic neutron scattering to probe the low-frequency densities of states of water hydrating small ‘model peptides’ (N-acetyl-leucine-methylamide, NALMA, and N-acetyl-glycine-methylamide, NAGMA) at low temperatures (Russo et al., JACS 133, 4882-4888; 2011 – paper here). At 200K they find that the hydration water for the hydrophilic NAGMA is similar to high-density amorphous ice, while that of the hydrophobic NALMA is more like low-density amorphous ice. Something similar has been reported at 100 K by Paciaroni et al. (Phys. Rev. Lett. 101, 148104; 2008), but was in that case attributed to curvature of the biomolecular surface – which is evidently not the case for these small molecules.

Aquaporins seem to play a crucial role in water regulation in arid periods during the life cycle of the major malaria vector mosquito Anopheles gambiae, according to Kun Liu of the Johns Hopkins Malaria Research Institute in Baltimore and colleagues (K. Liu et al., PNAS 108, 6062-6066; 2011 – paper here). The authors don’t say whether this makes these AQPs a potential target for controlling the spread of malaria, though I suppose that is a possible implication.

There’s still more to be understood about what hydrogen bonds are, as evidenced by a recent IUPAC working group set up to redefine them (see here). Angelos Michaelides at UCL (who I have to thank for my water-crested football shirt) and colleagues have now refined the quantum picture of the H-bond, showing how quantum nuclear effects due to the anharmonicity of the bond and the small proton mass can alter the bond strength, weakening weak H-bonds (like those in water) and strengthening strong ones (X.-Z. Li et al., PNAS 108, 6369-6373; 2011 – paper here).

There are one or two other papers I’ve still to get to, including some that folks have kindly sent to me. Apologies for that – more soon, I hope.

Coarse-grained models

2011-02-24T03:45:00.000-08:00

More on the mechanisms of urea-induced protein denaturation, this time from Ruhong Zhou at IBM and his colleagues in Beijing (M. Gao et al., J. Phys. Chem. B 114, 15687; 2010 – paper here). In simulations, they look at the populations of water and urea molecules around each residue in hen egg-white lysozyme, and find that some of the hydrophobic core residues stay virtually dry as unfolding proceeds in 8M urea. Moreover, the urea molecules are bound preferentially to uncharged rather than to charged residues. So the picture is that the protein swells to a molten globule state while keeping largely dry inside, because it is the urea rather than water that penetrates. this may not be a wholly general order of events, however – depending on the detailed shape and structure of the protein, water might sometimes penetrate first, as found for example by Bennion and Daggett (PNAS 100, 5142; 2003).

John Klassen and colleagues at the University of Alberta present an interesting comparison of protein-ligand dissociation constants in the hydrated and dehydrated states (L. Liu et al., JACS 132, 17658; 2010 – paper here). The latter are obtained from gas-phase measurements at 25-66 C. The kinetic stability of the associated state is significantly reduced in the hydrated phase: water stabilizes the dissociative transition state and might thereby be considered a kind of lubricant that facilitates the departure of the ligand.

David Beauchamp and Mazdak Khajehpour predicate their study of water-water interactions on enzyme activity with the supposition that the hydrogen-bond distribution in pure water is bimodal, with bonds that are high- and low-angle (J. Phys. Chem. B 10/1021/jp107556s – paper here). They say this is supported by some simulations, and that it is consistent with the (contentious) two-state model of the liquid. They also say that salts have the ability to perturb this distribution. OK… so given these assumptions, they see what added salts do to the activity of ribonuclease t1, and say that their spectroscopic and kinetic results are consistent with the notion that salts that promote the high-angle bonds stabilize the more compact and less active forms of the enzyme. Interesting ideas, but it seems a big leap from the data to the microscopic interpretation.

I recently described work by Martin Gruebele, Martina Havenith and colleagues on the mechanism of antifreeze glycoproteins, in which they argued that the biomolecules can effect long-range changes in water dynamics to inhibit freezing (S. Ebbinghaus et al., JACS 132, 12210; 2010). The authors now report similar findings for a 37-residue alpha-helical antifreeze protein from winter flounder (S. Ebbinghaus et al., Biophys. J. Biophys. Lett. in press). The find using CD and FRET on native and mutant versions that the antifreeze activity seems to be connected to a kinking of the helix, and that this is coupled to a suppression of bulk-like dynamics in the solvation water over a range of at least 3 nm, as indicated by THz spectroscopy.

Years ago, Royer et al. showed that a group of water molecules at the interface between the subunits of the dimeric haemoglobin of Scapharca clams seem implicated in the molecule’s allosteric cooperativity (Royer et al., PNAS 93, 14526; 1996). David Leitner and colleagues at the University of Nevada at Reno now look in detail at the dynamics of this cluster of waters using MD simulations based on the crystal structures (R. Gnanasekaran et al., J. Phys. Chem. B 114, 16989; 2010 – paper here). They find that those in the oxy form (11 molecules) exhibit slower relaxation than those (17) in the deoxy form, and that the water cluster, although rather static on ps timescales, can enhance energy transport across the interface of the subunits via vibrations.

The close and reciprocal interactions of water and protein dynamics, especially at low temperatures, seems to be echoed in the case of hydrated lipid bilayers, according to Peter Berntsen and colleagues at Chalmers University in Göteborg (J. Phys. Chem. B 10.1021/jp110899j – paper here). They have used dielectric rexlaxation measurements below 250 K to show that at low temperatures the water dynamics becomes increasingly dominated by the movements of the lipids, and is super-Arrhenius-like at low hydration levels.

Fast proton transport along peptide backbones can be assisted by water bridges, according to ab initio calculations by Po-Tuan Chen of the National Taiwan University of Science and Technology and colleagues (J. Phys. Chem. B 10.1021/jp107219r – paper here). They say that a two-molecule water bridge can make the transport between two adjacent carbonyl oxygens almost barrierless.

In a preprint (not sure where it is destined, but it looks like JCP format), David Chandler and his coworkers present a coarse-grained lattice model to implement the Lum-Chandler-Weeks dewetting theory of hydrophobic interactions (P. Varilly et al., arxiv: 1010.5750 – paper here). The model captures the essential features of the model at far less computational cost than full MD simulations, in particular modelling the solvent fluctuations that are essential for the dewetting mechanism.

With much the same objective of computational cheapness, Ken Dill at UCSF and colleagues present a new solvation model that they call semi-explicit self-assembly (C. J. Fennell et al., PNAS 108, 3234; 2011 – paper here). They basically construct a solute’s solvation shell as some combination of pre-computed solvation shells for simple spheres in explicit TIP3P water. They have so far only tested it here on simple small molecules such as sugars.

And Valeria Molinero and colleagues at the University of Utah have a coarse-grained model of DNA solvation with explicit water and ions (R. C. DeMille et al., J. Phys. Chem. B 115, 132; 2011 – paper here). It reproduces base-pair specificity and is computationally faster by two orders of magnitude than atomistic simulations.

There is a curious paper in Nature Structural and Molecular Biology by Nathaniel Nucci and colleagues at the University of Pennsylvania (NSMB 18, 245; 2011 – paper here) on an NMR technique to identify residence times of specific clusters of water molecules around proteins. I say curious, because these useful results are presented, particularly in a News & Views article in Nature (V. J. Hilser, Nature 469, 166; 2011 – paper here), as “challenging current dogma about protein hydration”. It seems this challenge comes from the fact that the results show that not all ‘bound’ water exchanges slowly with the surrounding solvent. But a wide range of exchange times is surely already well established, especially from simulations – the old crystallographic picture in which ‘hydration water’ is all securely bound and long-lived seemed long dead. Still, it is interesting that Nucci et al., whose method relies on confining the proteins (here ubiquitin) within reverse micelles to slow the hydration dynamics, found that water molecules with similar residence times seem to cluster on the protein surface, so that the molecules in each cluster form independent networks which exhibit intra-cluster cooperativity.

In another preprint, Giancarlo Franzese and colleagues at the University of Barcelona offer something of a mini-review of hydration structure and dynamics at protein surfaces, along with some Monte Carlo simulations that investigate cooperativity and dynamical transitions of a water monolayer hydrating a protein surface at low temperatures (arxiv preprint 1010.4984; paper here).

On the still-evolving picture of pure liquid water: Alessandro Cunsolo at Brookhaven and his colleagues study it using QENS to look at single-particle diffusion rates at 200 MPa as a function of temperature, and find that their results point to the proposed existence of a second critical point at about 220 K, and of the Widom line which ends at this point (J. Phys. Chem. B 114, 16713; 2010 – paper here).

Meanwhile, Richard Henchman and Sheeba Jem Irudayam of Manchester University in the UK propose a ‘topological’ definition of hydrogen bonding in water that offers a new description of water structure and dynamics (investigated in simulations using TIP4P/2005 water) based on the character of the H-bond network (J. Phys. Chem. B 10.1021/jp105381s – paper here). They say that in this description almost all the water molecules are H-bonded and that there are an appreciable number of ‘defects’ in which molecules are acceptors for one (trigonal) and three (trigonal bipyramidal) hydrogens rather than two.

Less is more

2011-02-14T02:28:00.000-08:00

In the spirit of maintaining continuity (do some folks really look at this site every week, as I’m told?), I will aim to post more regularly rather than exhaustively. That’s to say, this is not a complete list for what I’ve seen out there, but more will follow soon.

Sheh-Yi Sheu at National Yang-Ming University in Taiwan and Dah-Yen Yang at the Institute for Molecular Science in Okazaki, Japan, present a method for deducing the free energy of the hydration shell for a biomolecule from simulations (J. Phys. Chem. B 10.1021/jp105164t – paper here). They say that water in a protein (here myoglobin) hydration shell follows fractional Brownian motion.

Flavoproteins are electron-transfer proteins involved in a range of biological processes, including cell apoptosis and DNA repair. The nature of solvation at the active sites is of central importance for their function. Dongping Zhong and colleagues at Ohio State have used ultrafast spectroscopy to characterize the dynamics of the water network at the functional site in three redox stats of a representative flavoprotein, flavodoxin (C.-W. Chang et al., JACS 192, 12741 (2010) – paper here). Rather neatly, they are able to use the intrinsic cofactor of this protein as the fluorescent probe for the experiments. They can monitor changes in the relaxation and rigidity of the local water network between the different states, for example a retardation of the relaxation from around 2.6 to 40 ps between the oxidized to semiquinone state. They propose an intimate and biologically relevant coupling between the flexibility of the solvation network and the protein.

Gating of ion channels due to cooperative drying has been suggested as the underlying mechanism for such functions. Fangqiang Zhu and Gerhard Hummer at NIH explore this notion for the ligand-gated ion channel GLIC of the bacterium G. violaceus, for which the crystal structure of the open state is solved (PNAS 107, 19814; 2010 – paper here). They find that the pore is typically water-filled in the open state, but that a very small decrease in the channel radius can induce cooperative drying. It seems that the emptying of the pore is a response to, rather than the driving force for, changes in the pore width.

Alla Oleinikova, Ivan Brovchenko and their colleague G. Singh at Dortmund have calculated the heat capacity of hydration water of hydrophobic and hydrophilic peptides from simulations (A. Oleinikova et al., Europhys. Lett. 90, 36001; 2010 – paper here). They say that around 330 K there is a sharp change in structure from a percolating to a fragmented H-bonded network, and that this coincides with a point at which the heat capacity changes from being dominated by water interactions within the hydration shell to a situation where the hydration-shell-to bulk interactions are more important. At this stage, the ‘detachment’ of the hydration network from the peptide in effect makes the biomolecule more hydrophobic.

Anrew White and Shaoyi Jiang at the University of Washington have studied the hydration of glycine and two (zwitterionic) analogues di- and trimethylglycine using MD (J. Phys. Chem. B 115, 660; 2011 – paper here). They say that all three molecules affect the water structure out to the second hydration shell, but trimethylglycine has the greatest (retarding) effect on water dynamics and, perhaps surprisingly, does not aggregate but remains well solvated even at high concentrations. This might help to account for trimethylglycine’s antifouling properties and its suppression of protein aggregation.

There is sill a tussle going on about whether bulk water at ambient temperatures is best considered in a homogeneous or two-phase framework. Lars Pettersson and Anders Nilsson have recently teamed up with theorists including Jens Norskov at Stanford to perform ab initio MD calculations which point to a mixture of low- and high-density regions at ambient conditions (A Møgelhøj et al., arxiv preprint 1101.5666; paper here). But Niall English and John Tse dispute this, saying that such inhomogeneities are of very short range and transient, being just the ordinary density fluctuations one would expect to see in an equilibrium system (Phys. Rev. Lett. 106, 037801; 2011 – paper here).

Raymond Dagastine and colleagues at the University of Melbourne report a very striking claim: that air bubbles interact with (probably virtually all) solid surfaces via a repulsive van der Waals interaction (R. F. Tabor et al., Phys. Rev. Lett. 106, 064501; 2011 – paper here). As a bubble approaches a surface under hydrodynamic flow, they say, it will therefore start to deform and flatten at the point where the repulsive force equals the Laplace pressure. Repulsive vdW forces are well known in theory, but it seemed previously that rather special combinations of materials were needed to realise them.

Yes, I'm still here

2011-02-03T06:35:00.000-08:00

Apologies for the long silence. This blog is still active, but Christmas (among other things) got in the way and then I face the Sysiphean task of catching up. That task is not by any means completed here, but I want to flag up that Water in Biology hasn’t expired. Much more as soon as I can manage it.

Bruce Berne, Richard Friesner and Lingle Wang at Columbia have recently introduced the notion that ligand binding in protein receptor pockets is largely driven by the displacement of water molecules that sit in an unfavourable position in the pocket, which are replaced with groups on the ligand that are complementary to the protein surface (Young et al., PNAS 104, 808; 2007; Abel et al., JACS 130, 2817; 2008). In a new paper (Wang et al., PNAS 108, 1326; 2011 – paper here) they consider what their model, called WaterMap, has to say about regions of the binding pocket that are initially dry, being highly unfavourable environments for water. Including an interaction term in the model that represents the formation of a (hydrophobic) protein-ligand interface in dry regions, they can compute binding affinities in good agreement with experiment.

Dave Thirumalai at Maryland and his coworkers offer a striking view of how amyloid fibrils self-assemble from interdigitated beta-sheets (G. Reddy et al., PNAS 10.1073/pnas.108616107 – paper not yet online). They present a MD study of the association of beta-sheets in two amyloidogenic proteins of very different sequence, one polar and the other hydrophobic. They say that in the former case the association of the sheets is mediated by one-dimensional water wires at the interface between them, which are gradually expelled. But for the hydrophobic peptides the sheets come together in something like an abrupt drying transition, as postulated previously for some protein-folding and aggregation processes. This happens much faster (nearly 1,000-fold) than the previous case, since the trapped water wires for the polar peptide create a barrier to rapid assembly. Thus, although the final structures are very similar, the mechanisms and dynamics are quite different. It would seem that this paper ties in with a new one by Ken Dill and colleagues on the mechanisms of amyloid assembly into fibrils, of which I’ve only seen the abstract (which suggests that there’s not a big emphasis on the role of the solvent here beyond the involvement of hydrophobicity) (J. D. Schmit et al., Biophys. J. 100, 450-458; 2011 – paper here).

Cytochrome c oxidase (CcO) acts as a proton pump in which the transmembrane proton motion is thought to be facilitated by a proton wire involving strategically placed water molecules. The roles of these waters are investigated by Shelagh Ferguson-Miller and colleagues at Michigan State based on high-resolution crystals structures of two mutant forms of bacterial CcO (Liu et al., PNAS 108, 1284; 2011 – paper here). In both mutants, where proton transfer is inhibited to different degrees, the overall structural changes are very small but one or more of the bound waters is eliminated. The story is not, however, quite as simple as a mere break in the water wires, but involves subtle conformational changes between oxidized and reduced forms of the metal centres: an indication that, while bound water undoubtedly plays an active role in the catalytic function, in this case that role resists reduction to a simplistic picture.

Human telomeres contain G-rich sequences that form quadruplex structures in Hoogsteen hydrogen-bonded patterns. It’s not clear what influences the stability of this unusual motif, but John Trent and colleagues at the University of Louisville in Kentucky say that hydration plays a major part (M. C. Miller et al., JACS 132, 17105-17107; 2010 – paper here). They say that previous studies of the crystal structure of these sequences have been misleading because the dehydrating agents used to cause precipitation (PEGs) may give crystal structures that are not closely related to those in solution. Instead they use acetonitrile (which is water-soluble but does not engage in hydrogen-bonding) as the cosolvent for CD and NMR solution studies, and find that stabilization of the quadruplex seems to be caused more by dehydration than by steric crowding effects.

How hydration affects energy relaxation of cytochrome c after photoexcitation has been studied using ultrafast spectroscopy by Shuji Ye of the University of Science and Technology of China in Hefei and and Andrea Markelz of SUNY at Buffalo (J. Phys. Chem. B 114, 15151-15157; 2010 – paper here). One of the main conclusions is that hydration doesn’t in fact have a great deal of influence on the initial energy dynamics: there is an initial fast (around 300 fs) conversion from the electronically excited state to a vibrationally excited ground state, which is essentially hydration-independent. But the vibrational cooling then does involve interaction with the solvent, more or less in line with the existing notion that hydration water acts as a kind of plasticizer in this molecule.

Finally for now, and not really at all relevant to the real themes of this blog but too much of a curiosity for me to ignore, there are two papers on the arxiv investigating the notorious Mpemba effect, whereby hot water is said to sometimes freeze faster than cold: see here and here.

Pores for thought

2010-10-22T02:02:00.000-07:00

Two papers in Science look at the mechanics of proton conduction in the M2 pore of influenza viruses (F. Hu et al., Science 330, 505-508; M. Sharma et al., Science 330, 509-512; 2010 – papers here and here). Hu et al. say that the key is whether a complex of histidine groups (His37) in the tetrameric pore is or is not in contact with a water chain threading the pore, which changes in a pH-dependent manner. Previously it has been controversial whether the His37 group participates in an active fashion by protonation/deprotonation or merely alters the channel diameter electrostatically. Hu et al. say that the latter does happen, but is accompanied by increased rotational freedom of the His imidazole group to make contact with the ‘water wire’ and relay a hopping proton. Sharma et al. could be said to refine this picture by considering the interactions between all the His37s in the tetramer and their relation to the adjacent Trp41 residues. They say that the proton-conducting state is activated at low pH by ‘unlocking’ of the imidazole group in a way that is gated by Trp41 via pi-cation interactions.

More pores. Not all aquaporins are selective for water only – some will admit glycerol and other alcohols. David Savage at UCSF and colleagues have determined their X-ray crystal structures to figure out what determines the selectivity (D. Savage et al., PNAS 10.1073/pnas.1009864107 – paper here). The details are complex, but the basic features arguably those one might expect: in the region of the pore’s selectivity filter, the energetics of water transport are controlled by channel hydrophilicity, while selectivity for larger molecules such as glycerol is steric, governed by channel width.

Some other protein pores will also allow water and other small molecules to pass, such as the sodium-glucose cotransporter, which permits water flow in the presence of Na+ or glucose. This class of proteins allows passive water flow in the presence of an osmotic Na+ or glucose gradient, but also flow against such a gradient if Na+ or glucose is present. To what extent, then, is such flow passive, and to what extent actively pumped in the presence of these solutes? Michael Grabe at the University of Pittsburgh and colleagues investigate that question using MD simulations (S. Choe et al., Biophys. J. 99, L56-L58; 2010 – paper here). They find that water will pass through the sodium-dependent galactose cotransporter vSGLT both in the absence and the presence of galactose. In the former case the flow is passive (and occurs through the galactose-binding region), but that in the latter case the release of galactose ‘pushes’ water molecules through the pore in the same direction as its exit – as the authors put it, galactose acts as a Brownian piston that rectifies the passive water motion through the pore.

Comparable rectification of proton motion through a proton pumps such as bacteriorhodopin, resulting in a ‘proton diode’, is described by Klaus Gerwert and colleagues at Bochum (S. Wolf et al., Angew. Chem. Int. Ed. 49, 6889-6893; 2010 – paper here). This team draw on their detailed investigations of bR over recent years, and new studies of point mutations, to explain how conformational changes in a few residues can control access between internally bound and external water molecules in such a way as to bias the direction of proton flow in a general mechanism that they suspect might be more general to other proton pumps.

Biological processes involving proton motion are prime candidates for manifesting quantum-mechanical effects. A rather striking instance of this is claimed by George Reiter of the University of Houston and colleagues, who say that the zero-point motions of protons in are entirely responsible for the binding of water to A-DNA (G. Reiter et al., Phys. Rev. Lett. 105, 148101; 2010 – paper here). Changes in hydration seem to be what drive the A-to-B transition in DNA (the A phase forms in dehydrated conditions), and Reiter et al. say that this is accompanied by a change in the zero-point kinetic energy of the protons in the hydrated B-DNA that is sufficient in itself to motivate the transition. Whether the protons concerned are those of water molecules in the hydration shell or those in the DNA’s H-bonds (or, presumably, a bit of both) is not yet clear.

It’s many years ago now that David Tirrell, now at Caltech, developed ways to incorporate fluorinated amino acids into proteins using recombinant DNA technology – a feat popularized with reference to non-stick fried eggs. David has now teamed up with Ahmed Zewail and colleagues to investigate what fluorinated residues do to the hydration of such proteins, using ultrafast time-dependent fluorescent Stokes shift spectroscopy on fluorinated coiled-coil peptides (O.-H. Kwon et al., PNAS 10.1073/pnas.1011569107 – paper here). They find that the hydration dynamics are retarded around fluorinated residues, in marked contrast to an acceleration of the dynamics for the corresponding cases of hydrogenated residues, which are of comparable size.

