Monday, June 16, 2008

A mixed bag

Michael Fayer and colleagues at Stanford have looked at how high salt concentrations and nanoconfinement alter orientational relaxation of water’s hydrogen-bonded network using ultrafast IR spectroscopy [S. Park et al., J. Phys. Chem. B 112, 5279-5290; 2008 – paper here.] They find that structural rearrangements of the network are slowed in 6M NaBr, but only moderately – by a factor around 3. The effects of confinement in reverse micelles can be more pronounced, being up to 20 times slower when the ‘nanopools’ of enclosed water are just 1.7 nm across. Moreover, the relaxation then becomes non-exponential. The effect seems to be due more to the effects of confinement per se than to interactions with the charged lipid head groups.

Jim Hynes and Damien Laage have a paper [J. Phys. Chem. B 10.1021/jp802033r] reporting an improved method for determining water residence times in hydration shells in MD simulations, which works with anything from ions to proteins. The key, it seems, is a better handling of the ‘tolerance time’, which relates to frustrated attempts of a water molecule to escape from the first hydration shell.

The spectrum of the green fluorescent protein of the Pacific jellyfish Aequorea Victoria, widely used in molecular biology as a marker, has several absorption bands that are interpreted as resulting from protonation and ionization of certain residues. The excited-state dynamics are thought to involve a proton relay involving three protons that can shuttle along a chain involving a bound water molecule. Ricard Gelabert of the Universitat Autònoma de Barcelona and colleagues have studied this process using a nuclear quantum dynamical simulation, and they find that proton transfer can be extremely fast in this system, initially happening in a matter of femtoseconds (but slowing down in the final stages). Moreover, the three protons seem to travel synchronously along the relay. The transfer induces a conformational change that breaks the relay, and thus is irreversible. The paper [O. Vendrell et al., J. Phys. Chem. B 112, 5500-5511; 2008] is here.

Nikolai Smolin and Valerie Daggett in Seattle have studied the mechanism of a so-called type III antifreeze protein from polar pout (Macrozoarces americanus) using simulations (J. Phys. Chem. B 112, 6193-6202; 2008 – paper here). They’re trying to figure out which of the various possible mechanisms for AFPs seems to apply here, and find that hydration waters on the protein’s ice-binding surface are more tetrahedral and ice-like than those elsewhere in the hydration sphere, suggesting that there is a good epitaxial match that promotes the binding of the protein to incipient ice crystals, preventing their further growth. I’d be interested to know if/how one might rule out the possibility that the protein could in fact provide a site for ice nucleation this way, preventing the growth of large crystals via a proliferation of small ones.

Sinan Keten and Markus Buehler at MIT have an interesting paper in Phys. Rev. Lett. (100, 198301; paper here) on the strength of protein folds secured purely by hydrogen-bonding. They use concepts from conventional fracture mechanics to look at the rupture of H-bonded beta-sheet-like folds, which enables them to conclude that protein domains stabilized this way can’t have rupture forces greater than about 200 pN.

A couple of papers in Langmuir look at the nature of the water-solid interface. Bill Ducker and colleagues have studied the formation of nanobubbles at hydrophobic surfaces, using total-internal-reflection IR spectroscopy to confirm that there are genuine gas-phase molecules present in both air and CO2 bubbles, some as small as just a few nm across to judge from the AFM images also presented (X. H. Zhang et al., Langmuir 24, 4756-4764; 2008 – paper here). The pressures are estimated at around 1-1.7 atm, but while the air bubbles can be stable for days, CO2 bubbles persist for only an hour or two. So while these nanobubbles are not ubiquitous on hydrophobic surfaces, they do form quite routinely.

And Sergio Acuna and Pedro Toledo in Chile have measured short-range forces between glass surfaces in water, using the AFM (Langmuir 24, 4881-4887; 2008 – paper here here). They find a repulsion at short distances (an intervening water film of 3-4 molecular layers) that does not depend on pH or on ion concentration or size. They say that the mechanism of silica hairs, proposed by Israelachvili and Wennerström (Nature 379, 219-225; 1996), can’t explain their data, and that the oscillatory forces they see are due to sequential squeezing out of water layers. I don’t fully understand what the authors mean by attributing this to the ‘creation of a hydrogen-bonding network at the surface level’ – whether this is different from the bulk, say, and why one need invoke hydrogen bonding at all as opposed simply to the kinds of steric packing effects that create oscillatory solvation forces in any solvent.

The paper on water dynamics in cells by Marion Jasnin, Joe Zaccai and colleagues that I mentioned earlier is now published in EMBO Reports, and is available here.

To those who’ve sent me material: I firmly intend to comment on it soon!

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