Lintao Bu | Searcharxiv

arXiv2004

Probing vibrational energy relaxation in proteins using normal modes

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.

q-bio.BM↗

arXiv2004

Vibrational energy relaxation (VER) of a CD stretching mode in cytochrome c

We first review how to determine the rate of vibrational energy relaxation (VER) using perturbation theory. We then apply those theoretical results to the problem of VER of a CD stretching mode in the protein cytochrome c. We model cytochrome c in vacuum as a normal mode system with the lowest-order anharmonic coupling elements. We find that, for the ``lifetime'' width parameter $γ=3 \sim 30$ cm$^{-1}$, the VER time is $0.2 \sim 0.3$ ps, which agrees rather well with the previous classical calculation using the quantum correction factor method, and is consistent with spectroscopic experiments by Romesberg's group. We decompose the VER rate into separate contributions from two modes, and find that the most significant contribution, which depends on the ``lifetime'' width parameter, comes from those modes most resonant with the CD vibrational mode.

q-bio.BM↗