Some mini-proteins, such as the villin headpiece domains HP35 and HP36, with just 35 and 36 residues, have an unusual ability to fold quickly into a conformation with a securely buried hydrophobic core despite their small size. Takao Yoda of the Nagahama Institute of Bio-science and Technology and colleagues have used simulations to investigate how this happens (T. Yoda et al., Biophys. J. 99, 1637-1644; 2010 – paper here). The cores in the folded state are fully dehydrated, but some water molecules remain therein until the final stages of folding. This is an unusually large system for which the folding process has been followed in detail from a fully extended state in explicit solvent. Meanwhile, David Cerutti at Rutgers and coworkers have simulated the crystal structures of a scorpion toxin protein to probe the performance of different protein and water force-field models in predicting the observed structure (D. S. Cerutti et al., J. Phys. Chem. B 114, 12811-12824; 2010 – paper here). They find that the results are not very sensitive to the water model, and far more dependent on the protein model (FF99SB does best) in terms of correctly predicting the right contacts in the peptide chain.

Whether we can understand the various forces involved in protein folding sufficiently to design peptides and other heteropolymers to adopt specific conformations is of course one of the big challenges not only for protein design but for polymer chemistry more generally. Shekhar Garde and colleagues at RPI have studied how water-mediated interactions might be exploited in this endeavour (S. N. Jamadagni et al., J. Phys. Chem. B jp104924g – paper here). In particular, they explore the sequence space of model polymers containing one or two pairs of charged monomers, in cases where the other monomers are more or less hydrophobic, and at the effect of adding salt to such systems. The results reveal subtle factors at play: for example, ion pairs among hydrophobic monomers can stabilize hairpin conformations over collapsed globules via water-mediated Coulombic interactions, but this depends on where the charged monomers appear along the chain. And adding salt can open up these hairpins, whereas salt stabilizes the globular forms of hydrophobic homopolymers.

Some membrane-binding proteins induce curvature of the membrane (see H. T. McMahon & J. L. Gallop, Nature 438, 590; 2005) – for example, the so-called BAR domain of amphiphysin will remodel lipid vesicles into tubules. Greg Voth and colleagues have performed MD simulations to try to figure out how this works, and they find that, surprisingly, there is a layer of water intervening between BAR and the membrane even when the protein domain is strongly bound (E. Lyman et al., Biophys. J. 99, 1783-1790; 2010 – paper here). This implies that the charged region of BAR is screened from the lipid headgroups, so that the bending mechanism is not electrostatic.

How homogeneous are solutions of denaturing guanidinium salts? Recently, Mason and coworkers have reported evidence that the cations form nanoscale aggregates (e.g. P. E. Mason et al., PNAS 100, 4557; 2003). Using dielectric relaxation spectroscopy, Richard Buchner of the University of Regensburg question this conclusion (J. Hunger et al., J. Phys. Chem. B jp101520h – paper here). In other words, perhaps after all Gdm+ ions can ‘fit’ comfortably into the structure of bulk water without altering it – which would seem to support the ‘direct’ mechanism of denaturation whereby Gdm+ interacts with the protein backbone rather than loosening up the folded state by influencing hydration.

More evidence for the direct intermediation of water in enzyme action: Sason Shaik at the Hebrew University of Jerusalem and colleagues say that a water cluster in the binding site of heme oxygenase participates in its ring-opening degradation of heme groups (W. Lai et al., JACS 132, 12960-12970; 2010 – paper here). The water cluster organizes the substrate into the proper geometry, serves as a proton shuttle, and stabilizes the hydroxyl nucleophile that attacks the ring. And Dongping Zhong at Ohio State University and colleagues say that flavoproteins, which act as redox coenzymes, contain water networks in the active site with fast relaxation dynamics that probably controls the protein flexibility in a functionally relevant manner (C.-W. Chang et al., JACS 132,12741-12747; 2010 – paper here). Meanwhile, Peter Brzezinski at Stockholm University and colleagues offer evidence that water molecules are involved in proton transport through cytochrome c oxidase, which actively pumps protons across a membrane to sustain a proton-motive force for ATP synthesis (H. J. Lee et al., JACS ja107244g – paper here).

Mischa Bonn of the FOM Institute AMOLF in Amsterdam and colleagues say that the hydration region of lipid headgroups in monolayers contains two populations of water molecules, one with bulk-like relaxation and the other that relaxes faster (M. Bonn et al., JACS ja106194u – paper here). Their VSF spectroscopic measurements thus imply the presence of a group of water molecules that are strongly hydrogen-bonded to the headgroups, decoupled from the bulk, and potentially involved in rapid, in-plane proton transfer, as previous studies have suggested for lipid membranes.

How does the hydration of antifreeze proteins differ from that of regular proteins? Ann McDermott and colleagues at Columbia use NMR methods to study this question by investigating the hydration shells of ubiquitin and an ice-binding (type III) antifreeze protein at cryogenic temperatures (-35 C) (A. B. Siemer et al., PNAS 10.1073/pnas.1009369107 – paper here). They find that the ubiquitin hydration shell remains unfrozen and uncoupled to the ice lattice, whereas this is true of only parts of the AFP III shell: as one might expect, the ice-binding interface establishes direct contact with ice.

The ability of sufficiently narrow carbon nanotubes to admit water but exclude ions has been proposed as a basis for desalination technologies. But Daejoong Kim and coworkers at Sogang University in South Korea show that admission or exclusion of ions can be a subtle business. They say that at certain nanotube diameters, strong sodium hydration can lead to a preferential admission of potassium ions over sodium in mixed ionic solutions, while at other diameters sodium can be preferred, or that both ions can be increasingly excluded even as the tube diameter increases (J. J. Cannon et al., J. Phys. Chem. B jp104609d – paper here). So it is conceivable that selective filtration and separation might be achieved. It seems quite conceivable that Ilan Benjamin’s new analysis of the hydration of alkali-metal halides in hydrophobic environments, and the formation of ion pairs (J. Phys. Chem. B jp1050673 – paper here), might be relevant here to the state inside the nanotubes.

Finally, bulk water, and a suggestion that the structural picture here is still not fully resolved. Peter Hamm at the University of Freiburg and colleagues use the theoretical tools developed for the study of complex networks (such as those in social science) to reveal hidden topological aspects of the H-bonded network in MD simulations of liquid water (F. Rao et al., J. Phys. Chem. B jp1060792 – paper here). They say this approach reveals structural inhomogeneities, extending at least to the second hydration shell, that are not evident from methods that focus on a single scalar order parameter such as tetrahedrality. Needless to say, the same technique might be used to look at solute hydration shells.

Water in cavities

2010-09-17T02:12:00.000-07:00

How hydration affects ligand binding in protein cavities is a subtle business. Not only is it still imperfectly understood, but it seems possible that it might be hard to generalize about how the various enthalpic and entropic effects of dehydration of the cavity and the ligand balance out. Yet such issues could be central to the rational design of drugs. Andrew McCammon at UCSD and his coworkers have used MD simulations to try to bring some order to the problem (R. Baron et al., JACS 132, 12091-12097; 2010 – paper here). They point out that both positive and negative entropy changes have been reported previously for water entering protein cavities, and that the result probably depends both on the chemistry and the geometry of the cavity. The key question, they rightly say, is: does water have a passive or active role in cavity-ligand recogniton? They investigate that question using an idealized cavity-ligand combination with various permutations of surface charges on both, looking to develop ‘thermodynamic profiles’ of the binding events. And indeed, the signs and magnitudes of the enthalpy and entropy changes prove to vary widely for the different cases (their Figure 6 tells the story). One finding is that, coincidentally, the net free energy change is similar both for binding driven electrostatically and by hydrophobic interactions.

Similar issues are explored by Hongtao Yu and Steven Rick at the University of New Orleans, who calculate the entropy, enthalpy and free-energy changes on transferring a water molecule from the bulk to various types of protein cavity large enough to hold only a single water (J. Phys. Chem. B 10.1021/jp104209w – paper here). They look in particular at the effects of having different numbers of H-bond donors and acceptors in the cavity. It is again not easy to generalize, but it seems that the thermodynamic consequences of H-bond formation are greater than those exerted, via entropic effects, by the cavity size.

More on how denaturants work, this time from Ilja K. Voets at the University of Fribourg and colleagues (J. Phys. Chem. B 10.1021/jp103515b – paper here). They use light scattering, SANS, NMR, IR and UV-Vis spectroscopy to study how the size and flexibility of the lysozyme molecule changes in a mixed water/DMSO solvent at varying compositional ratios. They see three regimes, in which the protein is compact, wholly unfolded, and partially unfolded, and deduce that there are three major factors influencing these conformational changes: changes in water’s H-bonded structure induced by DMSO, the propensity of DMSO to act as an H-bond acceptor, and DMSO’s role as a poor solvent for polar groups and the polypeptide backbone but a good one for apolar sidechains.

Meanwhile, Yi Qin Gao at Texas A&M and colleagues look at urea denaturation (H. Wei et al., J. Phys. Chem. B 10.1021/jp103770y – paper here). Here the big debate has been whether urea acts indirectly, via its effect on water’s H-bonded network, or directly by interactions with the protein backbone. This group proposed previously that it’s a bit of both. Now they take that idea further by looking at urea denaturation of the chicken villin headpiece protein and some of its mutants. They consider in particular how urea affects the breaking of backbone hydrogen bonds and the penetration of water into the hydrophobic core. In both respects, the influence of urea seems again to be both direct and indirect. For example, the presence of urea seems to enhance water penetration of the core (just as it has been found previously to enhance the hydration of the interiors of carbon nanotubes), and that this enhancement is correlated with binding of urea to the protein surface. Moreover, as the protein unfolds, the exposed hydrophilic regions are stabilized by binding of urea. It seems, then, that the denaturing action cannot be explained by a ‘physical effect’ so much as by a ‘narrative’ of the dynamical process.

The mechanism(s) of anti-freeze glycoproteins also continue to be debated, and Martina Havenith at Bochum and her colleagues raise the intriguing idea that they owe their protective role to an ability to perturb the collective dynamics of water over long ranges, retarding them in the extended hydration shell in a way that suppresses freezing (S. Ebbinghaus et al., JACS 10.1021/ja1051632 – paper here). This proposal, based on terahertz spectroscopic data for an anti-freeze glycoprotein from an Antarctic fish, is quite different from any other that I know of, and could be quite different from the way anti-freeze proteins work – unlike AFP, AFGPs are flexible and don’t have a well-defined structure, so probably do not operate by binding to the surface of ice crystals.

One of my finer moments in my former life at Nature was getting Reza Ghadiri’s work on cyclic peptide nanotubes published in 1993 in the face of scepticism during the review process. The work was soon vindicated, and these self-assembling tubes showed evidence of being able to mediate transport of dissolved species through lipid membranes. Jianfen Fan at Soochow University in Suzhou and colleagues have now used MD to investigate the mechanism of water diffusion through such pores (J. Liu et al., J. Phys. Chem. B 10.1021/jp1039207 – paper here). Water molecules form a linear chain threading a hexapeptide channel, but the H-bonded structure is increasingly three-dimensional for wider cyclic molecules. Understanding the transport process could be valuable for, say, the potential use of self-assembling channels like this in water purification and desalination.

The dynamics and evolution of such water ‘filaments’ in pores and other biological systems, such as lipid membranes, are studied by Marek Orzechowski and Markus Meuwly at the University of Basel, using MD simulations (J. Phys. Chem. B 10.1021/jp1051003 – paper here). Their medium is, however, not explicitly a biological one: it is a monolayer of alkylsilica chains about 1 nm thick, like those used in some chromatographic columns; and the solvent is a water/acetonitrile mixture. They find that water filaments, containing typically tens of molecules, form intermittently in the alkyl layer, and can persist for around 1 ns before being dispersed by thermal fluctuations.

The transition of lipid membranes from a gel to a liquid-crystal phase may significantly alter the membrane’s interactions with water and aqueous ions, say Tomasz Róg at the Tampere University of Technology in Finland and coworkers (M. Stepniewski et al., J. Phys. Chem. B 10.1021/jp104739a – paper here). Both phases might exist in vivo, although the LC phase is the usual one. The authors’ simulations show that in the gel phase the lipid headgroups are partially dehydrated and sodium ions cannot penetrate to the interfacial region to bind to the carbonyl groups.

A new method for estimating hydration free energies of organic molecules with an implicit solvent is described by Maxim Federov of the MPI for Mathematics in the Sciences in Leipzig and coworkers (E. L. Ratkova et al., J. Phys. Chem. B 10.1021/jp103955r – paper here). It’s a modification of the RISM model of Chandler and Anderson, which provides a reasonably computationally cheap way of accounting for solvent structure along with some empirical parametrization of the solvation of specific chemical functionalities (alkyl, hydroxy, carbonyl etc.), ‘trained on’ and tested with small organics. No indication of whether it might be extended to macromolecules, although the authors intend to try it on bioactive compounds.

But the method for predicting hydration structures outlined by Karl Freed at Chicago and colleagues is explicitly geared towards proteins (J. J. Virtanen et al., Biophys. J. 99, 1611-1619; 2010 – paper here). They use simulations of the hydration of ubiquitin, lysozyme and myoglobin to calculate electron radial distribution functions for the different atom types, and then show that these can be used to generate electron densities – and from them, hydration structures – for other proteins. The electron distributions can also be used to calculate X-ray scattering intensity, and the authors intend to use this in future work to compare their predictions with experiment.

It’s the absence of water in the core of the ‘alpha-solenoid’ protein importin-beta that gives this spring-like molecule its astonishing elasticity, according to Helmut Grubmüller and colleagues at the MPI for Biophysical Chemistry in Göttingen (C. Kappel et al., Biophys. J. 99, 1596-1603; 2010 – paper here). Specifically, their simulations indicate that the hydrophobic core has a molten-globule-like conformation that governs its mechanical properties. As such, the protein occupies a middle ground between fully folded and intrinsically disordered, showing how what one might call ‘secondary unstructure’ determined by hydrophobicity allows fine-tuning of a biologically relevant physical property.

And not really ‘water in biology’ at all, but a neat experiment on water at a hydrophilic (mica) surface is reported by Jim Heath at Caltech and colleagues (K. Xu et al., Science 329, 1188-1191; 2010 – paper here). They deposit graphene sheets on mica, and observe islands on the surface with the AFM that appear to be water monolayers ‘sealed in’ by the graphene. These often have faceted edges, suggesting that they are ice-like even at room temperature, and they may be nucleated at surface defects. At 90 percent humidity a water monolayer appears to cover the entire mica surface, and a second adlayer may grow patchily on top.

Some hows and whys of protein folding

2010-08-16T05:46:00.000-07:00

Why do small proteins have such a wide range of folding times? Hue Sun Chan and colleagues at the University of Toronto make a case, using MD simulations, that a critical factor in folding time is the desolvation barrier (A. Ferguson et al., J. Mol. Biol. 389, 619-636; 2009 – yes, an ‘old’ paper, but one I fear I overlooked at the time; paper here). For simulations of 13 proteins, they find that the folding rates span two orders of magnitude if desolvation barriers are not included, but 4.6 orders with those barriers added, which is closer to the range seen experimentally. Moreover, folding in the presence of these solvation effects becomes more cooperative and more channelled, and at the same time sensitive to the native protein’s topological complexity. In other words, if you want to understand protein folding, you probably need explicit water.

Ionizable groups are in a sense ‘incompatible’ with the hydrophobic interiors of proteins, and destabilize the native state, but are nonetheless sometimes found there. Daniel Isom and colleagues at Johns Hopkins consider why (D. G. Isom et al., PNAS 10.1073/pnas.1004213107 – paper not yet online). They do so via mutagenesis experiments that introduce Glu groups into internal hydrophobic sites in staphylococcal nuclease, and measure their pKa values and the effects on protein stability. The Glu groups are accommodated without any major conformational reorganization, suggesting that the protein interior shields the charges surprisingly well, behaving like a material with high dielectric constant. It’s not clear why, although penetration of water is one possibility. Whatever the reason, the results suggest that proteins have somehow (and for some reason) evolved a substantial stability against the internalization of charged groups (albeit with sufficient intolerance not to incorporate them indiscriminately).

Cryoprotectants such as trehalose are also produced by some organisms as a defence against dehydration rather than freezing. But it’s not clear how this protection works. One popular idea is that the sugar simply replaces water molecules hydrating the polar groups of lipids in membranes, or of proteins, maintaining the biomolecules and their aggregates in a fluid state in the face of dehydration. For membranes, the aim must be to prevent the formation of a gel state during dehydration, since this leads to detrimental leakage upon rehydration. This notion is examined by Roland Faller at UC Davis and colleagues using MD simulations (E. A. Golovina et al., Langmuir 26, 11118-11126; 2010 – paper here). They find that the core tenets of the water-replacement hypothesis – replacement of water with trehalose, avoiding a transition to the membranes’ gel state – are borne out, but that the structure of the membrane is different in the presence of trehalose than when fully hydrated.

The precise nature of (charged) lipid hydration is studied by Tahei Tahara and colleagues at RIKEN’s Advanced Science Institute in Saitama, using vibrational sum-frequency generation (J. A. Mondai et al., JACS 10.1021/ja104327t – paper here). They aimed to resolve a discrepancy between hydrogen-down and hydrogen-up water orientations at the interface reported from earlier experiments and simulations, and find that the former seems to hold for cationic lipids and the latter for anionic ones – which I guess is what one would expect on the most simplistic electrostatic grounds.

Manuel Aguilar and colleagues in Spain and Mexico report on MD simulations of the hydration of the tripeptide Cys-Asn-Ser (C. Soriani-Correa et al., J. Phys. Chem. B 114, 8961-8970 (2010) – paper here). Hydration stabilizes a more extended structure of the tripeptide than in the gas phase, owing to the replacement of intramolecular hydrogen bonds with intermolecular ones to water molecules.

Sorin Lusceac and Michael Vogel at the TU Darmstadt use deuterium NMR to investigate water dynamics in the hydration shell of myoglobin in the region of the 200-220 K dynamical crossover (J. Phys. Chem. B 10.1021/jp103663t – paper here). They observe a gradual change from isotropic to anisotropic rotation as the temperature is lowered from around 230 K. At that temperature the hydration water has access to essentially a continuum of orientational states, while by 165 K it can adopt only a few, maybe two. But this change is gradual: there is no sign of a sharp phase transition around 225 K, which has previously been claimed as the temperature of an abrupt fragile-to-strong transition.

Hydration-water dynamics as a function of protein concentration at ambient temperature are studied by Stephen Meech and coworkers at the University of East Anglia using the ultrafast optical Kerr effect, which can probe picosecond time scales (K. Mazur et al., J. Phys. Chem. B 10.1021/jp106423a – paper here). Below 0.4M peptide concentration (for three dipeptides), the water dynamics are slowed (particularly for hydrophilic peptides) but the water retains a primarily tetrahedral geometry. Above this concentration the dynamics are slower still and the tetrahedral network is perturbed, presumably due to intermolecular H-bonding between the peptides.

In fact, David LeBard and Dmitry Matyushov at Arizona State University argue on the basis of numerical simulations (of three globular proteins) that protein hydration shells have sufficient average orientational ordering among the water molecules to constitute a ferroelectric shell that propagates 3-5 molecular layers into the solvent (J. Phys. Chem. B 114, 9246-9258; 2010 – paper here). They argue that this is consistent with THz dielectric measurements, and say the dynamics are dominated by a slow (nanosecond) component that freezes at the protein’s dynamical transition.

Fluorescent molecules are sometimes used to probe the dynamics of DNA and its hydration sphere. For example, coumarin can be inserted into the double helix in place on an entire base pair, attached to one strand while the other is simply without a base. But as Kristina Furse and Steven Corcelli of the University of Notre Dame point out, this is a non-trivial substitution. So they have used MD to investigate how much this substitution perturbs the native state of DNA and its surrounding water molecules and ions (J. Phys. Chem. B 10/1021/jp105761b – paper here). They find that the effects can be significant – widening of the minor groove, increased flexibility, and increased water mobility. They conclude that this is not a reliable way to study, for example, the highly constrained water in DNA’s minor groove.

Melanin pigments are widely distributed in living organisms – in humans they appear in skin, hair, eyes, brain and liver. Their macromolecular structures are still not fully characterized, but seem to be highly dependent on hydration: water fills the slit-like pore regions between stacked graphitic plates in the pigment aggregates. Maria Grazia Bridelli and Pier Raimondo Crippa at the University of Parma use FTIR spectroscopy to look at this water in melanins under different degrees of hydration (J. Phys. Chem. B 10.1021/jp101833k – paper here). They suggest that the traditional picture of water in melanins being divided into relatively labile and tightly bound fractions is simplistic, and that in fact the distribution of adsorption sites is very heterogeneous, with a large pore size dispersion, and the water environments ranging continuously from highly bound in small pores to more or less bulk-like.

Hua Guo at the University of New Mexico in Albuquerque and coworkers have previously reported a ‘promoted-water’ mechanism, involving an active-site bound water molecule, for the action of carboxypeptidase A (CPA) in proteolysis (D. Xu & H. Guo, JACS 131, 9780; 2009). Now, using quantum MD simulations, they find something similar for the CPA-catalysed cleavage of esters (S. Wu et al., J. Phys. Chem. B 114, 9259-9267; 2010 – paper here). An alternative, ‘anhydrous’ nucleophilic mechanism seems to be ruled out for proteolysis, and the authors say that while it is feasible for esterolysis, it has a considerably higher free-energy barrier than the promoted-water pathway.

