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 Рpaper 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.