Probing vibrational energy relaxation in proteins using normal modes

Details Probing vibrational energy relaxation in proteins using normal modes Probing vibrational energy relaxation in proteins using normal modes

2004-08-26

arxiv.org/abs/q-bio/0408023v2

Biology

Quantitative Biology

Biomolecules

20 pages, 8 figures, to appear in "Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems" edited by

Scientific paper

Vibrational energy relaxation (VER) of a selected mode in cytochrome c (hemeprotein) in vacuum is studied using two theoretical approaches: One is the equilibrium simulation approach with quantum correction factors, and the other is the reduced model approach which describes the protein as an ensemble of normal modes coupled with nonlinear coupling elements. Both methods result in estimates of VER time (sub ps) for a CD stretching mode in the protein at room temperature, that are in accord with the experimental data of Romesberg's group. The applicability of the two methods is examined through a discussion of the validity of Fermi's golden rule on which the two methods are based.

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