Saturday, December 22, 2007

Chem Rev article is now online

My review article on water in cell biology has now been published online in Chemical Reviews – it’s available here. Some minor corrections in the first five pages were omitted (I’m hoping these might yet be fixed), but such is life. Hope it’s useful.

Tuesday, December 11, 2007

Spherical water

More on the issue of urea denaturation of proteins comes from Paul Cremer and colleagues at Texas A&M (Chen et al., JACS 129, 15104; 2007). They have used vibrational sum frequency spectroscopy to look at the orientation of urea molecules at the surface of bovine serum albumin. They find that the orientation depends on the surface charge on the protein: it flips from pointing the amines towards the surface at high pH (negative surface charge) to pointing the carbonyls at low pH (positive surface charge). That’s interesting. But the authors’ argument that this supports an indirect model for denaturation, where the urea primarily acts via a restructuring of the hydration sphere rather than direct surface bonding, seems rather vague and not at all obvious at this point.

Sergey Buldyrev at Yeshiva University and coworkers (Kumar, Debenedetti, Rossky, Stanley) have found water-like behaviour in a rather un-water-like system (PNAS, doi:10.1073/pnas.0708427104). They’ve looked at a fluid of spherically symmetric particles with two interaction length scales – a hard core and a soft repulsive ‘ramp’ – and see water-like anomalies such as expansion on cooling, as well as cold-induced ‘denaturation’ of a hard-sphere polymer chain. This suggests that this dual-scale characteristic might be the most fundamental feature that gives water its ‘uniqueness’.

Ivan Brovchenko’s paper on water percolation effects in DNA polymorphism, which I mentioned several weeks back, has now been published in JACS: doi:10.1021/ja0732882.

Tuesday, December 4, 2007

More water tuning, and out with the structure-breakers

I couldn’t hope for a better illustration of how biomolecular hydration can be used to fine-tune function than that provided in a paper in Science by Keith Hodgson at Stanford and coworkers (30 November, Vol. 318, p.1464). They have used sulphur XAS to look at the iron-sulphur sites in the high-potential iron-sulphur protein (HiPIP) and in ferredoxin (Fd). Both have much the same iron-sulphur cluster, yet that in HiPIP gets oxidized and that in Fd gets reduced at physiological potentials. The authors conclude that this difference is due to different degrees of Fe-S covalency, which in turn depends on the hydration state. In other words, function here has in some sense rather little to do with the protein’s primary structure, but depends instead on the hydration environment.

Maria Ricci in Rome and her colleagues have a great paper in J. Phys. Chem. (Vol. 111, p.13570) on the structure of NaCl and KCl solutions as deduced by neutron scattering. They find that K ions have more orientationally disordered hydration shells than Na ions, while Cl ions tend to form H-bonded bridges between waters. In both cases the H-bonded structure of water is significantly disrupted, but not in a way that yields to any simplistic description as ‘structure-making’ or ‘structure-breaking’. As a result, the authors say, those old ideas “are not helpful in understanding how these ions interact with water at the molecular level.” Hear, hear. Let’s hope that message gets out.

There’s what looks to be a very nice paper in Biophys. J. (Vol. 93, p.4116) from Bryan Patel, Pablo Debenedetti, Frank Stillinger and Peter Rossky on the way hydrophobic hydration acts to cause protein denaturation at low and high temps and at high pressure. I’ve only seen the abstract of this so far, but the comment that “an explicit treatment of hydrophobic hydration is sufficient to produce cold, pressure, and thermal denaturation” implies that this paper covers a lot of important ground in this controversial area.

In a paper in J. Phys. Chem. B (doi:10.1021/jp077110d), Julio Martinez and Pieter Stroeve suggests that they can resolve previously discrepant findings about the nature of the interface between water and a hydrophobic surface. They have used surface plasmon resonance to study this interface for a self-assembled monolayer, and report that it evolves slowly: at first, nanobubbles are formed, but these disappear after about 10 minutes. Equilibrium is not reached, however, until about 30 hours later. In this equilibrium state, there is apparently an ‘organic layer’ at the interface, by which they seem to mean a film of organic contaminants. Something like that was reported by Evans et al. in Physica A 339, 101 (2004). I’m not sure this will be the final word, or quite what it implies for hydrophobic interactions, but it does seem to offer a reason why previous results have differed.

There’s going to be more to be said too about the issue of ions at the air-water or hydrophobe-water surface. Pavel Jungwirth and coworkers made a small splash earlier this year with a PNAS paper that claimed to find surface acidification. Greg Voth predicted that some time ago (se below, ‘Acid on top’, But others insist that hydroxide ions preferentially segregate at the surface. Jan Engberts now tells me that “Jungwirth has now performed MD simulations, with the help of my previous post-doc Ronen Zangi, now at Columbia [with Bruce Berne]. And they largely reproduce our previous results, i.e. hydroxide binding....The idea is now to write a joint paper. I am not sure what comes out of it.” Watch this space… And meanwhile, Dominic Horinek and Roland Netz have a simulation paper in Phys. Rev. Lett. (Vol. 99, 226104) which reports that large, polarisable halide ions are adsorbed preferentially at the surface of a hydrophobic SAM.