Hofmeister effects get subtler the harder you look. The series is reversed, say Pavel Jungwirth and colleagues in Prague and Lund, when ammonium halides are substituted by tetraalkylammonium cations (J. Heyda et al., J. Chem. Phys. B 10.1021/jp101393k – paper here). This effect is predicted by their MD simulations, and confirmed by experiment, and may be rationalized from a consideration of the different hydration structures of the cations.

Dissolved salts seem generally to increase water’s surface tension, and in ways specific to particular anions and cations that mirror the respective Hofmeister effects. Why? Irving Langmuir suggested that there is ion depletion at the interface; now we know that the effects may be subtle, especially at hydrophobic rather than free interfaces. Yan Levin and colleagues in Brazil have a shot at developing a first-principles theory based on an electrostatic approach to calculating Gibbs adsorption isotherms for the ions (A. P. dos Santos et al., Langmuir 26, 10778-10783; 2010 – paper here). They say that ‘kosmotropic’ (I know) anions are depleted at the interface, while chaotropic anions are absorbed (the theory is actually, as far as I can see, silent about the actual hydration structures of the ions). It predicts well the observed trends in surface tensions seen for the corresponding sodium salts.

Amphiphilic proteins tend to segregate to the air-water interface. Berk Hess of the MPI Mainz and colleagues say that the key driving force for small peptides of this type is the dehydration of hydrophobic residues, and that the effect scales linearly with the size of the molecules (O. Engin et al., J. Phys. Chem. B 10.1021/jp1024922 – paper here).

Roumiana Tsenkova at Kobe University and colleagues have proposed that studying water dynamics in biological systems using near-IR spectroscopy can provide a way of monitoring changes in an organism’s biological state – a method they call ‘aquaphotomics’ (see R. Tsenkova, J. Near Infrared Spectrosc. 17,303-313; 2009). They now propose that the technique can identify infection of soybean leaves with soybean mosaic virus in vivo, two weeks before the normal visual signs of infection in the plant (B. Jinendra et al., Biochem. Biophys. Res. Commun. 397, 685-690; 2010 – paper here). Two new NIR bands in the water region turn out to be highly sensitive to infection. The mechanism seems unclear; the authors say only that the virus seems to alter hydration hydrogen-bonded structures in a way that brings the water closer to bulk-like.

Another coarse-grained model for water is presented by Qiang Cui and colleagues at Wisconsin-Madison (Z. Wu et al., J. Phys. Chem. B 10.1021/jp1019763 – paper here). This groups four water molecules into a single site, represented as three electrostatic charges (which approximate the cluster’s dipole and quadrupole moments) and a non-electrostatic ‘soft’ interaction. The model is, however, optimized for the bulk and is considered unlikely to be applicable to ice; one imagines the same might be true of hydration structures in which local cluster geometries are non-bulk-like. A simple, computationally cheap model geared specifically to hydration is offered by Piotr Setny and Martin Zacharias (J. Phys. Chem. B 10.1021/jp102462s – paper here), in which solute-solvent and solvent-solvent interaction energies are calculated in a mean-field approximation on a BCC grid. The model performs well for predicting hydration energies of some drug molecules and for reproducing buried-water distributions in proteins.

I recently came across a nice review article by Felix Sedlmeier, Roland Netz and colleagues at TU Munich on ‘water at polar and nonpolar solid walls (F. Sedlmeier et al., Biointerphases 3(3), FC23-FC39 (2008) – paper here), which looks at what MD simulations have to tell us about statics, dynamics, rheology and so forth. And on this topic, Shu Nie and coworkers at Sandia Labs describe, on the basis of scanning tunnelling microscopy studies, an intriguing interfacial structure for a wetting water layer on Pt(111), in which the ice-like bilayer commonly reported is modified due to the appearance of 5-and 7-membered rings in the first wetting layer (S. Nie et al., Phys. Rev. Lett. 105, 026102; 2010 – paper here).

Water channels and flu resistance

2010-07-06T01:30:00.000-07:00

What happens to hydrophobic interactions in the presence of charge? Bruce Berne and colleagues at Columbia have used MD simulations to explore that question (L. Wang et al., J. Phys. Chem. B 114, 7294-7301; 2010 – paper here). They find that the binding affinity of a hydrophobic particle to a hydrophobic plate, when it is placed between two such plates, is decreased if the plates are charged. Indeed, with increasing charge density the plates can become hydrophilic-like, expelling the particle from the interplate region.

Allan Friesen and Dmitry Matyushov at Arizona State University have considered the polarity of the interface between water and hydrophobic particles, which they model as hard spheres surrounded by a Lennard-Jones layer (arxiv.org/1004.1728 – paper here). (They call these particles, a little confusingly, ‘cavities’, presumably because they open up cavities in the solvent.) They find that there is a significant increase in the local polarity of the water at the interface, meaning that any charges in the solute particle are significantly screened. Moreover, dipolar relaxation in the first hydration shell is slowed significantly, with a relaxation time of around 50 ps.

Hirofumi Sato and colleagues at Kyoto University have used an approach called multicentre molecular Ornstein-Zernicke equation theory to calculate the hydration structure of bacteriorhodopsin (and a simpler serine coiled coil) (K. Hirano et al., J. Phys. Chem. B 114, 7935-7941; 2010 – paper here). I’ve not come across this method and don’t fully understand it – I’m rather surprised that a first-principles method like this, using the O-Z equation, can be applied to such a complex system. But given that it is 20 years since I last set eyes on the O-Z equation, it is very probable that I’m behind the times. In any event, the authors say that the solvent distribution they calculate agrees well with that found from XRD, and they can pull out the relative strengths of the hydrogen-bonding interactions, for example of the bound water molecules close to the Schiff base of bR.

The efficacy of the antiflu drug amantadine (AMT) is undermined by resistance that has been reported as developing in influenza A. A possible mechanism of resistance is documented by Kunqian Yu of the Shanghai Institute of Materia Medica and colleagues (G. Qiu et al., J. Phys. Chem. B 114, 8487-8493; 2010 – paper here). Their MD and quantum molecular mechanics calculations indicate that AMT binds in the pH-gated proton channel M2, as indeed it was designed to do. Here the drug disrupts a water wire that allows protons to cross the pore, and thereby inhibits its function. But AMT can occupy different positions in the channel, and in the resistant mutant SN13 it binds at a site that does not ‘snip’ the water wire: protons can still get through.

In photosystem II, water acts as a ligand, which is oxidized by a Mn4Ca cluster. It’s not been clear exactly where this water is bound, and that is what Robert Stranger and colleagues at ANU set out to establish using density functional calculations (S. Petrie et al., Angew. Chem. Int. Ed. 49, 4233-4236; 2010 – paper here). They find six waters bound close to the Mn cluster through the catalytic cycle, of which the two substrate waters fit in a cleft between two Mn atoms and the Ca.

The thermodynamics and kinetics of water confined between hydrophobic plates is investigated using MD with a simple monoatomic water model by Limei Xu and Valeria Molinero (J. Phys. Chem. B 114, 7320-7328; 2010 – paper here). They consider the conditions under which drying is induced, and look at the marginal situation in which there are rapid fluctuations between a wet and dry state. One obviously has to ask to what extent the quantitative conclusions here would apply to more sophisticated water potentials, but I’m also left to wonder whether the authors have really made proper contact with the vast earlier literature on liquid-vapour phase transitions in confined systems.

Shiang-Tai Lin at the National Taiwan University and colleagues present a method for calculating the entropy and energy of molecular liquids from the trajectory of MD simulations, which they apply to water using various potentials (S.-T. Lin et al., J. Phys. Chem. B 10.1021/jp103120q – paper here). They show that the technique has rapid convergence: these thermodynamic quantities can be computed from just 10 ps of simulation time.

Evan Williams and colleagues at Berkeley have used infrared photodissociation spectroscopy to investigate water-structuring effects of sulphate ions hydrated within clusters of up to 80 water molecules at 130 K (J. T. O’Brien et al., JACS 10.1021/ja1024113 – paper here). They present these results within the context of ‘structure-making and –breaking’ in the Hofmeister series, although naturally it is an open question to what extent the structures seen here reflect those in bulk solution at ambient temperatures. They say they see the spectral signature of bulk-like water – or more precisely, of free OH groups at the cluster surfaces analogous to those at the bulk surface – for clusters with more than about 43 water molecules, equivalent to the third solvation shell. The authors say that in fact their results imply that, although a sulphate ion ‘patterns’ water molecules ‘to a distance much farther than the first solvation shell’, this does not alter the number and strength of the hydrogen bonds beyond the first shell. But it is not really clear what the consequences for Hofmeister effects are, beyond the suggestion by Williams et al. that experiments that probe only rotational dynamics may miss some of the more subtle ‘patterning’ (presumably ordering) effects evident in this spectroscopic study.

Andrei Sommer and his colleagues have extended their previous investigations of the anticancer effects of red light and green tea (thought to be operating via photo-induced changes in the ordering of interfacial water – see here) (A. P. Sommer et al., Photomed. Laser Surg. 28, 429-430; 2010 – paper here). They find that the two things administered together retard the growth of HeLa cells. The mechanism remains speculative.

MD simulations with explicit water are computationally intensive, for which reason Piotr Setny and Martin Zacharias at the TU Munich have developed a computationally efficient way to model hydration (J. Phys. Chem. B 10.1021/jp102462s – paper here). It is a lattice cellular automaton that calculates solute-solvent and solvent-solvent interaction energies using a mean-field approach, which can calculate whether a particular grid cell at the solute surface is hydrated. It performs well in terms of predicting hydration energies for drug molecules, as well as locating buried water molecules in cavities.

Water molecules passing through carbon nanotubes can be pulled by methane molecules across the potential barriers created by tapering junctions where two tubes of different radii are joined, according to simulations by H. Li at Shandong University in Jinan, China, and colleagues (H. Q. Yu et al., J. Chem. Phys. B 10.1021/jp102810j – paper here). The ‘dragging’ effect is mediated by van der Waals interactions, they say.

Drying-induced pore gating?

2010-06-09T03:09:00.000-07:00

Morten Jensen and colleagues at D. E. Shaw Research in New York show using MD simulations of a potassium channel that hydrophobic gating – dewetting transitions in the hydrophobic pore interior – appear to be a viable mechanism for these and perhaps many other ion channels (M. Ø. Jensen et al., PNAS 107, 5833-5838; 2010 – paper here). This is one of the most persuasive cases I’ve seen for this very interesting possibility, building as it does on the full atomistic structure of the pore protein.

S. Khodadadi at Akron and colleagues have an interesting paper about the hydration of tRNA (Biophys. J. 98, 1321-1326; 2010 – paper here). They use neutron scattering and dielectric spectroscopy to measure the hydration dynamics of this molecule, and find that these are slower than those for typical proteins, but faster than DNA. This, they say, challenges the ‘slaving’ hypothesis, ‘which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water’. But is that really what it assumes? People have written various things about this, and I’d have to go back and check the papers they cite, but I’d not understood ‘slaving’ to mean something quite so simple – rather, it implies only that the dynamics of the solute and solvent are interdependent. Certainly, I don’t know that anyone would suggest the dynamics of hydration water are bulk-like and unaffected by the nature of the macromolecule. Still, interesting results.

As Thomas Elsaesser at the Max Born Institute in Berlin point out (L. Szyc et al., J. Phys. Chem. B 10.1021/jp101174q – paper here), the residence times of hydration water molecules around DNA actually show an analogously broad distribution to those around proteins, and fluctuations in the hydrogen-bond network happen on fast (fs to ps) timescales. They have looked at how vibrational energy pumped into the phosphate groups gets redistributed into DNA’s hydration shell, which acts as a heat sink. This happens quickly too: within a few fs, while energy transfer within the DNA molecule is slower (timescales around 20 ps).

Returning to proteins, Stefania Perticaroli and colleagues at Perugia find using depolarized light scattering that the water dynamics in dilute solutions of lysozyme display two distinct timescales: fast (>ps) bulk-like relaxation, and slow (a few ps) due to hydration water (S. Perticaroli et al., J. Phys. Chem. B 10.1021/jp101896f – paper here).

One possible mechanism for the operation of antifreeze proteins is to bind to the surface of ice crystallites and stop them growing further. According to Knight and DeVries, this should also imply that the AFP’s should inhibit the melting of ice. Yeliz Celik at Ohio University and colleagues have presented experimental evidence for this (PNAS 107, 5423-5428; 2010 – paper here). They find that ice can be superheated up to 0.44 C in AFP solutions.

Does the electric field at a charged surface induce an ice-like hydrogen-bonding pattern in water? No, accortding to Tahei Tahara and colleagues at RIKEN’s Advanced Science Institute in Saitama, Japan (S. Nihonyanago et al., JACS 132, 6867-6869; 2010 – paper here). They use a form of vibrational sum frequency generation spectroscopy to look at the water structure in the Gouy-Chapman layer at the surface of a charged lipid monolayer, and say that it looks bulk-like.

Well, by this measure perhaps. But FT-IR and DSC measurements of water confined between lamellar bilayers of AOT surfactant suggest that the water here has three components: some is bulk-like, some closely linked to the surfactant head groups, and a layer about 0.5 nm between the two where the bulk H-bond network is disrupted (E. Prouzet et al., J. Phys. Chem. B 10.1021/jp101176v – paper here).

Another nice example of water in the active site playing a key role in enzymatic activity: Karol Kaszuba at the Tampere University of Technology in Finland and colleagues say that water in the binding site enables the high stereoselectivity of a beta-adrenergic receptor, a potential target for beta-blockers, by mediating H-bonding interactions between different enantiomers of the beta-blocker nebivolol (K. Kaszuba et al., J. Phys. Chem. B 10.1021/jp909971f – paper here).

Many simulations have shown single-file filling of and transport through carbon nanotubes. Now Wim Wenseleers and colleagues at Antwerp claim to have seen this experimentally for the first time (S. Cambré et al., Phys. Rev. Lett. 104, 207401; 2010 – paper here). They see the signature of such behaviour in the splitting of a Raman mode, for nanotubes of diameters down to 0.548 nm. But interestingly, the details of the filling (as revealed by the Raman shift) shows a complex, non-monotonic dependence on diameter, owing to variations in tube chirality.

Martina Havenith at Bochum and her coworkers have been using THz spectroscopy to reveal some interesting new features of hydration. Now she, Dominik Marx and their colleagues have used MD simulations to figure out precisely what manner of intermolecular motions are being probed by this technique (M. Heyden et al., PNAS 10.1073/pnas.0914885107 – not yet online). They conclude that ‘a modification of the hydrogen-bond network, e.g. due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules’ – and that this spectroscopy particularly probes strongly correlated molecular motions.

Here’s something that should stir up discussion: J. Raúl Grigera and Andres McCarthy in Argentina have conducted MD simulations of the pressure induced denaturation of proteins such as lysozyme and apomyoglobin, and say that they think the unfolding is caused by weakening of hydrophobic interactions owing to a change in water structure (weakening of the H-bonding network) (Biophys. J. 98, 1626-1631; 2010 – paper here). Other studies have tended to emphasize the penetration of water into the hydrophobic interior. Besides my now almost knee-jerk suspicion of explanations invoking ‘water structure’, I am forced to wonder, first, if such changes would be profound enough at the kbar pressures used here, and second, to what extent the hydrophobic interaction is really dependent on the H-bond network as opposed to being a more general solvophobic effect.

Nanobubbles – ah, one day I hope to bring together the various and diverse findings reported about their behaviour. In some studies (e.g. Jin et al., J. Phys. Chem. B 111, 2255; 2007), it has been claimed that nanobubbles will form in mixtures of non-aqueous solvents (that have some amphiphilic properties) with water. That notion is investigated by Xuehua Zhang and coworkers at the University of Melbourne (A. Häbich et al., J. Phys. Chem. B 114, 6962-6967; 2010 – paper here). They find that the behaviour of such mixtures is inconsistent with light scattering by bubbles (for example, there is no change in scattering on degassing), and they attribute the scattering instead to the presence of impurities.

Microbubbles are the focus of a study by Derek Chan, also at Melbourne, and colleagues (I. U. Vakarelski et al., PNAS 10.1073/pnas.1005937107; paper here). They use AFM measurements to look at the factors that influence bubble coalescence, particularly the hydrodynamic interactions between microbubbles. Curiously, they say that the hydrodynamics can induce a dynamic coalescence mode which operates as two bubbles separate.

Going back to January, Jan Swenson and colleagues at Chalmers University of Technology in Sweden claim to have identified a slow relaxation process in water (four orders of magnitude slower than the normal viscosity-related relaxation) due to collective motions of the hydrogen-bonded network (H. Jansson et al., Phys. Rev. Lett. 104, 017802; 2010 – paper here). They say that this type of relaxation has been identified before in mono- and polyalcohols, such as glycerol (R. Bergman et al., J. Chem. Phys. 132, 044504; 2010). The researchers see it in water in measurements of the dielectric response. They can’t really say much yet about what causes it, although the suggested connection to the ‘chain-like’ structures proposed by Huang et al. (PNAS 106, 15214; 2009) is speculative in the extreme.

See also Jan’s recent paper with José Teixeira (J. Chem. Phys. 132, 014508; 2010 – paper here) on the relaxation behaviour of supercooled water through the no-man’s-land between 150 and 235 K. They propose a crossover between cooperative α-relaxation at higher temperatures and ‘local’ β-relaxation at low temperatures.

Also, I don’t believe I mentioned previously a paper by Alenka Luzar and colleagues published last November (Phys. Rev. Lett. 103, 207801; 2009 – paper here) on the dynamics of alignment of a hydrated nanoparticle in an electric field. This process is important for applications such as dielectrophoresis and the electrical control of optical properties. Using MD simulations, the researchers conclude that the torque exerted by a typical experimentally realizable field strength is greater than kT (so alignment is possible even at the nanoscale) and greater than that estimated using continuum methods. Moreover, the alignment times are fast – of the order of a few hundred picoseconds.

Greg Voth and colleagues run a check on the self-consistent charge density functional tight binding (SCC-DFTB) method that has been used for quantum simulations of water in various systems, including some biological ones (C. M. Maupin et al., J. Phys. Chem. B 114, 6922-6931; 2010 – paper here). They look at what the method predicts for hydrated protons, and find that it puts the excess proton in a Zundel ion (H5O2+) in the resting state – unlike some other quantum chemical methods, and in contrast to what experiments have suggested. This presumably raises questions about the validity of the method.

Brad Bauer and Sandeep Patel at the University of Delaware also present a kind of model validation study for different water potentials, looking at how these affect the hydrophobic attraction of two flat plates (J. Phys. Chem. B 10.1021/jp101995d – paper here). They find that while many of the structural and dynamic aspects are the same for all the potentials studied – average density, fluctuations, hydrogen bonding – the potential of mean force for attraction between the plates is reduced when the water is polarizable.

Another validation study for simulations of biomolecules is described by Klaus Liedl at Innsbruck and colleagues (J. Phys. Chem. B 114, 7405; 2010 – paper here). They look at how simulations of the X-ray structure of the protein fXa, a key enzyme in blood coagulation, are affected by different choices of sets of water molecules in the hydration sphere. They conclude that only by judicious placement of water molecules around the protein, using available crystal structure data, will ensure a reasonable sampling of phase space when studying the protein’s dynamics. Otherwise, the simulations may take an unfeasible time for the hydration environment to equilibrate. One can’t, apparently, just plunge the protein into a bulk-like solvent environment and assume that it’ll find its own way to the right hydration structure.

A few more to come, but this is enough for now.

Two announcements of publications:
There is a special volume of the Journal of Electron Spectroscopy and Related Phenomena (177 (2-3), March 2010) devoted to water and hydrogen bonds investigated through inner-shell spectroscopies.
And the long-overdue collection of papers stemming from a conference on ‘water and life’ in Varenna in 2005 is now out:
Water and Life: The Unique Properties of H2O, eds Lynden-Bell, Ruth M., Conway Morris, Simon, Barrow, John D.,Finney, John L., and Harper, Charles L., Jr. Boca Raton, Florida: CRC Press / Taylor & Francis Group, 2010. More details here. I just received my copy, and it looks still relevant despite the long delay in publication.

Another catch-up

2010-04-28T02:19:00.000-07:00

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.

Denaturants again

2010-02-16T01:26:00.000-08:00

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.

The post-Christmas glut

2010-02-02T02:28:00.000-08:00

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.

How do spores survive?

2009-11-06T16:04:00.000-08:00

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.

Water in drug design... and why green tea keeps you young?

2009-09-29T04:33:00.000-07:00

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.

Nanobubbles: birth, motion, and consequences

2009-08-25T15:18:00.000-07:00

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.

How proteins loosen up

2009-07-27T04:36:00.000-07:00

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.

