Tuesday, January 22, 2008

Updates to the review

Inevitably, my review article has sins of omission and miscomprehension. I hope to put these right as they are pointed out to me.

One of the more serious is that I attributed to Meyer et al. [PNAS 102, 6839; 2005] the observation that a long-ranged electrostatic attraction can be established between two plates coated with lipids due to delamination of the monolayer and the formation of charged patches. This observation was in fact first reported by Jacob Klein and his coworkers in Phys. Rev. Lett. 96, 038301 (2006) and J. Phys. Chem. B 109, 3832-3837 (2005), though that work was overlooked in the Meyer et al. paper.

David Chandler has explained to me in more detail what is involved in the dewetting transition that he has postulated to occur as hydrophobic surfaces come together [Lum et al., J. Phys. Chem. B 103, 4570; 1999]. This transition has a signature that has not been necessarily sought in some of the simulations of protein aggregation looking for this effect, for example those by Bruce Berne’s group. David says:

“Bruce Berne is doing fine work. The empirical results he has collected are significant, and they are instructive when viewed in context. Problems can arise when the context is misunderstood, as I think they have been in some of Bruce’s writings. Case in point is that the ‘de-wetting’ mechanism of hydrophobic collapse does NOT require the presence of a vapor bubble BEFORE the collapse occurs, though that chronology is what Bruce takes to be the signature of the effect. Rather, an extended hydrophobic surface creates a loose fluctuating water interface. When the surface attracts that interface, the average interface position is close to the surface (i.e., no ‘vapor’ is explicitly seen). But that’s the average. More significantly, because the surface is soft (i.e., can fluctuate with little free energy cost), it becomes possible for water to move aside and thus possible for two hydrophobic surface to collapse upon one another. Consistent with this statement is that ensembles of trajectories and free energy functions show that the ‘reaction’ coordinate for hydrophobic assembly of two extended hydrophobic surfaces, whether idealized or ‘realistic’, has a significant contributor from water dynamics. That effect is the story of de-wetting that I have been trying to explain in my papers. I don’t think subsequent work has demonstrated this idea to be of limited applicability, though I do think many folks have misinterpreted what I have said. In a nutshell: in the matter of what liquid water does to make things happen, it’s the fluctuations that matter.”

Other papers relevant to the general topic of water in molecular biology that have been brought to my attention are:

A. Y. Mulkidjanian & D. A. Cherepanov, “Probing biological interfaces by tracing proton passage across them”, Photochem. Photobiol. Sci. 5, 577-587 (2006)
A. Y. Mulkidjanian, J. Heberle & D. A. Cherepanov, “Protons @ interfaces: Implications for biological energy conversion”, Biochim. Biophys. Acta 1757, 913-930 (2006)
J. Dzubiella, J. M. J. Swanson & J. A. McCammon, “Coupling nonpolar and polar salvation free energies in implicit solvent models”, J. Chem. Phys. 124, 084905 (2006)
L.-T. Cheng, J. Dzubiella, J. A. McCammon & B. Li, “Application of the level-set method to the implicit salvation of nonpolar molecules”, J. Chem. Phys. 127, 084503 (2007)
X. Gong, J. Li, H. Lu, R. Wan, J. Li, J. Hu & H. Fang, “A charge-driven molecular water pump”, Nature Nanotechnol. 2, 709-712 (2007)

There is also a nice crop of new papers that I should mention:
S. Joseph & N. R. Aluru, “Why are carbon nanotubes fast transporters of water?”, Nano. Lett. doi:10.1021/nl072385q (2008) [the answer is attributed to the presence of a depletion layer of water at the interface with the nanotube wall]
C. F. Lopez, R. K. Darst & P. J. Rossky, “Mechanistic elements o protein cold denaturation”, J. Phys. Chem. B doi:10.1021/jp075928t (2008) [in a nutshell: “low temperature leads to solvent-induced packing effects at the protein surface, and this more favourable water-protein interaction in turn destabilizes the overall protein structure”]
M. Lagi, X. Chu, C. Kim, F. Mallamace, P. Baglioni & S.-H. Chen, “The low-temperature dynamic crossover phenomenon in protein hyration water: simulations vs experiments”, J. Phys. Chem. B doi:10.1021/jp710714j (2008) [more on the explanation for the 220K dynamical transition of proteins in terms of the residual influence of a liquid-liquid critical point, an idea developed previously by these authors]
H. Chen, Y. Moreau, E. Derat & S. Shaik, “Quantum mechanical/molecular mechanical study of mechanisms of heme degradation by the enzyme heme oxygenase: the strategic function of the water cluster”, J. Am. Chem. Soc. doi:10.1021/ja076679p (2008) [more on the roles of ‘bound water’ in enzymatic catalysis]
D. K. Hore, D. S. Walker & G. L. Richmond, “Water at hydrophobic surfaces: when weaker is better”, J. Am. Chem. Soc. doi:10.1021/ja0755616 (2008) [uses MD simulations to conclude that “the degree of water structuring in the immediate vicinity of the oil-water junction is highest when the hydrophobic phase is least polar”]