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.
Tuesday, January 6, 2009
Thursday, December 18, 2008
A nice Christmas package
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.
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.
Tuesday, December 9, 2008
A lot about interfaces
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.
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.
Friday, November 14, 2008
Some DNA - and is the 220 K transition real?
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.
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.
Tuesday, October 7, 2008
Pores, membranes, and knots
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.
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.
Wednesday, September 17, 2008
Are nanopipes more slippery?
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.
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.
Wednesday, September 10, 2008
Getting up to date
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?
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?
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