Small molecules and protein folding

2009-06-22T00:53:00.000-07:00

The role of small molecules – denaturants and osmolytes – in protein folding is much in need of a good review article (or have I missed one?). Julio Fernández and colleagues have used single-molecule force spectroscopy to look at how the osmolyte glycerol interacts with ubiquitin as the protein is mechanically unfolded (S. Garcia-Manyes et al., PNAS 10.1073/pnas.09020106 – not yet online). Glycerol stabilizes the protein against unfolding, and apparently also promotes hydrophobic collapse of the unfolded conformation. They think that while glycerol stabilizes the folded state via direct interaction with the protein, ethanol seems to exert a weaker stabilizing effect via an indirect interaction involving the disruption of ‘water structure’. The promotion of hydrophobic collapse in the presence of glycerol (which is not seen for ethanol) seems to be a separate effect, perhaps due to the enhanced destabilization of exposed hydrophobic surface due to the polar surface area of glycerol.

The electronic state of water molecules confined in a close-packed rodlike micelle lattice is significantly different from that in the gas and bulk liquid phases, according to Jan-Erik Rubensson and colleagues at Uppsala University (J. Gråsjö et al., J. Phys. Chem. B 113, 8201; 2009 – paper here). They have probed this question using soft X-ray absorption and emission, and say that the water molecules among micelles are stabilized relative to the bulk, perhaps because of interaction with the chloride counterions in solution.

Pablo Debenedetti and coworkers have also studied nanoconfined water, here in a slit-like space between two hydrophilic silica surfaces using MD simulations (S. R.-V. Castrillón et al., J. Phys. Chem. B 10.1021/jp9025392 – paper here). They find rotational slowing within 0.5 nm of the surfaces, and translational slowing within 1 nm.

The difference in hydrophobic interactions in acidic solutions relative to salt solutions is investigated by Greg Voth and colleagues (H. Chen et al., J. Phys. Chem. B 113, 7291; 2009 – paper here). They say that in acid (HCl) solution they see interactions between the hydrophobe surface and the hydrated protons, owing to the amphiphilic character of the latter. This could explain why hydrated protons are anomalous in the Hofmeister series, promoting solubilization of nonpolar solutes despite having a similar radius to salting-out cations such as potassium and ammonium.

And on matters Hofmeister, Bernd Rode and colleagues at the University of Innsbruck have carried out quantum simulations of the hydration of beryllium ions, and find that the tetrahedral first hydration shell has very slow exchange dynamics (S. S. Azam et al., J. Phys. Chem. B 10.1021/jp903536k – paper here). They refer to this as a strong ‘structure-forming’ behaviour – I can see what they mean, but does it invite confusion with the already confused issue of ‘structure-making’?

The dynamic Stokes shift – the slower decay of a frequency-shifted fluorescent probe molecule – close to protein surfaces relative to the bulk solution has been attributed in the past to much slower water motions in the hydration shell. But Bertil Halle and Lennart Nilsson question this interpretation in a new paper (J. Phys. Chem. B 113, 8210; 2009 – paper here). They say that the slower decay can be understood by a solvent polarization effect, and does not probe hydration dynamics at all.

Zoran Arsov at the Josef Stefan Institute in Ljubljana and colleagues report the weakening of hydrogen bonds in water confined between lipid bilayers, using a form of FTIR (Z. Arsov et al., ChemPhysChem 10.1002/cphc.200900185 – paper here). The water films separating bilayers in the lamellar phases (phospholipids DMPC and POPE) studied here are very thin – 2 and 0.6 nm respectively. So a disruption of bulk structure is presumably to be expected. They suggest that this perturbation may contribute to the attractive hydration force between the bilayers.

There has been a long debate, going back to Faraday and Tyndall, on whether ice has a liquid-like layer on its surface and if so, what this looks like. Xiao-Yang Zhu and colleagues at Minnesota have investigated this with interfacial force microscopy (M. P. Goertz et al., Langmuir 10.1021/la9001994 – paper here). They see a liquid-like layer tens of nanometres thick, but suggest that it is in fact viscoelastic.

More catching up

2009-06-16T01:45:00.000-07:00

Changes in my circumstances have delayed this one, and of course the longer I delay, the worse it gets. I bring things somewhat up to date here, but there’s still more to come.

First, an ad: there is an RSC Faraday Discussion on ‘Wetting Dynamics of Hydrophobic and Structured Surfaces’ in Richmond, Virginia on 12-14 April 2010. Given the list of organizers and invited speakers, it is sure to be very good. Details are here.

More on water flow inside carbon nanotubes, which is attracting increasing interest because of the possibilities for water purification and desalination. John Thomas and Alan McGaughey at Carnegie Mellon find in MD simulations that the water structure changes significantly for tubes of 0.83 to 1.39 nm – from single chains to stacked pentagons and hexagons and finally to bulk-like (Phys. Rev. Lett. 102, 184502; 2009 – paper here). This seems to significantly affect the (pressure-driven) flow velocity in a non-monotonic way, particularly when the liquid has a layer-like profile.

Thomas Angel and his coworkers have looked at the roles of water molecules in photosensitive rhodopsin-like G protein-coupled receptors (T. E. Angel et al., PNAS 10.1073/pnas.0903545106 – paper here). They find that waters associated with highly conserved residues seem to be crucial to function, in particular providing the plasticity needed to transmit a signal from the retinal binding pocket to the intracellular surface.

Sow-Hsin Chen and coworkers find, using QENS, that lysozyme remains flexible (‘soft’) at low temperatures (210-240 K) when moderate pressure (around 1 kbar) is applied (X.-q. Chu et al., J. Phys. Chem. B 10.1021/jp900557w – paper here). Surprisingly, the dynamics under these conditions are actually faster than those under ambient conditions, and reflect those of the hydration water.

And speaking of low-temperature environments, David Wharton and Craig Marshall have outlined some of the survival strategies of Antarctic organisms in a nice brief review in J. Biol. 8, 39; 2009 – paper here. And Todd Sformo at the University of Alaska at Fairbanks has told me about a very interesting paper reporting an Arctic gnat that simultaneously uses freeze tolerance and freeze avoidance in different parts of its body – these strategies are usually mutually exclusive (T. Sformo et al., J. Compar. Physiol. B: Biochem. System. Envir. Physiol. 10.1007/s00360-009-0369-x; 2009 - paper here. (You see, this is the kind of nice stuff I fear I’m missing all the time…)

Huib Bakker’s group has used THz and femtosecond IR spectroscopy to study proton hydration (K. J. Tielrooij et al., Phys. Rev. Lett. 102, 198303; 2009 – paper here). They find that protons induce a drop in dielectric constant corresponding to an effect on 19 water molecules per proton. Four of these are involved in direct solvation, being irrotationally bound to the proton, but the others are perturbed by becoming implicated in proton motion.

Staying with proton transport, Greg Voth and colleagues have used the MS-EVB method to look at proton transfer in human carbonic anhydrase II (C. M. Maupin et al., JACS 10.1021/ja8091938 – paper here). The proton transfer here, between a zinc-bound OH group and the His64 residue, is the rate-limiting step, and involves a water cluster in the active site. There are some insights here into the ways proteins may use hydrophobic interfaces to control and facilitate proton transport. And Ana-Nicoleta Bondar at the University of California at Irvine and colleagues have studied how protons achieve long-distance transport in bacteriorhodopsin from the acceptor residue Asp85 to the extracellular proton release group (P. Phatak et al., JACS 10.1021/ja809767v – paper here). Bound water molecules in the active site are again implicated.

Prashanth Athri and W. David Wilson at Georgia State University show how interfacial water can help the DNA-binding agent DB921 to bind in the minor groove despite an imperfect geometric match (JACS 10.1021/ja809249h – paper here). These results might offer clues to exploiting water mediation in designing DNA-binding molecules.

More on urea and denaturation: Frank Gabel at the Institut de Biologie Structurale in Grenoble and colleagues have used SANS and SAXS to study the binding of urea to denatured ubiquitin (JACS 10.1021/ja9013248 – paper here). They find that acid-induced denaturation recruits about 20 urea molecules from solution to bind to the protein, supporting the view that these direct interactions between protein and denaturant are the cause of denaturation.

Some studies of water at lipid membranes. M. D. Fayer and colleagues at Stanford look at the hydration of AOT reverse micelles, compared to the lamellar phase, using ultrafast IR spectroscopy, and conclude that short-range, direct interactions with the head groups, rather than more general nanoconfinement effects, seen to be responsible for the orientiation retardation of water molecules (D. E. Moilanen et al., JACS 131, 8318; 2009 – paper here). And Zhancheng Zhang and Max Berkowitz at UNC have looked at the slowing of water orientational relaxation in the hydration layer of phospholipids bilayers using MD (J. Phys. Chem. B 113, 7676; 2009 – paper here). Berkowitz and Changsun Eun have also looked (via MD) at the hydration of lipid headgroups attached to two parallel graphene plates, as a model for interactions between bilayers (J. Phys. Chem. B 10.1021/jp901747s – paper here). They find a repulsive interaction between the plates that has three regimes, dependent on the plate separation. At small distances (0.75-1 nm) the repulsion is steric. At intermediate distances (1-1.6 nm) it results from dehydration of the head groups, and at large separations (1.7-2.4 nm) – well, I must be missing something in my rapid reading here, but all I can glean is that this is water-mediated too.

Alenka Luzar and colleagues have compared MD simulations of the hydration of monosodium glutamate with the recent neutron data from Sylvia McLain et al. (J. Phys. Chem. B 110, 21251; 2006). They find that the simulations could not reproduce the reduction in water-water correlations seen experimentally, pointing to some of the shortcomings of the classical potentials used (C. D. Daub et al., J. Phys. Chem. B. 113, 7687; 2009 – paper here). And Janusz Stangret and colleagues have characterized the hydration of carboxylate ions using FTIR spectroscopy (E. Gojlo et al., J. Phys. Chem. B 10.1021/jp811346x – paper here). They find that two water molecules induce symmetry-breaking of the carboxylate group, providing non-equivalent proton donors to the oxygen atoms.

Jacob Petrich and colleagues at Iowa State describe a new method for probing the dynamics of proteins – specifically, measuring the solvation correlation function – by monitoring the fluorescence from two coumarins with different lifetimes (S. Bose et al., J. Phys. Chem. B 10.1021/jp9004345 – paper here).

Benoît Roux at Chicago and coworkers consider the ‘topological control hypothesis’ for selective ion binding to proteins, which postulates that selectivity is controlled primarily by the number of ligands coordinating the ion – which can in turn be predicted from the average coordination structure in bulk water – and not from their chemical nature (H. Yu et al., J. Phys. Chem. B 10.1021/jp901233v – paper here). They find, perhaps not surprisingly, that this hypothesis has some serious limitations in predicting binding free energies.

Kelly Gaffney and coworkers at Stanford use ultrafast IR spectroscopy to look at hydrogen-bond dynamics in sodium perchlorate solution (S. Park et al., J. Phys. Chem. B 10.1021/jp9016739 – paper here). They find that the dynamics support an orientational jump model in which the making and breaking of H-bonds is the predominant control on reorientation times. MD simulations also indicate that the anion hydration shells have two distinct shells, and that the molecules in the inner shell donate one H-bond each to the perchlorate ion.

Nicolas Giovambattista, Peter rossky and Pablo Debenedetti have been trying to map out the phase behaviour of water confined between hydropholic, hydrophobic and heterogeneous plates at various temperatures and pressures (Phys. Rev. E 73, 041604; 2006 and J. Phys. Chem. C 11, 1323; 2007). They have now extended this work by looking at the effects of varying the T and P simultaneously between 220-300 K and –0.2 to 0.2 GPa (J. Phys. Chem. B 10.1021/jp9018266 – paper here). It’s hard to summarize all the information in this rich paper, but one general conclusion is that the plates become effectively less hydrophobic (the vapour phase is suppressed) as the temperature drops. An underlying motive for this work is to understand the pressure- and cold-denaturation of proteins and how this is tied up with invasion of hydrophobic cavities by water.

Catching up

2009-05-06T00:50:00.000-07:00

I have been on travel and caught up with numerous other things for several weeks, which not only means I have been unable to post but also that I’ve doubtless missed some interesting things over the recent period. If so, apologies for that – and feel free to let me know! But note also that my email address at Nature won’t be active for much longer, as I am very shortly leaving my role there as a writer – I’m no longer able to keep that going alongside the other demands on my time. I will no doubt keep writing occasionally for Nature nonetheless, but will be henceforth reachable at p.ball@btinternet.com.

To business, and in no particular order from the stack of papers in my pile…

Martina Havenith and her coworkers at Bochum have continued their highly revealing work on hydration structures using terahertz spectroscopy. In a new paper (B. Born et al., JACS 131, 3752 (2009) – paper here) they look at the hydration networks around various small peptides at low hydration levels, and find that the collective motions of peptide + solvent that seem to characterize protein hydration shells disappear below a minimum number of hydration waters, which appears to be well below that required for monolayer coverage.

This issue of solvent-protein dynamical correlations is also studied by Nigel Scrutton and colleagues at the University of Manchester (D.J. Heyes et al., Angew. Chem. Int. Ed. 48, 3850; 2009 – paper here). They find that proton tunnelling in protochlorophyllide oxireductase, a light-driven enzyme involved in chlorophyll biosynthesis, requires protein motions that appear to be slaved to the solvent, whereas hydride transfer in this species does not. It seems significant that proton, but not hydride, transfer occurs only close to the protein’s glass transition temperature, when the protein-solvent coupling is likely to be most acute.

In my recent ChemPhysChem paper (here), I referred to some recent work on denaturants by Jeremy England and coworkers, inadvertently describing it as though it came out of Vijay Pande’s lab (J. L. England, V. S. Pande & G. Haran, JACS 130, 11854; 2008). Actually I gather it was done mostly at the lab of Gilad Haran at the Weizmann Institute in Israel. Apologies for that oversight. Gilad has told me of his recent work on protein collapse using single-molecule FRET (G. Ziv & G. Haran, JACS 131, 2942; 2009 – paper here; and G. Ziv et al., Phys. Chem. Chem. Phys. 11, 83; 2009 – paper here). The former paper argues that the action of denaturants operates primarily by modulating the collapse of the denatured state, rather than acting on the transition from molten globule to folded state.

A recent special issue of J. Phys. Chem. B on aqueous solutions and interfaces (113(13)) has given me a lot to catch up with. Sotiris Xantheas and Greg Voth give a nice overview here. Among the interesting papers therein, Greg profiles the case for the amphiphilic nature of the hydrated proton at the interface with hydrophobic media (S. Iuchi et al., J. Phys. Chem. B 113, 4017; 2009 – paper here); Janamejaya Chowdhary and Branka Ladanyi use MD to investigate the dynamics of hydrogen-bond making and breaking (113, 4045; 2009 – paper here), and Yves Rezus and Huib Bakker use femtosecond IR spectroscopy to look at how various amphiliphilic small molecules alter water structure in the bulk (113, 4038; 2009 – paper here). Rezus and Bakker find that trimethylamine-N-oxide seems to be special in the latter regard, increasing the rate of reorientation of mobile water, which might be interpreted as a sign that it increases the number of defects in the H-bonded network.

On much the same topic, Greg Voth and colleagues have used MD to look at the interactions of hydrophobic, nonpolar solvents in aqueous salt (NaCl) and acid (HCl) solution (H. Chen et al., J. Phys. Chem. B ASAP; paper here). They find unusual solvated-proton structures in the acid which are bound to the hydrophobes, again supporting the idea that the hydrated protons act as amphiphiles. This might explain why protons seem anomalous in the Hofmeister series. And Michael Brindza and Robert Walker at the University of Maryland use SHG to look at solvation mechanisms of small molecules (p-nitroanisole, indoline) at the interface of polar solids and various liquids, offering a broader context for understanding what water in particular does in such cases (JACS 131, 6207; 2009 – paper here). Alenka Luzar and her coworkers have used MD to look at the solvation of monosodium glutamate, making a comparison to experimental data on this system (C. D. Daub et al., J. Phys. Chem. B ASAP; paper here). On the whole the agreement is good with the neutron-diffraction data, but there are some important differences – for example, the simulations couldn’t reproduce the experimentally observed reduction in water-water correlations – that presumably point to inadequacies of using classical potentials. (Incidentally, my spellchecker tirelessly insists that ‘solvation’ should be ‘salvation’ – forgive me if I don’t fail to catch them all…)

Alenka’s comparison with experiment here relies heavily on Alan Soper’s neutron data and its analysis using empirical potential structure refinement, which was conducted for those data by Alan with Sylvia McLain and Anthony Watts. Sylvia has sent me a paper in which she, with Soper and Watts alongside Jeremy Smith and Isabella Daidone, use this same technique to deduce the nature of hydration and interaction between various amino acid dimmers (S. E. McLain et al., Angew. Chem. Int. Ed. 47, 9059; 2008 – paper here). This is extremely interesting, as it challenges the conventional view that the main driving force for association is the interaction of hydrophobic regions. In contrast, this study finds that it is the charged sites on the peptides that dominate the association, and that interaction decreases as hydrophobicity increases. Could the same apply in protein folding itself?

Sason Shaik and his collaborators have now published the full analysis of the role on internal waters in the action of cytochrome P450 StaP (Y. Wang et al., JACS ASAP; 2009 – paper here), the preliminary account of which I discussed in my CPC paper.

Anders Nilsson, Lars Pettersson and their coworkers have now published the work that I referred to in a Nature article last year, in which they challenge the view that X-ray and neutron diffraction data uniquely support the conventional tetrahedral-coordinate picture of water structure (K. T. Wikfeldt et al., J. Phys. Chem. B 113, 6246; 2009 – paper here). Needless to say, this remains highly controversial stuff.

Pedro de Pablo and colleagues at Madrid have reported some very striking results on the desiccation of viruses. They say that drying of two different viruses causes the ejection of DNA and, in one case, collapse of the remaining capsid owing to capillary forces of the water menisci inside (C. Carrasco et al., PNAS 106, 5475; 2009 – paper here).

A couple more papers on nanoconfined water, in hydrophobic but less explicitly biological environments. Sow-Hsin Chen and colleagues say that supercooled water, which shows a density minimum under confinement in hydrophilic mesoporous materials, has none such in a hydrophobic material (Y. Zhang et al., J. Phys. Chem. B ASAP: paper here). And Gene Stanley and colleagues look at the H-bond dynamics of TIP5P water in a hydrophobic nanopore slit (S. Han et al., Phys. Rev. E 79, 041202; 2009 – paper here). They say that the H-bonds are shorter-lived in this case than in the bulk, and the relaxation time is smaller, but the general qualitative behaviour is much the same (e.g. the temperature-dependence of the average H-bond lifetime, and non-exponential lifetime distributions).

Ahmed Zewail and Ding-Shyue Yang recently reported ultrafast electron crystallography of water at low temperatures (c. 150 K) at the surface of graphite (PNAS 106, 4122; 2009 – paper here). It’s not strictly relevant to water in biology, perhaps, but an issue that I’ve started to follow increasingly and which touches on water’s general ability to order at interfaces. The results imply that, perhaps contrary to expectation (especially when compared with hydrophobic H-terminated silicon), this hydrophobic surface doesn’t disrupt a highly ordered interfacial structure. It seems this may be because the graphite surface is stepped, which apparently allows it to template a cubic-ice structure.

I recently wrote a column for Nature Materials (8, 250; 2009 – see here) on hydrophobicity at larger scales than the molecular, and in particular on the discussions of wetting by water of nano- and microstructured surfaces via Wenzel or Cassie states. This is relevant to biology insofar as it bears on the question of wettability of, e.g. insect legs and lotus leaves. There is a nice recent simulation paper on the topic by Takahiro Koishi at the University of Fukui and colleagues (PNAS doi:10.1073/pnas.0902027106 – not yet online), which describes the different conditions (of surface topology and so forth) under which Wenzel and Cassie wetting exist, and the possibility of their coexistence. And Abraham Marmur has flagged up his paper from last year (Langmuir 24, 7573; 2008 – paper here) in which he too looks at general geometric considerations that might promote such high-contact-angle states.

Here’s an intriguing thing that had escaped my notice until now: it seems that voltages may be generated in carbon nanotubes along the tube axis when water flows through them (see S. Ghosh et al., Science 299, 1042; 2003 – paper here). That’s suggestive from the perspective that views nanotubes as simple analogues of hydrophobic protein channels. Already it seems that this idea has been explored for power conversion (Y. C. Zhao et al., Adv. Mater. 20, 1772; 2008). Now Quanzi Yuan and Ya-Pu Zhao of the Institute of Mechanics in Beijing offer an explanation for the phenomenon in terms of the alignment of water molecules in the hydrogen-bonded chain within the nanotube (JACS ASAP; paper here).

More on this general topic from Bo Liu at the Graduate University of the Chinese Academy of Sciences in Beijing and coworkers, who describe simulations of a model system in which end-functionalized short carbon nanotubes are embedded in a phospholipid bilayer as mimics of aquaporin (B. Liu et al., Nano Lett. 9, 1386; 2009 – paper here). Two charges are placed near the tube midpoints, to simulate the NPA region of aquaporin where water selectivity and proton gating is thought to happen. But proton conduction couldn’t be studied explicitly in these classical MD simulations. That aside, the device seems to work more or less as planned, in theory. But can we make it?

Well, that’s not the end of it, but my desk looks a whole lot better.

There’s more to life than sequence

2009-03-13T02:07:00.000-07:00

I have been meaning for some time to write about an interesting paper in JACS by Naoki Sugimoto’s group in Kobe. It found its way into an article that I wrote this week for Nature’s online news. So I’ve decided to simply post this article here – it’s not all strictly relevant to water in biology, but hopefully is interesting stuff anyway. This is the version before editing, which has more detail.

Shape might be one of the key factors in the function of mysterious ‘non-coding’ DNA.

