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.

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