Study of Vibrational Energy Transfer in Proteins

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Anharmonic dynamics of a protein molecule was studied by molecular dynamics simulations, (1)in terms of the intramolecular vibrational energy transfer, and (2)second through moving normal mode coordinates.(1)A small excess kinetic energy was added to a specified normal mode, and the process of the energy transfer to other modes was observed. It was found that the vibrational energy was transferred by two distinct mechanisms depending on temperature. At near zero temperature, the vibrational energy is transferred ass a process of the Fermi resonance. As the temperature increases, the resonance type transfer is dominated by the off-resonance energy transfer through various mode coupling terms.(2)A set of normal mode coordinates is defined at each time instant of the trajectory by principal component analysis (PCA) with a small time window. The time evolution of the normal mode coordinates defines the moving normal mode coordinates. Translation of he origin of he coordinates was decomposed into diffusion and vibrational motions. Significant parts of both types of motions occur in the large-amplitude normal mode space. Rotation of the large-amplitude normal mode space was characterized by fast relaxation completed within the time window of PCA, but was confined in a small space spanned by a limited number of large-amplitude normal modes.