Everyone knows what DNA looks like. Its double helix decorates countless articles on genetics, has been celebrated in sculpture, and was even engraved on the Golden Record, our message to the cosmos on board the Voyager spacecraft.

The entwined strands, whose form was deduced in 1953 by James Watson and Francis Crick, are admired as much for their beauty as for the light they shed on the mechanism of inheritance: the complementarity between juxtaposed chemical building blocks on the two strands, held together by weak ‘hydrogen’ bonds like a zipper, immediately suggested to Crick and Watson how information encoded in the sequence of blocks could be transmitted to a new strand assembled on the template of an existing one.

With the structure of DNA ‘solved’, genetics switched its focus to the sequence of the four constituent units (called nucleotide bases). By using biotechnological methods to deduce this sequence, they claimed to be ‘reading the book of life’, with the implication that all the information needed to build an organism was held within this abstract linear code.

But beauty has a tendency to inhibit critical thinking. There is now increasing evidence that the molecular structure of DNA is not a delightfully ordered epiphenomenon of its function as a digital data bank but a crucial – and mutable – aspect of the way genomes work. A new study in Science [1] underlines that notion by showing that the precise shape of some genomic DNA has been determined by evolution. In other words, genetics is not simply about sequence, but about structure too.

The standard view – indeed, part of biology’s ‘central dogma’ – is that in its sequence of the four fundamental building blocks (called nucleotide bases) DNA encodes corresponding sequences of amino-acid units that are strung together to make a protein enzyme, with the protein’s compact folded shape (and thus its function) being uniquely determined by that sequence.

This is basically true enough. Yet as the human genome was unpicked nucleotide base by base, it became clear that most of the DNA doesn’t ‘code for’ proteins at all. Fully 98 percent of the human genome is non-coding. So what does it do?

We don’t really know, except to say that it’s clearly not all ‘junk’, as was once suspected – the detritus of evolution, like obsolete files clogging up a computer. Much of the non-coding DNA evidently has a role in cell function, since mutations (changes in nucleotide sequence) in some of these regions have observable (phenotypic) consequences for the organism. We don’t know, however, how the former leads to the latter.

This is the question that Elliott Margulies of the National Institutes of Health in Bethesda, Maryland, Tom Tullius of Boston University, and their coworkers set out to investigate. According to the standard picture, the function of non-coding regions, whatever it is, should be determined by their sequence. Indeed, one way of identifying important non-coding regions is to look for ones that are sensitive to sequence, with the implication that the sequence has been finely tuned by evolution.

But Margulies and colleagues wondered if the shape of non-coding DNA might also be important. As they point out, DNA isn’t simply a uniform double helix: it can be bent or kinked, and may have a helical pitch of varying width, for example. These differences depend on the sequence, but not in any straightforward manner. Two near-identical sequences can adopt quite different shapes, or two very different sequences can have a similar shape.

The researchers used a chemical method to deduce the relationship between sequence and shape. They then searched for shape similarities between analogous non-coding regions in the genomes of 36 different species. Such similarity implies that the shapes have been selected and preserved by evolution – in other words, that shape, rather than sequence per se, is what is important. They found twice as many evolutionarily constrained (and thus functionally important) parts of the non-coding genome than were evident from trans-species correspondences using only sequence data.

So in these non-coding regions, at least, sequence appears to be important only insofar as it specifies a certain molecular shape and not because if its intrinsic information content – a different sequence with the same shape might do just as well.

That doesn’t answer why shape matters to DNA. But it suggests that we are wrong to imagine that the double helix is the beginning and end of the story.

There are plenty of other good reasons to suspect that is true. For example, DNA can adopt structures quite different from Watson and Crick’s helix, called the B-form. It can, under particular conditions of saltiness or temperature, switch to at least two other double-helical structures, called the A and Z forms. It may also from triple- and quadruple-stranded variants, linked by different types of hydrogen-bonding matches between nucleotides. One such is called Hoogsteen base-pairing.

Biochemist Naoki Sugimoto and colleagues at Konan University in Kobe, Japan, have recently shown that, when DNA in solution is surrounded by large polymer molecules, mimicking the crowded conditions of a real cell, Watson-Crick base pairing seems to be less stable than it is in pure, dilute solution, while Hoogsteen base-pairing, which favours the formation of triple and quadruple helices, becomes more stable [2-4].

The researchers think that this is linked to the way water molecules surround the DNA in a ‘hydration shell’. Hoogsteen pairing demands less water in this shell, and so is promoted when molecular crowding makes water scarce.

Changes to the hydration shell, for example induced by ions, may alter DNA shape in a sequence-dependent manner, perhaps being responsible for the sequence-structure relationships studied by Margulies and his colleagues. After all, says Tullius, the method they use to probe structure is a measure of “the local exposure of the surface of DNA to the solvent.”

The importance of DNA’s water sheath on its structure and function is also revealed in work that uses small synthetic molecules as drugs that bind to DNA and alter its behaviour, perhaps switching certain genes on or off. It is conventionally assumed that these molecules must fit snugly into the screw-like groove of the double helix. But some small molecules seem able to bind and show useful therapeutic activity even without such a fit, apparently because they can exploit water molecules in the hydration shell as ‘bridges’ to the DNA itself [5]. So here there is a subtle and irreducible interplay between sequence, shape and ‘environment’.

Then there are mechanical effects too. Some proteins bend and deform DNA significantly when they dock, making the molecule’s stiffness (and its dependence on sequence) a central factor in that process. And the shape and mechanics of DNA can influence gene function at larger scales. For example, the packaging of DNA and associated proteins into a compact form, called chromatin, in cells can affect whether particular genes are active or not. Special ‘chromatin-remodelling’ enzymes are needed to manipulate its structure and enable processes such as gene expression of DNA repair.

None of this is yet well understood. But it feels reminiscent of the way early work on protein structure in the 1930s and 40s grasped for dimly sensed principles before an understanding of the factors governing shape and function transformed our view of life’s molecular machinery. Are studies like these, then, a hint at some forthcoming insight that will reveal gene sequence to be just one element in the logic of life?

References

1. Parker, S. C. J. et al., Science Express doi:10.1126/science.1169050 (2009). Paper here.
2. Miyoshi, D., Karimata, H. & Sugimoto, N. J. Am. Chem. Soc. 128, 7957-7963 (2006). Paper here.
3. Nakano, S. et al., J. Am. Chem. Soc. 126, 14330-14331 (2004). Paper here.
4. Miyoshi, D. et al., J. Am. Chem. Soc. doi:10.1021/ja805972a (2009). Paper here.
5. Nguyen, B., Neidle, S. & Wilson, W. D. Acc. Chem. Res. 42, 11-21 (2009). Paper here.

Making sense of solvent slaving

2009-03-03T09:08:00.000-08:00

In my previous post I mentioned work by Pablo Debenedetti on ‘toy models’ of water. The places to look are: Buldyrev et al., PNAS 104, 20177 (2007) (here) for the solvation thermodynamics of ‘spherical’ water; and Patel et al., Biophys. J. 93, 4116 (2007) (here) and J. Chem. Phys. 128, 175102 (2008) (here) for water-explicit lattice models of proteins.

And in discussing recent work on the mechanism of urea-induced protein denaturation, I neglected to mention Bruce Berne’s PNAS paper from late last year with Ruhong Zhou, Dave Thirumalai and Lan Hua (105, 16928; paper here). That paper on MD simulations for lysozyme anticipated the more recent work showing that denaturation seems to be caused by direct urea-protein interactions: the urea displaced water from the first hydration shell and penetrates into the hydrophobic core to give a ‘dry globule’.

The notion that protein dynamics are ‘slaved’ to those of the hydration shell has been floating around for some time now. Hans Frauenfelder and colleagues have now brought considerable focus to the idea (PNAS doi:10.1073/pnas.0900336106; paper here) with dynamical measurements using dielectric spectroscopy, Mossbauer and neutron scattering. They find that large-scale protein motions follow the fluctuations of the solvent and are dependent on solvent viscosity. There are two classes of fluctuation in the solvent, alpha and beta, with different timescales. It seems that the former are ‘structural’ in nature and control protein shape; the latter are those to which the protein’s internal motions are slaved.

Jianxing Song at the National University of Singapore, who I met in Hangzhou, has sent me three papers on the intriguing solubilisation of ‘water-insoluble’ proteins in pure water. He and his coworkers found this effect in 2006 for a range of diverse proteins (M. Li et al., Protein Science 15, 1835 (2006) – paper here; M. Li et al., Biophys. J. 91, 4201 (2006) – paper here). They attributed it to the tendency of the ‘insoluble’ proteins to form partially folded states with many exposed hydrophobic residues, such that only a very low ionic strength is sufficient to screen out repulsive interactions and cause aggregation. In pure water, however, those electrostatic interactions remain sufficiently strong to suppress aggregation and precipitation. Jianxing has now provided an overview of this work, expanding on the importance of pH for this effect, in FEBS Letters (doi:10.1016/j.febslet.2009.02.022; paper here).

Roberto Righini at the University of Florence and colleagues have used IR spectroscopy to identify and quantify the various aqueous species that solvate the polar heads of phospholipids in bilayers (V. V. Volkov et al., J. Phys. Chem. B doi:10.1021/jp806650c; paper here). And Davide Donadio and coworkers in California have shown how electronic charge fluctuations show up in the IR spectra of water close to nonpolar surfaces (here graphite) (D. Donadio et al., J. Phys. Chem. B doi:10.1021/jp807709z; paper here). Still in that neck of the woods, Chuan-Shan Tian and Ron Shen have used sum-frequency-IR spectroscopy to sort out the nature of hydrogen-bonding at the air-water interface (JACS 131, 2791 (2009) – paper here). And Heather Allen and colleagues at Ohio State University have used this and other spectroscopic techniques to study hydration structure of the air-water interface for various divalent nitrates (M. Xu et al., J. Phys. Chem. B doi:10.1021/jp806565a; paper here).

Haiping Fang in Shanghai continues his exploration of how water and solutes can be manipulated within the confinement of carbon nanotubes. He and colleagues now show, using MD simulations, how a single charge outside a nanotube can be used to move a hydrated peptide inside it, regardless of whether the peptide itself is charged (P. Xiu et al., JACS 131, 2840 (2009) – paper here). This is due to the dipole-orientational ordering of the water molecules caused by confinement and interaction with the external charge.

There’s more, but later.

What does denaturation mean?

2009-02-05T08:27:00.000-08:00

At a recent symposium in honour of John Finney, who ‘retires’ (quote marks sure to be apt) this year, I heard Bertil Halle talk about the work described in a new paper (M. Davidovic et al., JACS 10.1021/ja8056419 – paper here), in which he and his colleagues argue that – if I am not being too liberal with the message here – cold-induced protein denaturation is not really denaturation at all, but rather the formation of a solvent-pentrated compact state. They report here that the hydration dynamics of BPTI, ubiquitin, apomyoglobin and beta-lactoglobulin, as monitored with NMR spin relaxation, shows that only apomyoglobin – that is, the only ‘modified’ protein here – truly denatures in picolitre emulsion droplets cooled to minus 35 C. Thus, they argue that cold denaturation is not equivalent to heat denaturation, and is perhaps not a well-defined state at all.

I have the abstract only of a simulation study of (partially) denaturation of human alpha-lactalbumin by Doug Tobias and colleagues (N. Sengupta et al., Biophys. J. 95, 5257; 2008 – paper here). So I can’t say too much about it, except that I assume this to be heat-induced, and that the results seem to show quite subtle effects on solvation dynamics. It seems that the partially denatured structure is rather patchily and ‘imperfectly’ solvated, with the solvent influx not keeping pace with the exposure of new surface in the protein.

Pablo Debenedetti was also at John’s symposium, and reported some most intriguing work on ‘toy’ models of water – spherical with two length scales, and four-coordinate on a square lattice – that offered insights into the possible origins of some behaviours both in the bulk and as a solvent. Forgive me, I will try to track that down when I have a free moment. Meanwhile, Pablo’s latest paper in J. Phys. Chem. B. (S. Romero-Vargas Castrillon et al., 10.1021/jp809032n – paper here) involves rather more ‘realistic’ water. They look at how water behaves in confinement between the silica surfaces of beta-cristobalite, primarily as a function of the parametrized surface Coulombic charge (k). When the surfaces are wholly apolar – no surface charge – they template an ice-like layer with slow dynamics. When the surfaces are strongly hydrophilic (high charge), the dynamics are also slow, but for a different reason: a dense, disordered water layer forms, with strong H-bonds. Both the diffusion coefficient and the rotational relaxation are thus non-monotonic with k.

Jan Engberts has brought my attention to a deeply interesting paper in Acc. Chem. Res. by Stephen Neidle of UCL and coworkers (Acc. Chem. Res. 42, 11-21; 2009; paper here) on the water mediation of DNA-ligand interactions. They describe how the binding of various small molecules in the minor groove can’t be easily understood on the basis of shape complementarity, but can be rationalized in terms of water-bridging in the hydration shell. This concept has already been used to identify drug candidates with high binding affinity and biological activity, which are now in clinical trials. This is probably the most striking example I have come across of how hydration structures can be used to inform drug development, something that I said in my Chem. Rev. paper was very much under-utilized owing to a lack of understanding. Perhaps that statement is now too strong. In any event, this looks like very important work.

Takashi Hayashi of Osaka University and coworkers report X-ray structures of cytochrome P450cam (which catalyses hydroxylation of camphor), showing how a propionate side chain acts as a gate that helps expel water from the active site (T. Hayashi et al., JACS 10.1021/ja807420k; paper here).

Mark Berg and colleagues have simulated the dynamics of water and ions near DNA in order to explain Stokes-shift data (S. Sen et al., JACS 131, 1724 (2009); paper here). It seems that the anomalous power-law dynamics seen experimentally can be accounted for by the water motions alone, the bottom line being that ‘water near DNA is strongly perturbed and is quite unlike bulk water.’

Damien Laage, Guillaume Stirnemann and Casey Hynes add to the overwhelming body of argument for dispensing with any notion of ‘iceberg’ hydration around hydrophobic groups (J. Phys. Chem. B 10.1021/jp809521t; paper here). They show that, contrary to what Rezus and Bakker recently claimed (Phys. Rev. Lett. 99, 148301; 2007), no water molecules are actually immobilized by hydrophobic solutes. Their model suggests that only a moderate degree of reorientational slowing, owing to slower hydrogen-bond exchange, is sufficient to explain both the ultrafast spectroscopic and the NMR data.

Mauricio Alcolea Palafox and coworkers in Madrid have simulated the hydration shells of thymidine and its derivative D4T (an alternative substrate for HIV-1 reverse transcriptase) from first principles (J. Phys. Chem. B 10.1021/jp806684v; paper here). And Dor Ben-Amotz and colleagues at Purdue look at the hydration shells of halide ions using Raman spectroscopy to probe the OH stretch (J. Phys. Chem. B 10.1021/jp808732s; paper here). They say the results support earlier work showing that the H-bonds between the halide ions and water are weaker than those in water.

How do protons get through bacteriorhodopsin?

2009-01-06T09:18:00.000-08:00

I’ve just received a copy of the special issue of ChemPhysChem (here) on water at molecular interfaces (Vol. 9, 2635-2879), containing presentations from the DFG Forschergruppe 436 meeting in Dortmund last July. I won’t list everything in it – there is too much that is all worth reading.

One of the contributions, from Klaus Gerwert and colleagues, looks at how vectorial proton transport is achieved in bacteriorhodopsin via a network of water molecules (p.2772). That is also the topic of a recent paper from Qiang Cui of the University of Wisconsin and colleagues (P. Phatak et al., PNAS 105, 19672; 2008 – paper here), who look specifically at the much-debated question of what the proton storage site in bR is. They argue, against the conclusions of Gerwert and coworkers (e.g. Nature 439, 109; 2006), that the proton is kept on a pair of glutamate residues (Glu 194/204), not on a nearby water cluster. I daresay the debate will continue.

Jeremy Smith and colleagues have looked at another aspect of the problem – the possible role of a bound water molecule on the cytoplasmic side of the retinal Schiff base chromophore in the initial transfer of a proton from this chromophore to Asp85, the first step in its motion to the extracellular side (A.-N. Bondar et al., J. Phys. Chem. B 112, 14729; 2008 – paper here). They report calculations which suggest that a water molecule bound to the ‘back’ of retinal in this way helps to direct proton transfer to Asp85 rather than towards Asp212 on the other side of the channel. A surprisingly subtle and indirect form of ‘water-tuning’.

Feng Gai and colleagues at the University of Pennsylvania have added to the unfolding (forgive me) story of how hydration influences amyloid aggregation (S. Mukherjee et al., J. Phys. Chem. B 10.1021/jp809817s – paper here). They have manipulated the degree of hydration of two amyloid-forming peptides by encapsulating them in reverse micelles, and find that aggregation is enhanced when hydration is lessened.

Ronen Zangi, Ruhong Zhou and Bruce Berne report simulations that support what seems to be a growing view that urea’s denaturing action results from direct interaction with hydrophobic surfaces and not any kind of ‘chaotropic’ effect on ‘water structure’ (R. Zangi et al., JACS 10.1021/ja807887g – paper here). They find that urea weakens hydrophobic interactions both in a hydrophobic model polymer and between hydrophobic (and graphene) plates, owing to its binding to the surface and acting as a kind of surfactant.

A nice Christmas package

2008-12-18T08:28:00.000-08:00

There are some important and provocative papers in this batch…

Teresa Head-Gordon and her coworkers have extended their recent work on quasi-elastic neutron scattering in peptide hydration shells (e.g. Russo et al., J. Phys. Chem. B 108, 19885 and 109, 12966 (2005); Russo et al., Biophys. J. 86, 1852 (2004)) by using MD simulations to explore the way in which the hydration dynamics are affected by the heterogeneous, amphiphilic nature of most protein surfaces (M. E. Johnson et al., J. Phys. Chem. B doi:10.1021/jp806183v – paper here). The notion they proposed earlier is that the dynamics are most perturbed at the interfaces of hydrophobic and hydrophilic patches, due to the frustration created by different styles of hydration in the adjacent regimes. This now seems to be borne out by the simulations, where the water dynamics seen experimentally are reproduced for an amphiphilic peptide but not a hydrophilic one. The strongest dynamical perturbations are found for the first hydration shell of hydrophobic residues.

Jeetain Mittal and Gerhard Hummer have used simulations to try to clarify exactly what goes on at the interface of a hydrophobic surface and water (PNAS doi:10.1073/pnas.0809029105 – paper here). They are in particular examining the vexed question of whether there is a depletion layer in water density close to the surface, as proposed first by Frank Stillinger and invoked in the Lum-Chandler-Weeks model of dewetting-induced hydrophobic collapse (K. Lum, D. Chandler & J. D. Weeks, J. Phys. Chem. B 103, 4570; 1999). Experiments have now shown some evidence for a depletion layer perhaps 1-2 Å thick. But is there a sharp transition between a liquid-like and vapour-like phase, or a gradual thinning? In the former case, capillary waves are expected to blur the interface, so it’s hard to tell the difference. Mittal and Hummer find, for a purely repulsive spherical solute particle, that the interface is indeed rather sharp, but broadened by capillary waves in line with what theory predicts for a free air-water interface. The ‘dry’ layer looks to be instantaneously about 2 Å or so thick. The result is a flickering interface with patches that are intermittently dry and wet (in proportions that depend on the solute size), and transitions between them that are slow on a molecular timescale. This is all very illuminating, but I’m hard to satisfy – what happens when van der Waals forces between solvent and surface are included, I wonder?

Roland Netz at the TU Munich and his colleagues have also explored the depletion-layer problem from a very different angle. They have used MD simulations to examine how the slip length for water flow past a hydrophobic surface depends on the contact angle (D. M. Huang et al., Phys. Rev. Lett. 101, 226101; 2008 – paper here). Experimental studies in this area have given confusing and conflicting results, with slip lengths orders of magnitude different for surfaces that seem very similar. But the simulations show a rather systematic (though nonlinear) dependence of slip length on static contact angle. Moreover, they see depletion layers of molecular dimensions, whose average width varies with the ¼ power of the slip length. Thus, anything that influences the width of the depletion layer (dissolved gases) should have a marked effect on the slip length.

I referred recently to a study that challenged the notion of a dynamical transition for protein hydration water at 220 K and its interpretation as a fragile-to-strong crossover (S. Khodadadi et al., J. Phys. Chem. B 112, 14273-14280; 2008). Now here comes another one, from Michael Vogel at the Technical University of Damstadt (Phys. Rev. Lett. 101, 225701; 2008 – paper here). He has used deuterium NMR to study reorientational dynamics of hydration water for elastin and collagen, and sees no sign of a transition at 225 K. There is one at 200 K, but Vogel says that it corresponds to the onset, at lower temperatures, of thermally activated jumps in tetrahedral coordination, perhaps related to defect motion in the hydrogen-bonded network.

Fabio Sterpone and colleagues in Rome argue that the thermostability of proteins is primarily determined by protein-water interactions, with the intra-chain interactions between packed portions of the polypeptide being of only secondary importance (F. Sterpone et al., J. Phys. Chem. B doi:10.1021/jp805199c – paper here). They looked, using simulations, at the thermal stability and flexibility of three homologous proteins – one mesophilic, one thermophilic, and one hyperthermophilic. As thermal stability increases, so the proteins seem to be encased in an increasingly persistent hydration shell linked by hydrogen bonds. The idea, crudely speaking, seems to be that this shell supplies an increasingly robust protective coat against the penetration of water into the folded protein.

