Vibrational Frequency Shifts and Relaxation Rates for a Selected Vibrational Mode in Cytochrome c

Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome C.

The vibrational energy relaxation of a selected vibrational mode in cytochrome c--a C-D stretch in the terminal methyl group of Met80--has been studied using equilibrium molecular dynamics simulation and normal mode analysis methods. As demonstrated in the pioneering work of Romesberg and co-workers, isotopic labeling of the C-H (to C-D) stretch in alkyl side chains shifts the stretching freque...

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 ∼ 30 cm, th...

Vibrational frequency shifts in dense molecular fluids

Vibrational energy relaxation of isotopically labeled amide I modes in cytochrome c: theoretical investigation of vibrational energy relaxation rates and pathways.

With use of a time-dependent perturbation theory, vibrational energy relaxation (VER) of isotopically labeled amide I modes in cytochrome c solvated with water is investigated. Contributions to the VER are decomposed into two contributions from the protein and water. The VER pathways are visualized by using radial and angular excitation functions for resonant normal modes. Key differences of VE...

Simulating Vibrational Energy Flow in Proteins: Relaxation Rate and Mechanism for Heme Cooling in Cytochrome c

The rate and mechanism of the kinetic energy relaxation of directly excited heme in cytochrome c was investigated using classical molecular dynamics simulation. The kinetic energy relaxation was found to be a biphasic exponential decay process with relaxation time constants of 1.5 ps for the fast process and 10.1 ps for the slow process. Approximately 60% of the kinetic energy relaxes on the sh...