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.
Tuesday, December 9, 2008
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?
Wednesday, August 20, 2008
Inside chaperonins, and dewetting for amyloids
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.
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.
Wednesday, August 6, 2008
Some new perspectives on old debates
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.
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.
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