At the recent Hangzhou workshop I heard about the work of Shengfu Chen of Zhejiang University and colleagues on anti-fouling films that incorporate heterogeneously charged peptides. The idea is that the ability of these films to resist non-specific protein adsorption is linked to the nature of hydration of the surface chemical groups: the ‘more’ hydration there is, the stronger the disrupting influence of an incoming adsorbate and thus the more its attachment is inhibited. Shengfu and his workers in Washington and Taiwan develop this idea in a paper here (J. Phys. Chem. B doi:10.1021/jp8065713). They introduce a method for deducing the number of water molecules hydrating a given solute, and find that the greater the ‘hydration capacity’ of a solute, the greater its ability to resist protein adsorption in anti-fouling films.

Haiping Fang, my co-chair at that meeting, has an intriguing paper on the effect on water flux through a nanotube on the nature of the ‘outside structure’, in this case meaning whether the nanotube threads through a single, double or multiple sheets of graphene (X. Gong et al., Phys. Rev. Lett. 101, 257801; 2008 - paper here). In simulations, they find that the flux of water can be quite different in the various cases. For example, with two graphene sheets separated by a vacuum, the flux and flow both increases as the separation increases. And if water surrounds the nanotube in the space(s) between sheets, the flux is lowered. They deduce that interactions between water molecules inside the nanotube and the species outside the tube are responsible for the differences, emphasizing how sensitive, in this confined geometry with more or less single-file molecular traffic (where molecular motions are strongly correlated), the water transport is to the internal configurations of water molecules.

It seems clear that nanobubbles can form on hydrophobic surfaces, and very likely that these play a key role in the long-ranged hydrophobic interaction that is sometimes observed between such surfaces. The question has remained of how such bubbles, with a very high radius of curvature, can be stable when that curvature creates a large Laplace pressure which should lead to rapid diffusive efflux of gas out of the bubble. Michael Brenner and Detlef Lohse have considered this question (Phys. Rev. Lett. 101, 214505; 2008 – paper here). They say that the outflux can be balanced by an enhanced influx of gas at the contact line of bubble and surface, owing to the attraction of dissolved gas to the hydrophobic surface. They acknowledge that this is a non-equilibrium situation which suggests that in the long term the bubbles should disappear. But there haven’t yet been any long-term studies of closed systems to see whether that is the case.

Apparently sobering news from Michael Levitt and colleagues: MD simulations for protein structure refinement perform worse in explicit solvent than implicit solvent (G. Chopra et al., PNAS doi:10.1073/pnas.0810818105 – paper here). This seems to be because the potential in explicit solvent is more rugged, and so there is more chance of getting stuck in local minima unless the simulation is very long. So there are some situations in which it is still best not to consider the hydration shell molecule by molecule.

Angel Garcia at RPI and coworkers have calculated the stability diagram of the well-studied Trp-cage miniprotein (D. Paschek et al., PNAS 105, 17754; 2008 – paper here). They derive some insights into the role of hydration in pressure-induced denaturation, which they link in part to tighter packing of water around nonpolar atoms as pressure increases.

The debate over the ‘pH’ of the air-water interface continues. First-principles empirical-valence-bond calculations by Greg Voth and colleagues seem to indicate that the preference of hydrated protons for the surface (as claimed in their earlier work) is energetically (rather than entropically) promoted, due to the amphiphilic nature of the hydrated proton (S. Iuchi et al., J. Phys. Chem. B doi:10.1021/jp805304j – paper here). They say that much the same applies for a water-hydrophobe interface too.

A lot about interfaces

2008-12-09T07:21:00.000-08:00

Janamejaya Chowdhary and Branka Ladanyi at Colorado State have used MD simulations to look at the dynamics of H-bonds at a water-hydrocarbon interface (J. Phys. Chem. B ASAP doi:10.1021/jp; paper here). They find that the reorientation of the O-H bond is anisotropic, and quantify the effects of cooperativity in the dynamics.

Robert Woods and colleagues at the University of Georgia study how bound water mediates the binding of concanavalin A to its target carbohydrate ligand (R. Kadirvelraj et al., JACS ASAP; paper here). Or rather, they look at a modified ligand of the natural trisaccharide, with a hydroxylethyl side chain that may or may not displace a conserved water in binding of the natural ligand. The crystal structure reported here shows that this water is retained, though its position is distorted. This helps to explain the previous thermodynamic data on ligand specificity for Con A, showing that there is no entropic component for the synthetic ligand arising from water displacement.

Roger Tam and colleagues in Ottawa have looked at the inhibition of ice recrystallization by mono- and disaccharides (JACS ASAP; paper here). Specifically, they look for correlates of ice-growth inhibition in the degree of hydration of the sugars, and find that, rather than using the total number of tightly bound water molecules, a better predictor of inhibiting ability is a hydration index in which the hydration number is divided by the molar volume. The researchers conclude that the inhibition arises from a disruption of water ‘pre-ordering’ at the ice-water interface.

Joe Zaccai and colleagues have measured water dynamics in human red blood cells using quasielastic incoherent neutron scattering (A. M. Stadler et al., JACS ASAP; paper here). In line with their previous work on E. coli, they find that most (90%) of the cell water has similar translational diffusion to the bulk, while about 10% is slower, this presumably being the water hydrating haemoglobin.

Sherwin Singer and colleagues at Ohio State have looked at the hydration dynamics of myoglobin using MD simulations (T. Li et al., J. Phys. Chem. B 10.1021/jp803042u; paper here). Specifically, they look at the time-dependent fluorescence Stokes shift after photoexcitation of the Trp-7 residue, a measure of the relaxation dynamics of the chromophore’s environment. The question is whether the water dynamics are due to constraint of the water by interactions with the protein, or whether they are controlled by the dynamics of the protein itself. This distinction should be revealed by arresting the protein in the simulations. Singer and colleagues find that doing so significantly changes the Stokes shift, suggesting that the intrinsic protein flexibility is important. They caution, however, that this does not necessarily imply that the water dynamics exhibit no intrinsic slow component of relaxation; rather, the protein and water dynamics are so intimately coupled that either slow water dynamics or slow protein dynamics (or both) could alter the Stokes shift.

Shekhar Garde and colleagues at RPI have conducted simulations of hydrophobically induced polymer collapse near to the interface with air or a hydrophobic wall (S. N. Jamadagni et al., J. Phys. Chem. B 10.1021/jp806528m – paper here here). They find that the driving force for collapse is smaller at the water-alkane interface, and all but vanishes at the air-vapour interface, where the polymer remains unfolded. They think that both the weaker hydration of the polymer and the enhanced density fluctuations of water at the interface produce faster conformational switches in the folded chain. The results throws up lots of interesting questions, most obviously of course what this implies for the conformational flexibility of two peptide chains approaching one another via the hydrophobic interaction.

Hangjun Lu and colleagues at Zhejiang Normal Univerity have looked at how an external charge of +1e near a carbon nanotube will affect the filling and emptying by water (H. Lu et al., J. Phys. Chem. B 10.1021/jp802263v – paper here here). It seems that the charge stabilizes the water-filled state when it is at the midpoint of the nanotube, but much less so if it is moved towards the ends. The implication is that this is a method that might be exploited by protein channels to control water transport via the positioning of ionized residues.

The freezing-point depression of water that hydrates phospholipid membranes has been studied using NMR by Dong-Kuk Lee at Seoul National University of Technology and coworkers (D.-K. Lee et al., Langmuir 24, 13598 (2008) – paper here). They find that water molecules still show liquid-like signatures below -20 C in bilayers, and that the freezing behaviour is depressed still further by cholesterol, a known cryoprotectant.

I have a kind of follow-up to my Chem. Rev. article in a forthcoming issue of ChemPhysChem, which has now appeared online (here). This will form part of a special issue on the subject of water at interfaces, stemming from a meeting of the DFG Forschergruppe 436 in Dortmund last summer.

Some DNA - and is the 220 K transition real?

2008-11-14T12:43:00.000-08:00

At the end of October I had the pleasure of chairing the workshop on Water at Biological Interfaces in Hangzhou, China. It was a truly enjoyable and satisfying experience. Thanks to everyone who participated, and especially to the hosts at Zhejiang University and in Shanghai.

Happily, the papers have not been proliferating too rapidly while I was away…

Thomas Truskett at Texas at Austin and his colleagues have taken another look at the ‘hydrophobic collapse’ of polymers posited by Lum, Chandler and Weeks (G. Goel et al., J. Phys. Chem. B 112, 13193-13196; 2008 – paper here). They have used MD simulations of simple bead-spring polymers in water to probe how polymer collapse dependson the strength of van der Waals attractions. Provided that these are not too strong, they seem to have rather little influence on the potential of mean force for polymer collapse that arises from putative dewetting ‘cavity’ effects.

Alessandro Paciaroni of the Università degli Studi di Perugia and colleagues say that the low-energy vibrational mode density of states of the hydration water of maltose binding protein at 100 K are similar to those of amorphous ice, and quite different from crystalline ice (A. Paciaroni et al., Phys. Rev. Lett. 101, 148104; 2008 – paper here).

A potential to describe interactions between two hydrophobes that posits two minima – one for direct contacts, the other for an intervening water layer – seems empirically to work well in protein structure prediction. But why? Florin Despa and Stephen Berry have studied this question for the model case of methane (Biophys. J. 95, 4241; 2008 – paper here). They say that the ‘water-mediated’ minimum can be understood as the interaction of dipoles on the methane molecules induced by the (oriented) water layer.

Joe Dzubiella at TU Munich has looked at the effects of salt bridge on the conformation of a short, helical alanine-based peptide, rationalizing the denaturing effects of NaCl and NaI in terms of ion binding to specific residues and changes in hydration (JACS doi:10.1021/ja805562g – paper here).

Kristina Furse and Steven Corcelli at the University of Notre Dame have looked at the question of why the dynamics of probe molecules (e.g. fluorescent) at the interface of water with proteins or DNA seem to be significantly slower than those in bulk aqueous solution (JACS doi:10.1021/ja803728g – paper here). The issue is whether this slowing is dominated by changes in solvation water dynamics or by the dynamics of the biomolecules. The MD studies reported here, for the fluorescent probe molecule Hoescht 33258 bound to DNA, support the latter interpretation.

More on the roles of water bound in the active sites of enzymes on their catalytic mechanism. Yanli Wang and Tamar Schlick of New York University look at a DNA polymerase Dpo4, where a crucial deprotonation step seems to be mediated by two bridging water molecules (JACS 130, 13240-13250; 2008 – paper here).

Takeshi Yamazaki at the National Institute for Nanotechnology in Edmonton, Canada, and his colleagues have looked at the role of hydration in the formation of amyloid aggregates (Biophys. J. 95, 4540-4548; 2008 – paper here). This is a topic starting to attract a considerable amount of attention, as I’ve mentioned earlier. Yamazaki and colleagues say that there is a large entropic driving force to aggregation stemming from hydration, which they say implicates hydrophobic cooperativity as a dominant factor. I’ve only seen the abstract for this.

Alexei Sokolov at the University of Akron and his coworkers have combined dielectric spectroscopy and neutron scattering to probe the hydration dynamics of hydrated lysozyme powder between 180 and 300 K (S. Khodadadi et al., J. Phys. Chem. B 112, 14273-14280; 2008 – paper here). They see a smooth, super-Arrhenius relaxation for both the protein and its hydration shell across this entire temperature range, with no anomaly at around 220 K, which challenges the interpretation of this anomaly by S.-H. Chen and colleagues as a fragile-to-strong crossover. Rather, they think this apparent anomaly is just an artefact of the protein dynamics reaching the resolution limit of neutron spectrometry. That seems destined to provoke debate.

Jim Hynes and Damien Laage have extended their previous analysis in Science (311, 832; 2006) of the molecular reorientation mechanism of pure water (Laage & Hynes, J. Phys. Chem. B 112, 14230-14242; 2008 – paper here). They argue that the reorientation has only a small diffusive component, and occurs mostly through large-angle jumps prompted by H-bond rearrangements. The rate-limiting step is not the breaking of the H-bond itself, but the translational motion and bond elongation involved in the departure of the ‘old’ partner and the arrival of the ‘new’ one.

A curious but interesting paper by Julia Berashevich and Tapash Chakraborty of the University of Manitoba examines the influence of hydration water on the electrical and magnetic properties of DNA, mostly with an eye on the implications for DNA-based spintronic devices (J. Phys. Chem. B 112, 14083-14089; 2008 – paper here). H-bonding of the bases to water molecules creates unbound pi electrons which can contribute to conductance, and the spin-spin interactions of unbound electron pairs can result in a magnetic-field dependence of conductance.

Pores, membranes, and knots

2008-10-07T13:10:00.000-07:00

Nikolai Ivashin of the Institute of Physics in Minsk, Belarus, and Sven Larsson at Chalmers University in Sweden have investigated the role of an interstitial water molecule (water-A) in the primary charge-separation process of a bacterial photosynthetic reaction centre (J. Phys. Chem. B 112, 12124-12133; 2008 – paper here). It seems that water-A donates a proton to a side-chain group, and receives one from another, during the photoexcitation process, stabilizing the charge-transfer state. Water-A cannot rotate in the ground state, but this becomes possible in the photoexcited state – but if I read this rightly, it’s not clear that this is an essential part of the process.

Robert Harrison and coworkers at Georgia State University have compared the radial distribution functions of hydration water molecules from 105 protein crystal structures with that of bulk water (X. Chen et al., J. Phys. Chem. B 112, 12073-12080; 2008 – paper here). The two differ, but actually not by very much: the first and second maxima are sharper for hydration water, but appear at much the same separations. Certainly, the hydration-water rdfs are not ice-like.

Tetsuo Okada of the Tokyo Institute of Technology and coworkers have used XAFS to investigate the hydration structure of alkali metal cations and of bromide in aqueous solution and in a solution of ovalbumin (T. Ohki et al. J. Phys. Chem. B 112, 11863-11867; 2008 – paper here). They find little difference between the two cases, and conclude that the positive free energy of transferring the ions from water to the protein solution comes from perturbations only of the second hydration shell and/or beyond.

Chang Won and N. R. Aluru of the University of Illinois at Urbana-Champaign have studied water inside the nanoscale channels of boron nitride nanotubes (JACS 10.1021/ja803245d – paper here). Their simulations show that formation of a Stone-Wales defect in the wall structure – basically the conversion of four adjoining hexagons into two pentagons and two heptagons – will trigger the severing of a hydrogen-bonded chain of water molecules through a narrow tube (0.69 nm width) and create a vapour-like bubble localized at the defect, reducing water transport through the tube. This is further evidence of the acute sensitivity of water transport in these nanoscale pores to small perturbations (and thus the possibility of gated flow).

In a preprint shortly to be published in J. Phys. Chem. B, Valeria Molinero and Emily Moore of the University of Utah say that water can usefully be treated as an element intermediate between carbon and silicon (paper here). This somewhat rough and ready ‘monatomic’ water model does a surprisingly good job of capturing many of the key properties, and should supply a computationally cheap coarse-grained description for simulations.

Ulrich Schmidt and colleagues at the German Cancer Research Centre in Heidelberg show how ‘hydrophobic mismatching’ – a difference in the thickness of a membrane protein’s transmembrane hydrophobic domain and the thickness of the membrane itself – can facilitate the non-specific clustering of membrane proteins commonly found in vivo (U. Schmidt et al., Phys. Rev. Lett. 101, 128104; 2008 - paper here).

There is an interesting set of papers in the latest Faraday Discussions. Especially,
James Beattie and colleagues weigh in to the debate on the acid/base nature of interfacial water by reporting that zeta potential measurements show the air-water interface to be basic (Faraday Discuss. doi:10.1039/b805266b; paper here). They say that they see the same behaviour at all inert hydrophobic interfaces.

Francois-Xavier Coudert and colleagues report Monte Carlo simulations of water droplets confined in the nanoscale channels of zeolites (Faraday Discuss. doi:10.1039/b804992k; paper here). In hydrophobic pores the water leaves few dangling OH groups, while in hydrophilic pores it opens up to form weak hydrogen bonds with the zeolite oxygens.

And Maria Ricci and her colleagues argue that confined water shows similarities to supercooled water, in particular a shortening of hydrogen bonds
(M. A. Ricci et al., Faraday Discuss. doi:10.1039/b805706k; paper here).

In reference to the Beattie paper above, Greg Voth and colleagues further the contrary view, using the empirical valence-bond model, that hydrated protons are preferentially segregated at water-hydrophobic interfaces (S. Iuchi et al., J. Phys. Chem. B doi:10.1021/jp805304j; paper here). I confess that I am not optimistic about finding some reconciliation of all this in the near future, but I hope someone will.

Jeremy England and Vijay Pande have expanded on their recent JACS letter investigating the way water may be organized inside chaperonins, supporting the view that the cavity of GroEL may create a microenvironment that enhances the hydrophobic effect (Biophys. J. 95, 3391-3399; 2008 – paper here).

Andrew McCammon and colleagues at UC San Diego have looked at the thermodynamics of lipid partitioning between membranes and solution (A. A. Gorfe et al., Biophys. J. 95, 3269-3277; 2008 – paper here). They conclude that the hydrophobic effect here is primarily enthalpy-driven.

Joe Dzubiella at TU Munich has an interesting preprint) describing how a protein knot might trap a water molecule – I’ve discussed this and related work in my column in the October issue of Nature Materials.

Are nanopipes more slippery?

2008-09-17T05:42:00.000-07:00

Several recent papers have shown both theoretically and experimentally that water flows through nanopipes (such as carbon nanotubes) more quickly than would be expected by extrapolating normal macroscopic pipe flow to the nanoscale (see, for example, J. C. Rasaiah et al., Ann. Rev. Phys. Chem. 59, 713-740; 2008). This, along with the exclusion of ions from very narrow pores, has raised hopes that nanotube membranes might be used for efficient desalination. One day New Scientist is going to publish a feature from me on this, but they have been sitting on it for months (as is their wont). Now Nick Quirke at Imperial College in London and colleagues have found enhanced transport, by a factor of up to 45, for water and other liquids (ethanol, decane) through wider carbon nanotubes than studied previously (M. Whitby et al., Nano Lett. 8, 2632-2637; 2008 - paper here). The reasons are not yet fully understood, but are likely to depend on the specifics of the fluid-wall interaction. This doesn’t obviously help much with desalination, but bodes well for ultrafiltration.

But John Thomas and Alan McGaughey at Carnegie Mellon sound a warning bell. Their MD simulations (J. A. Thomas & A. J. H. McGaughey, Nano Lett. 8, 2788-2793; 2008 – paper here) find significantly lower flow enhancement than reported previously in experiments (e.g. Holt et al., Science 312, 1034-1037; 2006; Majumder et al., Nature 438, 44; 2005). Thomas and McGaughey suggest that the experiments might have miscalculated the true flow area, or might have been affected by external driving forces such as electric fields.

Two papers this week probe the nature of nanoconfined water. Manu Sharma, Giulia Galli at UC Davis and their coworkers have calculated theab initio IR spectra of confined water, and say that some of the features seen experimentally are due to electronic charge fluctuations at the interface (M. Sharma et al., Nano Lett. 8, 2959-2962; 2008 – paper here). They also suggest that the frequency shifts of some spectral peaks relative to the bulk are due to confinement-induced changes in the hydrogen-bond network. And Jean Philippe Renault at CEA Laboratory of Radiolysis in Gif-sur-Yvette and colleagues use pump-probe IR spectroscopy to look at those effects on hydrogen bonds for water in porous glasses (I assume silica) with pores of 1, 13 and 50nm width (R. Musat et al., Angew. Chem. Int. Ed. doi:10.1002/anie.200802630; paper here). There are apparently modifications of the relaxational dynamics even for the largest pores. The bottom line reiterates a familiar notion: “the microscopic properties of water are influenced by the space it occupies.”

Roland Netz and colleagues at TU Munich have studied the friction and adhesion of polypeptides on hydrophilic and hydrophobic diamond surfaces using MD simulations (A. Serr, D. Horinek & R. R. Netz, JACS 130, 12408-12413; 2008 – paper here). They find stick-slip motion due to making and breaking hydrogen bonds (with little sign of cooperativity) on the hydrophilic surface, but smooth motion on the hydrophobic one.

Getting up to date

2008-09-10T01:48:00.000-07:00

I don’t like to do this, but a combination of holidays and a glut of papers means that, in order to have any chance of getting this blog up to date, I am going to have to provide a mere listing of relevant papers here, without further comment or explanation. I hope that the titles will speak for themselves; there is a wealth of nice stuff here. Normal service will be resumed as the days draw in.

1. PNAS advance online publication
Burst analysis spectroscopy: A versatile single-particle approach for studying distributions of protein aggregates and fluorescent assemblies
Jason Puchalla, Kelly Krantz, Robert Austin and Hays Rye
(Paper here).

2. J. Phys. Chem. B 112, 11106–11111, 2008. 10.1021/jp803956s
Hydrophobic Interactions in Urea_Trimethylamine-N-oxide Solutions
Sandip Paul and G. N. Patey
(Paper here).

3. J. Am. Chem. Soc. 10.1021/ja8021297
Interfacial structure of acidic and basic aqueous solutions
C. Tian et al.
(Paper here).

4. J. Phys. Chem. B 112, 11440-11445, 2008. 10.1021/jp803819a
Anomalously increased lifetimes of biological complexes at zero force due to the protein-water interface.
Y. V. Pereverzev et al.
(Paper here).

