Tuesday, November 6, 2007

Protein-water coupling: confirmations and complications

With far too much to catch up with here, I shall do little more than list things that have crossed my radar screen. Lots happening, all interesting…

Alla Oleinikova, Nikolai Smolin, and Ivan Brovchenko have a paper in Biophys. J. (93, 2986) entitled “Influence of Water Clustering on the Dynamics of Hydration Water at the Surface of a Lysozyme”, in which they use MD simulations to look at the coupling of water and protein dynamics as the degree of hydration changes. In line with their earlier work, they see maximal dynamical coupling when the water coverage corresponds to a percolating water network on the protein surface.

Ivan and Alla have also told me about their forthcoming book, Interfacial and Confined Water, to be published by Elsevier, which will look at water’s behaviour at hydrophilic and hydrophobic surfaces in general but with clearly a pretty strong focus on biomolecules, including these ideas about percolation transitions in the hydrogen-bonded network.

The hydration dynamics at a protein surface are also the topic of a paper from Dongping Zhong and colleagues at Ohio State University (PNAS doi:10.1073/pnas.0707647104). They have used ultrafast spectroscopy to map out the hydration dynamics from place to place on the surface of various mutants of sperm whale myoglobin, and find two distinct dynamical regimes: one with dynamical timescales of 1-8 ps, the other with around 20-200 ps. These regimes are strongly correlated with the protein’s structure and composition, confirming the intimate relationship between hydration dynamics and protein fluctuations.

But at the same time, this story gets more complex. Martin Weik has sent me a forthcoming paper to be published in PNAS (doi:10.1073/pnas.0706566104) called “Coupling of protein and hydration-water dynamics in biological membranes”. Here they use inelastic neutron scattering and MD simulations to look at the relationship between water dynamics and fluctuations of lipids and bacteriorhodopsin in the purple membrane between 120 and 260 K. They find that the two seem to be decoupled, at least below 260 K, in contrast to the situation for soluble proteins and their hydration layers. In other words, there is no coupled ‘glass-like’ transition of the water and membrane protein: the onset of water motion as the temperature is raised through 200 K does not coincide with a dynamical transition of bR. That adds a whole new layer of complexity to the ongoing story of protein-water dynamics: membranes change the game.

Time to change the subject, then. The hydration of DNA tends to get far less attention than that of proteins, but evidently has interesting stories attached. It seems fairly clear now that the regular double helix depends on the presence of water, though that tends to be glossed over in biochemical texts. Hermann Gaub and colleagues have now made that point in a very forceful manner (JACS doi:10.1021/ja074776c). They have used an AFM tip attached to one strand to drag a length of double-stranded DNA from water into a poor (nonpolar) solvent, octane - whereupon the ds-DNA unzips spontaneously. This happens too in MD simulations. That, the authors say, might be exploited by helicases, which need only force the DNA into a hydrophobic binding pocket to make it unwind. A lovely and striking result.


Anonymous said...

hey there...

Isobe Ltin said...

Alla have also told me about their forthcoming book.
meet and greet at Luton