Tuesday, February 27, 2007

Dynamics fast and slow

How do motions of a peptide chain depend on those of water molecules in the hydration shell? It's clear enough that the solvent dynamics can span a wide range of timescales, depending on how the water molecules interact with the protein. But in unfolded and molten-globule states, it has been suggested that there are rapid fluctuations between various helical and beta-sheet-like states that are 'lubricated' by picosecond rearrangements of the hydrogen-bonding network in water. This lubrication, enabled by the rapidity of H-bond making and breaking, is presumed to enable protein folding. Neil Hunt and coworkers at the University of Strathclyde now say that they've seen such motions, with timescales of a few tenths of a picosecond, in the alpha-helix-to-random-coil transition of a homo-polypeptide (poly-L-lysine) using optical Kerr-effect spectroscopy. The paper is here.

Motions in the hydration shell that are one or two orders of magnitude slower have been studied by Dongping Zhong and colleagues at Ohio State, in a paper here. They're looking at apomyoglobin, and specifically at the water dynamics around a tryptophan group (Trp7), which serves as a convenient fluorescent chromophore. Through both experiment and simulation, they find slow relaxation on timescales of 5-87 ps. Previous studies of such slow dynamics have offered divergent interpretations. Ahmed Zewail and coworkers have suggested that these dynamics are due to the effect of the protein's potential field on the hydration water (J. Phys. Chem. B 107, 13218; 2003). Bertil Halle thinks that these water dynamics close to a protein aren't so different from those in the bulk (PNAS 102, 13867; 2005). Zhong and colleagues say that the slow relaxation is due to strongly coupled water-protein motions. If either the water or the protein is frozen in the simulations, the slow component disappears. I guess that supports the contention of Bizzarri and Cannistraro that the dynamics of the protein and solvent are so strongly coupled that they ‘should be conceived as a single entity' (J. Phys. Chem. B 106, 6617-6633; 2002).


Omer said...

Links doesn't seem to work. Maybe you could show a reference to each one?


sasisanker said...

Hi Philip
The short coming of the model proposed by Zewail and his co-workers are recently highlighted by the work of Golosov et al. See J.Phys. Chem, B, 2007 and also in recent studies J. Chem. Phys, Vol 127, 0555101, 207. These emphasize that surface water in higly dynamic.