5. J. Phys. Chem. B 112, 11396-11401, 2008. 10.1021/jp8015886
Quantum mechanical studies of residue-specific hydrophobic interactions in p53-MDM2 binding
Y. Ding et al.
(Paper here).

6. J. Am. Chem. Soc. 130, 11854-11855, 2008. 10.1021/ja803972g
Chemical denaturants inhibit the onset of dewetting.
J. L. England et al.
(Paper here).

7. J. Am. Chem. Soc. 10.1021/ja8034027
Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations.
D. R. Nutt & J. C. Smith.
(Paper here).

8. J. Phys. Chem. B 112, 10786–10790, 2008. 10.1021/jp804694u
Polarization of Water in the First Hydration Shell of K+ and Ca2+ Ions
Denis Bucher and Serdar Kuyucak
(Paper here).

9. ASAP J. Phys. Chem. B ASAP Article, 10.1021/jp802795a
Hydration Water and Bulk Water in Proteins Have Distinct Properties in Radial Distributions Calculated from 105 Atomic Resolution Crystal Structures
Xianfeng Chen, Irene Weber and Robert W. Harrison
(Paper here).

10. ASAP J. Phys. Chem. B ASAP Article, 10.1021/jp711924f
Trapped Water Molecule in the Charge Separation of a Bacterial Reaction Center
Nikolai Ivashin and Sven Larsson
(Paper here).

11. J. Am. Chem. Soc. 130, 11582–11583, 2008. 10.1021/ja803274p
Specific Ion Binding to Nonpolar Surface Patches of Proteins
Mikael Lund, Lubos_ Vrbka and Pavel Jungwirth
(Paper here).

12. J. Am. Chem. Soc. 130, 11578–11579, 2008. 10.1021/ja802341q
Dissecting Entropic Coiling and Poor Solvent Effects in Protein Collapse
Frauke Gräter, Pascal Heider, Ronen Zangi and B. J. Berne
(Paper here).

13. ASAP J. Am. Chem. Soc. ASAP Article, 10.1021/ja8022434
Electron Capture by a Hydrated Gaseous Peptide: Effects of Water on Fragmentation and Molecular Survival
James S. Prell, Jeremy T. O’Brien, Anne I. S. Holm, Ryan D. Leib, William A. Donald and Evan R. Williams
(Paper here).

14. ASAP J. Chem. Theory Comput. ASAP Article, 10.1021/ct800121e
Dissecting the Hydrogen Bond: A Quantum Monte Carlo Approach
Fabio Sterpone, Leonardo Spanu, Luca Ferraro, Sandro Sorella and Leonardo Guidoni
(Paper here).

15. J. Am. Chem. Soc. 129, 2504 -2510, 2007. 10.1021/ja0659370 S0002-7863(06)05937-3
Effect of Field Direction on Electrowetting in a Nanopore
Dusan Bratko, Christopher D. Daub, Kevin Leung and Alenka Luzar
(Paper here).

16. J. Chem. Phys. 127, 174515 (2007); DOI:10.1063/1.2784555
Investigations on the structure of dimethyl sulfoxide and acetone in aqueous solution
S. E. McLain, A. K. Soper and A. Luzar
(Paper here).

(These latter two are older ones I’ve just discovered.)

17. Faraday Discussions 141, 1-12, 2008
Water-mediated ordering of nanoparticles in an electric field
D. Bratko, C. D. Daub & A. Luzar
Not yet on the web; doi:10.1039/b809135h

18. Biophysical Journal 95, 2916-2923, 2008
Hydration Affects Both Harmonic and Anharmonic Nature of Protein Dynamics
H. Nakagawa , Y. Joti , A. Kitao and M. Kataoka
(Paper here).

19. Langmuir 24, 9183–9188, 2008. 10.1021/la8014578
Teflon is Hydrophilic. Comments on Definitions of Hydrophobic, Shear versus Tensile Hydrophobicity, and Wettability Characterization
Lichao Gao and Thomas J. McCarthy
(Paper here).

20. PNAS 105, 12725-12729, 2008
NMR evidence of a sharp change in a measure of local order in deeply supercooled confined water
F. Mallamace, C. Corsaro, M. Broccio, C. Branca, N. González-Segredo, J. Spooren, S.-H. Chen & H. E. Stanley
(Paper here).

21. PNAS 105, 13391-13396, 2008
Dehydration of main-chain amides in the final folding step of single-chain monellin revealed by time-resolved infrared spectroscopy
T. Kimura, A. Maeda, S. Nishiguchi, K. Ishimori, T. Konno, Y. Goto & S. Takahashi
(Paper here).

22. J. Chem. Phys. 129, 034504, 2008
POLIR: Polarizable, flexible, transferable water potential optimized for IR spectroscopy
P. K. Mankoo & T. Keyes
(Paper here).

23. JACS 130, 9025-9030, 2008
Combined electrostatics and hydrogen bonding determine intermolecular interactions between polyphosphoinositides
I. Levental, A. Cebers & P. A. Janmey
(Paper here).

24. J. Phys. Chem. B 112, 5500-5511, 2008
Operation of the proton wire in green fluorescent protein. A quantum dynamics simulation
O. Vendrell, R. Gelabert, M. Moreno & J. M. Lluch
(Paper here).

25. PNAS 105, 9233-9237, 2008
A stringent test for hydrophobicity scales: two proteins with 88% sequence identity but different structure and function
A. E. Kister & J. C. Phillips
(Paper here).

26. J. Phys. Chem. B 112, 9532-9539, 2008
Effect of the air-water interface on the structure of lysozyme in the presence of guanidinium chloride
A. W. Perriman, M. J. Henderson, C. R. Evenhuis, D. J. McGillivray & J. W. White
(Paper here).

27. JACS 130, 10939-10946, 2008
Hydration and conformational mechanics of single, end-tethered elastin-like polypeptides
A. Valiaev, D. W. Lim, S. Schmidler, R. L. Clark, A. Chilkoti & S. Zauscher
(Paper here).

28. J. Phys. Chem. B 112, 10158-10164, 2008
Do probe molecules influence water in confinement?
B. Baruah, L. A. Swafford, D. C. Crans & N. E. Levinger
(Paper here).

29. J. Phys. Chem. B 112, 7702-7705, 2008
Stepwise hydration of protonated proline
C. Michaux, J. Wouters, E. A. Perpète & D. Jacquemin
(Paper here).

30. J. Phys. Chem. B 112, 7157-7161, 2008
Anion fractionation and reactivity at air/water:methanol interfaces. Implications for the origin of Hofmeister effects.
J. Cheng, M. R. Hoffmann & A. J. Colussi
(Paper here).

31. J. Phys. Chem. B 112, 7810-7815, 2008
Two-particle entropy and structural ordering in liquid water
J. Zielkiewicz
(Paper here).

32. PNAS 105, 7456-7461, 2008
Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
C.-E. A. Chang, W. A. McLaughlin, R. Baron, W. Wang & J. A. McCammon
(Paper here).

33. Mol. Phys. 106, 485-495, 2008
The distribution of acceptor and donor hydrogen-bonds in bulk liquid water
O. Markovitch & N. Agmon
(Paper here).

Some meeting news:
Alenka Luzar is organizing a session at Pacifichem 2010 that hits the bullseye of all the topics I try to cover here; see here.

And finally, a real oddity:
Geophys. Res. Lett. 35, L16710, doi:10.1029/2008GL034288, 2008
Magnetic effect on CO2 solubility in seawater: A possible link between geomagnetic field variations and climate
Alexander Pazur& Michael Winklhofer
(Paper here).
This looks at face value irrelevant to water in biology, except that if these weak-field effects are seen for seawater, would one not expect them for blood and cytoplasm? And in that case, would significant changes in air and CO2 solubility not be expected to have profound physiological implications? And am I therefore right to be deeply sceptical?

Inside chaperonins, and dewetting for amyloids

2008-08-20T10:26:00.000-07:00

If I were ever to do something as tendentious as deciding on a ‘paper of the week’, on this occasion it would be this one. Vijay Pande and colleagues at Stanford argue here that water trapped inside barrel-shaped enzymes called chaperonins could be crucial to the way they help proteins to fold (J. L. England et al., JACS doi:10.1021/ja802248m). This encapsulated water has generally been neglected previously. When the chaperonin complex GroEL+ES takes in an unfolded protein, it undergoes a conformational change to expose hydrophilic residues on its inner surface. Using MD simulations, Pande and colleagues show that this can be explained as a way of sequestering water in the cavity, which creates a stronger driving force for folding driven by hydrophobic interactions. Cavity hydrophilicity turns out to be well correlated with refolding rate, and fine differences found for various GroEL mutants can be explained on the basis of different spatial distributions of charged residues. The message is that this enzyme seems to mould the solvent micro-environment to favour folding in a generic way.

Joan-Emma Shea at UCSB and coworkers have teamed up with Bruce Berne, Ruhong Zhou and Lan Hua at Columbia to extend the latter group’s investigations of dewetting transitions in protein aggregation and folding to amyloids (M. G. Krone et al., JACS 130, 11066-11072; 2008 – paper here). They look at the formation of protofilaments from two parallel beta-sheets of segments of the Alzheimer amyloid-beta. Dewetting occurs in some but not all of the simulation trajectories – when it doesn’t, hydrophobic collapse is simultaneous with the expulsion of water from between the hydrophobic faces of the peptides. Dewetting always occurs when the van der Waals forces between the proteins and water are turned off, suggesting that these attractions may in reality be often sufficient to compensate for the loss of hydrogen-bonding in the confined water. Small changes in the simulation temperature can also tip the balance, suggesting both that the results of simulations like this may be highly sensitive to the nature of the molecular force fields used and also, I guess, that the balance between dewetting or not may be rather finely balanced in vitro/vivo as well as in silico.

More on the hydrophobic gap: Mark Schlossman at the University of Illinois at Chicago and colleagues have used X-ray reflectivity to probe the oil-water interface, both for heptane and for the extreme superhydrophobic case of perfluorohexane (K. Kashimoto et al., Phys. Rev. Lett. 101, 076102; 2008 – paper here). In both cases they find that any vapour-like depletion layer can be no thicker than 0.2 Å. It seems the evidence is now fairly overwhelming that a single hydrophobic surface in water is not in any meaningful sense ‘dry’.

Aggrecan, a proteoglycan with a ‘bottle-brush’ structure that is involved in the organization of the extracellular matrix of cartilage, seems to be extremely insensitive to salt, according to scattering experiments (SANS, SAXS, light) by Ferenc Horkay at NIH and colleagues (Phys. Rev. Lett. 101, 068301; 2008 – paper here). They find that the aggregation properties are very insensitive to calcium concentrations. This seems to be a necessary consequence of its biological role: aggrecan assemblies not only protect bone surfaces from wear and lubricate joints but also seem to provide a reservoir of calcium ions for bone mineralization. It’s interesting that nature could find a way of engineering such salt-independent properties into a polyelectrolyte – achieved, apparently, by virtue of the rigidity conferred by the side-chains.

I have tended naively to assume that we knew already all that needed to be known about the differences between heavy and light water. Clearly that isn’t so. Alan Soper and Chris Benmore use X-ray and neutron diffraction and simulation to refine the differences, and say that they have been underestimated. The OH bind length in water is longer than OD by about 3 percent, while the H-bond is about 4 percent shorter – making the H-O---H bond more symmetric than O-D---O (Phys. Rev. Lett. 101, 065502: 2008 – paper here).

Sony Joseph and Narayana Alura at the University of Illinois at Urbana-Champaign say that using electric fields to orient the dipoles of water molecules inside carbon nanotubes introduces a coupling between rotational and translational motions that creates a directional bias for diffusion, which can be used to pump the molecules through the tube (Phys. Rev. Lett. 101, 064502; 2008 – paper here). This is intriguing, although it seems to me that basically much the same result as was reported last year by Haiping Fang and colleagues (X. Gong et al., Nature Naotechnology 2, 709-712; 2008 – paper here).

Urban Johanson at Lund and coworkers have just published a high-resolution crystal structure of human aquaporin 5, with a fine view of the central pore (R. Horsefield et al., PNAS doi:10.1073/pnas.0801466105 – no link available yet). In contrast to other aquaporins, here the passage of gas molecules and ions seems to be prevented by a lipid occluding the central pore.

Bert de Groot at Göttingen has done a lot of work on the transport mechanism of aquaporins, and now he and coworkers have looked at the generic mechanism of ion permeation and gating in narrow peptide channels (G. Portella et al., Biophys. J. 95, 2275-2282; 2008 – paper here). I only have the abstract of this paper, but it appears they find that the free-energy barrier for ion permeation is predominantly entropic, arising from constraints on motion within the channels, rather than from the enthalpic cost of desolvation.

Some new perspectives on old debates

2008-08-06T02:00:00.000-07:00

Garegin Papoian has extended his previous studies of how water-mediated contacts influence protein folding, with a new paper with Christopher Materese and Christa Goldmon (C. K. Materese et al., PNAS doi:10.1073/pnas.0801850105 – paper here). The basic notion is that a variety of contacts in the folding peptide – hydrophobic, hydrophilic, salt bridges – are ‘tried out’ during the folding process and filtered down to a subset of preferred interactions in a hierarchical branching process. This paper shows that many of these contacts are mediated by bridging water molecules, and that subsets of such interactions are characteristic of certain basins in the folding landscape. It adds to the argument that explicit water is essential for a full picture of the folding process.

Valerie Daggett and colleagues at the University of Washington in Seattle have carried out simulations of aquaporin embedded in a lipid bilayer to study the role of protein fluctuations on water transport (N. Smolin et al., Biophys. J. 95, 1089-1098; 2008 – paper here). Their aim was to look at some of the apparent discrepancies in earlier studies of how water passes through the protein pore in a hydrogen-bonded wire (e.g. Tajkhorshid et al., Science 296, 525-530; 2002; de Greet & Grubmuller, Science 294, 2353-2357; 2001). The key action seems to happen in the narrow constriction at the centre of the channel called the NPA region. Here, the dynamics of two asparagine residues seem to play a crucial role in aligning the water molecules for transport to occur. But beyond the constriction is a ‘valve’ region in which two residues, His76 and Val155, act to control the flow by potentially swinging into the channel to block the passage of the water molecules. The emerging picture, then, is of a remarkably orchestrated collaboration of side-chain and water dynamics to regulate the progress of the water along the ‘wire’.

H. Nagase of Hoshi University in Tokyo and his coworkers have continued their exploration of the molecular mechanisms of anhydrobiosis and how trehalose acts as a bioprotectant in this regard (H. Nagase et al., J. Phys. Chem. B. 112, 9105-9111; 2008 – paper here). They have studied the crystal structure of trehalose anhydrate, and find that it contains a one-dimensional channel threading between the trehalose molecules which may be filled with water in the dihydrate form of solid trehalose. This water uptake facilitates the transformation from the anhydrate to the dihydrate, and effectively makes the crystalline form a potential source and sink of water. If I understand this rightly, I believe the idea is then that this ‘water sponge’ prevents uptake of water by the amorphous (glassy) phase of trehalose thought to be responsible for bioprotection, which would otherwise lower its glass transition temperature.

Fernando Bresme at Imperial College and his coworkers have returned to the controversial question of a ‘hydrophobic gap’ or depletion layer at the interface of water with a hydrophobic surface (Phys. Rev. Lett. 101, 056102; 2008 – paper here). They model this interface as that between water and dodecane or hexane, which they study using computer simulations. Their objective is to decouple the intrinsic width and density profile of the interface with the effect of fluctuations from capillary waves, which will blur the details. They find that at 300 K water at the interface resembles that at the air-water interface – despite the fact that there is no appreciable intervening vapour film because the system is far from the drying transition. And the interface is rather rigid: corrugations remain well below a molecular diameter. But the water structure is significantly perturbed, with layering similar to that seen at a hard surface. Of course, this leaves open the question of what a nanoscopic film of water looks like between two such surfaces (see below), let alone the issue of how (if at all) a more rigid hydrophobic surface changes the situation. But it does seem to support the growing consensus that any ‘hydrophobic gap’ is extremely narrow.

On the same issue, there’s an interesting exchange in Phys. Rev. Lett. between Ben Ocko and colleagues and Steve Granick and coworkers (B. Ocko et al., Phys. Rev. Lett. 101, 039601 and A. Poynor et al., 039602; 2008 – letters here and here). Poynor et al. claimed previously (Phys. Rev. Lett. 97, 266101; 2006) that they see a depletion layer 2-4 Å thick with a reduced water density of at least 40 percent of the bulk. Ocko et al. say that, if the hydrogen-rich methyl groups of the hydrophobic monolayer are taken into account, the density deficit is much reduced, and might in fact be explained instead by local water orientation. Poynor et al. reject the latter interpretation, but agree that, as they stated, their originals density depletion was cited only as an upper bound. They point out that there does now seem to be agreement that a depletion zone exists (and, I guess, that it is very narrow and certainly not gas-like), and argue that the focus now should be on the role of fluctuations in the interfacial density. David Chandler has argued that indeed it’s the fluctuations (as opposed to the average equilibrium state) that matter for any discussion of how dewetting might occur between two such surfaces.

I have been meaning for some time to mention a paper by Alexander Pertsin and Michael Grunze (Langmuir 24, 4750-4755; 2008 – paper here) on simulations of the shear behaviour of water films between hydrophilic surfaces. Perhaps the delay was fortuitous, because into this discussion there now comes an experimental paper by K. B Jinesh and Joost Frenken at Leiden (Phys. Rev. Lett. 101, 036101; 2008 – paper here). Pertsin and Grunze previously simulated water monolayers (Langmuir 24, 135; 2008 – paper here), and found that they could observe essentially solid-like configurations in the confined layer. They now say that solidification can happen for bilayers too when sheared quasi-statically (that is, with an infinitely small shear rate) – but only for a small range of wall-to-wall separation, where the separation between the two monolayers is favourable for the formation of hydrogen bonds between them. The solid-like shear behaviour also depends on the relative alignment and period of the wall lattices. And importantly, the solid-like shear behaviour does not involve film crystallization. For trilayers, there is no solid-like behaviour at all.

So then, a complex picture. Now, already this seems to complicate the picture reported by Zhu and Granick (Phys. Rev. Lett. 87, 096104; 2001), where oscillatory shear of electrolyte films between mica showed no solid-like signature. One might add that Jacob Klein and colleagues have also seen the retention of fluidity in sub-nanometre confined water films under shear (U. Raviv et al., Nature 413, 51-54; 2001). Yet Jinesh and Frenken claim to see a solid-like response in their friction-force measurements of water between a graphite surface and a tungsten tip. Specifically, they see stick-slip behaviour which seems to change, with increasing humidity, from that expected for graphite corrugation to that with a different periodicity (around 0.4 nm), similar to a lattice periodicity of ice. The film thickness here is not known for sure, but is less than about 2 nm. (I notice that they have made this claim before on the basis of different evidence, which has caused a little confusion.)

Now, I’ve seen some criticisms of this latest work – for example, that it seems to attribute thermodynamic transitions from dynamic mechanical measurements, that it ignores the possibility of surface reconstructions of bulk ice or of a tip-sample potential and the role of the lateral spring constant in the cantilever in determining the 0.4 nm periodicity. This is a tricky issue – it would be unfair to level unattributed criticisms at the work, but neither can I pretend I haven’t heard them. I guess I can only say that there seems to be a debate in store, and until that happens we might best regard the results as no more than suggestive. In any event, if Pertsin and Grunze are right, there is likely to be a great deal of further subtlety to the question, not least in terms of the lattice periodicities and the hydrophobicity/hydrophilicity of the surfaces.

Staying with fundamentals, Noam Agmon, Greg Voth and their colleagues present a new look at the details of proton transport in water – classically explained by the Grotthuss hopping mechanism but now known to be a more complex, cooperative process (O. Markovitch et al., J. Phys. Chem. B 112, 9456-9466; 2008 – paper here). Their quantum-chemical calculations offer a fine-grained picture involving a range of time and distance scales: a ‘dance’ that embraces proton motions and water reorientations in both the first and the second hydration shells of the central hydronium ion.

An interesting paper by Haoran Li and colleagues at Zhejiang University in Hangzhou (X. Hu et al., J. Phys. Chem. B doi:10.1021/jp8028903 – paper here) explores not a biologically relevant process per se – the iron-porphyrin-catalysed activation of methane and methanol – but one that has interesting parallels to the functions of some cytochromes and horseradish peroxidise. In both of those latter cases, water molecules have been found to play important roles, particularly by providing bridges for proton transport to or from the heme group. Water has also been found to assist metal-porphyrin-catalysed oxidation in trace amounts, but to suppress the reaction when present in greater amounts. Li et al. find that a water molecule near the iron porphyrin can either assist or inhibit the catalytic processes considered here, depending on where it sits.

Hydration dynamics, amyloids, and more

2008-07-23T02:41:00.000-07:00

My pile of water-related papers is stacking up worryingly, so let me now try to clear it. Thanks again to everyone who has sent me papers – it is always a pleasure to receive them.

Roberto Senesi and Antonino Pietropaolo at Rome and their colleagues have been producing a succession of papers in which they use inelastic neutron scattering to study the momentum distributions of protons in water in a variety of settings: in nano-confined systems (G. Reiter et al., Phys. Rev. Lett. 97, 247801; 2006 – paper here; and V. Garbuio et al., J. Chem. Phys. 127, 154501; 2007 – paper here), in supercooled water (A. Pietropaolo et al., Phys. Rev. Lett. 100, 127802; 2008 – paper here) and the ambient liquid and supercritical phase (C. Pantalei et al., Phys. Rev. Lett. 100, 177801; 2008 – paper here), and in a protein hydration shell (R. Senesi & A. Pietropaolo, Phys. Rev. Lett. 98, 138102; 2007 – paper here). The last of these is of course particularly relevant here. The authors study the momentum distributions for hydration protons around lysozyme both above (290 K) and below (180 K) the dynamical transition at around 220 K. At 290 K, the results are consistent with a hydration shell that is slightly denser than bulk water, with a smaller oxygen-oxygen distance that confines the protons in a double well, with the possibility of tunnelling between minima. This suggests that tunnelling may occur even at room temperature ion the hydration shell, with potential implications for biological function. That, of course, is something that would be picked up in simulations only in a full quantum-chemical treatment.

There’s an important paper by Johan Qvist and Bertil Halle in JACS (doi:10.1021/ja802668w paper here) on rotational dynamics of water in hydrophobic hydration shells, probed by deuterium NMR. They find for four partly hydrophobic solutes, including two peptides and two osmolytes, that below 255 K hydration water rotates with a lower activation energy, and faster if the temperature is low enough, than it does in the bulk. As they say, “these findings reverse the classical ‘iceberg’ view of hydrophobic hydration by indicating that hydrophobic hydration water is less ice-like than bulk water.” It will be good to put that idea finally to rest. Moreover, the two osmolytes have opposite effects on protein stability but the same effect on water dynamics, again challenging the common view that somehow ‘water structure’ is responsible for these effects. As the authors say, “Such poetic explanations may be misleading unless they are accompanied by a precise definition of water structure. Indeed, much of the confusion in the literature stems from indiscriminate use of the word ‘structure’. Furthermore, the connection between water dynamics and structure is non-trivial.” These NMR results do, however, seem to conflict with quasi-elastic neutron scattering studies (e.g. D. Russo et al., Biophys. J. 86, 1852; 2004), and Qvist and Halle suggest some reasons for that. A final word of caution: the small peptides here serve as models for unfolded proteins, while as Qvist and Halle say, “for folded proteins, the intricate surface topography features solvent-penetrated pockets with more substantial perturbations of water dynamics than at the convex parts of the surface.”

Poul Petersen and Rick Saykally have a new contrubution to the ongoing debate over whether the air-water surface is basic or acidic (Chem. Phys. Lett. 458, 255-261; 2008 – paper here). They use resonant UV second-harmonic generation spectroscopy to study the question, and find that the results are best understood as indicating a surface depletion of hydroxide and enhancement of hydrated protons. This paper gives a nice overview of the history of this issue and the current state of play, and offers a suggestion for why the results seem to conflict with the conclusions based on macroscopic measurements of zeta potentials at bubble surfaces.

More on gating of protein channels. Carmen Domene at Oxford and coworkers report a simulation study of potassium channels in which they look at how conformational changes in the constriction responsible for ion selectivity can also induce gating by in effect snipping the hydrogen-bonded chain of water molecules (C. Domene et al. JACS doi:10.1021/ja801792g; paper here). Dirk Gillespie at Rush University Medical Center had a recent paper on the mechanism of divalent selectivity in calcium channels (Biophys. J. 94, 1169-1184; 2008 – paper here). And he and his coworkers have a new paper using synthetic nanopores to investigate a theory for the mechanism of the anomalous mole fraction effect in ion channels, whereby two types of ion produce a lower conductance than the same concentration of either ion on its own (D. Gillespie et al., Biophys. J. 95, 609-619; 2008 – paper here). They show that single-file motion of the ions through the channel is not necessary to produce this effect.

At the recent meeting of the DFG Forschergruppe 436 in Dortmund I had the pleasure of meeting Rajesh Mishra and Roland Winter, who now have an interesting paper on the issue of amyloid polymorphisms of proteins, specifically on how cold denaturation and high pressure can dissolve protein aggregates (Angew. Chem. Int. Ed. doi:10.1002/anie.200802027 – paper here). I’ve not been able to read the full paper yet, but from talking to Rajesh I can see that this is a potentially very fruitful direction.

Also forthcoming in Angewandte Chemie, though I’ve not seen it online yet, is a paper by Martin Gruebele, Martina Havenith and colleagues entitled “Real-time detection of protein-water dynamics upon folding by terahertz absorption”, which does what it says on the can (the protein here is ubiquitin). The results provide more evidence of slaving of (some) protein dynamics to solvent motions – in this case, if I understand correctly, the coupling comes from the way hydrogen bonds between the unfolded protein backbone and water are broken and then remade as intramolecular H-bonds in the secondary structure.

In a somewhat related vein, Biman Bagchi and colleagues at the Indian Institute of Science in Bangalore have studied hydrogen-bond breaking in the hydration shell of lysozyme (B. Jana et al., J. Phys. Chem. B doi:10.1021/jp800998w – paper here). They see three different mechanisms for bond-breaking. In 80 percent of cases, the new acceptor water molecule comes from within the first coordination shell, and the old acceptor water molecule remains in the shell. Neither the incoming nor the outgoing acceptor molecules show diffusive motion. In 10 percent of cases, the new acceptor comes from the second coordination shell, with the donor being in the first. In the remaining 10 percent of cases, both of the acceptor molecules are initially in the first coordination shell, but the old acceptor moves out after bond breaking. In all cases, the donor molecule undergoes a large-angle reorientational jump on making the new bond.

Alfonso De Simone in Naples (currently at Cambridge) has sent me a couple of nice reprints. In a paper in Proteins (G. Colombo et al., Proteins 70, 863-872; 2008) he and his colleagues have looked at whether amyloid-like fibrils, here of ribonuclease A, retain native-like domains. Using MD simulations, they find that this is indeed the case in these fibrils: there are segments that retain monomer-like conformations, dynamics and hydration structures, explaining why the fibrils seem to retain some catalytic activity. They also discuss how hydration changes in polyglutamine stretches might promote hydrophobic collapse leading to aggregation (despite the fact that glutamine is generally considered to be hydrophilic). Alfonso says “a better inspection showed that the huge accessibility of glutamines to sidechain-sidechain H-bonds generated a chaotic and complex network. As a result of continuous forming and breaking of sidechain-sidechain H-bonds, the water was not able to interact stably with glutamines and presented very short residence times… Therefore the message is that dewetting can be triggered even by surfaces that are able to engage in a large number of H-bonds with water. Sometimes the dynamics of the interaction are even more important than the interaction itself.”

The other paper looks at the “Role of hydration in collagen triple helix stabilization” (A. De Simone et al., Biochem. Biophys. Res. Commun. 372, 121-125; 2008). They find, again vai MD simulations, a wide range of water residence times in the hydration layer, strongly influenced by the local peptide sequence. Moreover, the stabilizing effect of Arg and Hyp (hydroxyproline) residues on the triple helix is water-mediated.

Well, that does not clear my pile but it makes a dent. More as soon as I’m able.

Hangzhou Water 08

2008-07-03T08:55:00.000-07:00

Time, I think, for this announcement of a forthcoming meeting in China. Apologies that the web link below isn't up and running yet, but I'm sure it soon will be.

Workshop on Water at Biological Interfaces

Hangzhou Water08
Oct. 27-28, 2008, Hangzhou, China
http://www.sinap.ac.cn/water08/index.html

First Announcement & Call for papers

Hangzhou Water08 is sponsored by the Shanghai Institute of Applied Physics (SINAP), cosponsored by the Zhejiang University, Organized by Shanghai Institute of Applied Physics, Chinese Academy of Sciences, and supported by National Science Foundation of China and the Chinese Academy of Science, and Ministry of Science and Technology of the People’s Republic of China

Water at biological interfaces plays a crucial role in cell and molecular biology. It has become increasingly clear over the past two decades or so that water is not simply life’s passive solvent, but is an active and versatile matrix that engages and interacts with biomolecules in complex, subtle, and essential ways. Most dramatically, it affects the structure, dynamics, folding and unfolding, interactions and functions of proteins. Moreover, the structure and dynamics of protein hydration shells seem to feed back onto those aspects of the biomolecules themselves, so that biological function depends on a delicate interplay between what we have previously regarded as distinct entities: the molecule and its environment. A fundamental understanding of the properties of water at biological interfaces is also important for many practical issues, including environmental problems and technologies for desalination, purification and waste water recovery.

The workshop provides an excellent opportunity for researchers from different disciplines to review the latest progress on interfacial biological water, and exchange their experience, progress and ideas.

Chair: Philip Ball, Nature, 4-6 Crinan Street, London N1 9XW, U.K.
Co-Chair: Haiping Fang, Shanghai Institute of Applied Physics, CAS, Shanghai
Secretary: Shenfu Chen, Zhejiang University
Xiaoling Lei, Shanghai Institute of Applied Physics, CAS, Shanghai

Organizing Committee
1. Enge Wang, Institute of Physics, CAS, China
2. Xiangyang Liu, National University of Singapore, Singapore
3. Ruhong Zhou, IBM Watson and Columbia University, USA
4. Jichen Li, University of Manchester, UK
5. Yuhong Xu, Shanghai Jiao Tong University, China
6. Jun Hu, Shanghai Institute of Applied Physics, CAS, China
7. Fengshou Zhang, Beijing Normal University, China
8. Gang Pan, State Key Laboratory of Environment Aquatic Chemistry, CAS, China
9. Shaoping Deng, Zhejiang Gongshang University, China
10. Shenfu Chen, Zhejiang University

More Hofmeister headaches

2008-06-26T15:08:00.000-07:00

The debate rumbles on over Hofmeister effects. In a paper in Scholarly Research Exchange [doi:10.3814/2008/761829 – paper here], Terence Evens and Randall Niedz of the US Horticultural Research Laboratory in Florida say that many previous studies of ion-specific effects on protein precipitation are flawed because they fail to take into account the dependence of pH on the type and concentration of ions in solution, treating it as an independent variable. More generally, they say that individual ion effects can’t be deduced in any straightforward way from the effects of specific salts. In a nutshell, this seems to be the key message: ‘Is the sulphate ion more effective at protein precipitation than the chloride ion? It depends on the protein. It depends on protein concentration. It depends on the concentration of the respective ions. It depends on the proportions and concentrations of the other cations and anions in solution. It depends on the dissolved gases. It may or may not depend on the pH. It depends on temperature. These dependencies are conflated, confounded, lost or ignored in traditional Hofmeister series, but are fundamentally essential to realizing a deeper understanding of ion-specific effects.’ Discuss, as they say. It’s certainly a rather discouraging message on what is already a bewildering problem, but Evens and Niedz present results for ovalbumin and BSA that seem to bear out this complexity.

In a related vein, Shekhar Garde and colleagues at RPI have examined the thermodyanmcis of hydrophobic hydration, association and folding for a hydrophobic polymer in sodium chloride solution and aqueous trimethylamine oxide (TMAO), an osmolyte [M. V. Athawale et al., J. Phys. Chem B 112, 5661; 2008 – paper here]. They’ve found previously that NaCl weakens hydrophobic hydration and enhances association, while TMAO has little effect (Ghosh et al., J. Phys. Chem. B 109, 642; 2005 and Athawale et al., Biophys. J. 89, 858; 2005). Here they carry out temperature-dependent simulations to figure out if the effects are entropic or enthalpic. For TMAO, there is almost precise enthalpic-entropic compensation. For NaCl, changes in solvent-solvent, solvent-salt and salt-salt energy lead to a dominant enthalpic contribution at small length scales (that is, for small solutes), but the strengthening of hydrophobic interactions is entropic in origin at large length scales, being governed by the need to form a solvent-solute interface. This seems to offer further evidence that there is no single ‘explanation’ of Hofmeister-type effects.

Meanwhile, Agustín Colussi and colleagues at Caltech have returned to a more basic level of the problem: the fractionation of ions at the air-water interface (a loose proxy for the air-hydrophobe interface) [J. Cheng et al., J Phys. Chem. B 112, 7157; 2008 – paper here]. They have shown previously [J. Cheng et al., J. Phys. Chem. B 110, 25598; 2006] that aggregation of anions at the interface seems to increase with increasing ion radius. They now extend their experimental study to the cases of the large anion PF6- and the highly polarizable IO3-, and look also at the effect of adding methanol, which will migrate to the surface and cap it with methyl groups. The same relationship with ion radius is found, and the fractionation barely depends on the methanol content. The authors conclude that this fractionation happens not because the ions have any affinity with the surface but because they are expelled from the bulk.

Now forget the salts. Esben Thormann and colleagues at the University of Southern Denmark have looked again at a familiar model system: a polystyrene particle several microns across stuck to an AFM tip and brought close to hydrophobic and hydrophilic surfaces [E. Thormann et al., Langmuir doi:10.1021/la8005162 – paper here]. For approaching surfaces in the hydrophilic case, all looks fine: the interactions are described by DLVO theory. But for the hydrophobic case, bridging air bubbles form, as has often been hypothesized, leading to jump-in at a separation of around 10 nm due to the action of the meniscus. When the particle is retracted, the bubble becomes elongated until it ruptures at about 70 nm. In both cases there are also force plateaus at separations of up to a few hundred nm, which the researchers interpret in terms of bridging polymer molecules pulled out from the particle surface. All this argues for caution in regarding the system as a model of the biological case.

Let’s stick with these model surfaces for a bit. Some time ago I mentioned some ‘curious’ results of Andrei Sommer and colleagues at the University of Ulm on irradiation of water films on diamond. I found some difficulty there figuring out what the underlying hypothesis was. Andrei has now sent me more material on this. The basic motivation for the work is the fact, known for some time but unexplained, that the surfaces of diamond are somewhat conductive. Andrei and colleagues believe this is due to proton migration in thin surface films of water, which are formed in humid conditions. Their experiments [A. P. Sommer et al., Cryst. Growth. Design 7, 2298; 2007] show that for hydrogen-terminated diamond, the conductivity drcreases with increasing humidity. They think this is because the highly ordered water films that form at low humidity are disrupted, degrading proton motion, as the films get thicker. This idea challenges the widely accepted model for the surface conductivity, called the transfer doping model [M. I. Landstrass & K. V. Ravi, Appl. Phys. Lett. 55, 975; 1989], which would predict increased conductivity with increased humidity. Andrei and colleagues have recently debated this point with John Angus and colleagues in Science [V. Chakrapani et al., Science 318, 1424; 2007].

From the perspective of water in biology, Andrei suggests the key point is that the highly ordered (indeed, essentially crystalline) water nanofilms he identifies on the (hydrophobic) diamond surface offer “a unique platform for the systematic investigation of nanoscopic water layers.” In a forthcoming paper for Crystal Growth and Design, he and his colleagues Dan Zhu and Hans Fecht argue that these layers might even provide a platform for the origin of life, as I understand it by potentially templating the evolution of organic monolayers. Apparently Albert Szent-Györgyi suggested something similar in the 1970s, proposing such a role for crystalline interfacial water layers. Diamonds can be extremely ancient, and also extraterrestrial. All this is very intriguing, although as someone now programmed to approach with scepticism the notion of enhanced ordering of water at hydrophobic surfaces I think I would like to see some more direct evidence that the water molecules on diamond are indeed truly ordered, especially if the claim is that this extends beyond a monolayer. But I think they’re working on that.

Heme catalases convert hydrogen peroxide to water and oxygen. One type of such enzyme, so-called Clade 3 of the most abundant (monofunctional) class, contains a tightly bound NADPH molecule which seems to protect one of the intermediates of the ferryloxo group against deactivation to a catalytically inactive form. Reiner Sustmann at Duisburg-Essen and colleagues propose in a new paper (W. Sicking et al., JACS 130, 7345-7356; 2008 – paper here) that a bound water molecule plays a critical part in this process, both by supplying a hydroxyl group that binds temporarily to the porphyrin group and then assists the fast two-electron reduction of the intermediate ferryloxo species by NADPH via a series of proton shifts, to restore the catalase resting state and avoid diversion of the reaction towards the deactivated state. A nice example of the multiple, sophisticated roles that bound water can play in active sites.

Lei Zhou and Steven Siegelbaum at Columbia University present a new coarse-grained approach for conducting normal-mode analysis of the dynamics of proteins, which has a lower computational cost than trying to extract the dynamics from a full MD simulation with explicit water [Biophys. J. 94, 3461; 2008 – paper here]. They say that this method is more accurate than are existing coarse-grained NMA techniques, and gives good agreement with experimental results from quasieleastic neutron and light scattering.

In my last blog entry I referred to recent work on the excited-state dynamics of the green fluorescent protein. Dan Huppert and colleagues at Tel Aviv University have looked at essentially the same aspect of the problem: the role of the proton-transfer process [R. Gepshtein et al., Langmuir 112, 7203; 2008 – paper here]. They say that the non-exponential dynamics seem to stem from the distance-dependence of the proton transfer between the chromophore and a bound water molecule that acts as the acceptor. This distance has a relatively large spread of about 0.2 angstroms in GFP.

Finally, thanks to everyone who helped make my Chem. Rev. article a most-accessed paper for the period Jan-Mar 2008.

A mixed bag

2008-06-16T04:17:00.000-07:00

Michael Fayer and colleagues at Stanford have looked at how high salt concentrations and nanoconfinement alter orientational relaxation of water’s hydrogen-bonded network using ultrafast IR spectroscopy [S. Park et al., J. Phys. Chem. B 112, 5279-5290; 2008 – paper here.] They find that structural rearrangements of the network are slowed in 6M NaBr, but only moderately – by a factor around 3. The effects of confinement in reverse micelles can be more pronounced, being up to 20 times slower when the ‘nanopools’ of enclosed water are just 1.7 nm across. Moreover, the relaxation then becomes non-exponential. The effect seems to be due more to the effects of confinement per se than to interactions with the charged lipid head groups.

Jim Hynes and Damien Laage have a paper [J. Phys. Chem. B 10.1021/jp802033r] reporting an improved method for determining water residence times in hydration shells in MD simulations, which works with anything from ions to proteins. The key, it seems, is a better handling of the ‘tolerance time’, which relates to frustrated attempts of a water molecule to escape from the first hydration shell.

The spectrum of the green fluorescent protein of the Pacific jellyfish Aequorea Victoria, widely used in molecular biology as a marker, has several absorption bands that are interpreted as resulting from protonation and ionization of certain residues. The excited-state dynamics are thought to involve a proton relay involving three protons that can shuttle along a chain involving a bound water molecule. Ricard Gelabert of the Universitat Autònoma de Barcelona and colleagues have studied this process using a nuclear quantum dynamical simulation, and they find that proton transfer can be extremely fast in this system, initially happening in a matter of femtoseconds (but slowing down in the final stages). Moreover, the three protons seem to travel synchronously along the relay. The transfer induces a conformational change that breaks the relay, and thus is irreversible. The paper [O. Vendrell et al., J. Phys. Chem. B 112, 5500-5511; 2008] is here.

Nikolai Smolin and Valerie Daggett in Seattle have studied the mechanism of a so-called type III antifreeze protein from polar pout (Macrozoarces americanus) using simulations (J. Phys. Chem. B 112, 6193-6202; 2008 – paper here). They’re trying to figure out which of the various possible mechanisms for AFPs seems to apply here, and find that hydration waters on the protein’s ice-binding surface are more tetrahedral and ice-like than those elsewhere in the hydration sphere, suggesting that there is a good epitaxial match that promotes the binding of the protein to incipient ice crystals, preventing their further growth. I’d be interested to know if/how one might rule out the possibility that the protein could in fact provide a site for ice nucleation this way, preventing the growth of large crystals via a proliferation of small ones.

Sinan Keten and Markus Buehler at MIT have an interesting paper in Phys. Rev. Lett. (100, 198301; paper here) on the strength of protein folds secured purely by hydrogen-bonding. They use concepts from conventional fracture mechanics to look at the rupture of H-bonded beta-sheet-like folds, which enables them to conclude that protein domains stabilized this way can’t have rupture forces greater than about 200 pN.

A couple of papers in Langmuir look at the nature of the water-solid interface. Bill Ducker and colleagues have studied the formation of nanobubbles at hydrophobic surfaces, using total-internal-reflection IR spectroscopy to confirm that there are genuine gas-phase molecules present in both air and CO2 bubbles, some as small as just a few nm across to judge from the AFM images also presented (X. H. Zhang et al., Langmuir 24, 4756-4764; 2008 – paper here). The pressures are estimated at around 1-1.7 atm, but while the air bubbles can be stable for days, CO2 bubbles persist for only an hour or two. So while these nanobubbles are not ubiquitous on hydrophobic surfaces, they do form quite routinely.

And Sergio Acuna and Pedro Toledo in Chile have measured short-range forces between glass surfaces in water, using the AFM (Langmuir 24, 4881-4887; 2008 – paper here here). They find a repulsion at short distances (an intervening water film of 3-4 molecular layers) that does not depend on pH or on ion concentration or size. They say that the mechanism of silica hairs, proposed by Israelachvili and Wennerström (Nature 379, 219-225; 1996), can’t explain their data, and that the oscillatory forces they see are due to sequential squeezing out of water layers. I don’t fully understand what the authors mean by attributing this to the ‘creation of a hydrogen-bonding network at the surface level’ – whether this is different from the bulk, say, and why one need invoke hydrogen bonding at all as opposed simply to the kinds of steric packing effects that create oscillatory solvation forces in any solvent.

The paper on water dynamics in cells by Marion Jasnin, Joe Zaccai and colleagues that I mentioned earlier is now published in EMBO Reports, and is available here.

To those who’ve sent me material: I firmly intend to comment on it soon!