Affiliations: Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research Institute, Umemidai 8-1, Kizu-cho, Soraku-gun, Kyoto-fu, 619-0215, Japan | Graduate School of Science, Kyoto University, Japan
Abstract: We investigated the protein energy landscape using molecular dynamics simulation and normal mode analysis. The dynamical structure factor of a protein, staphylococcal nuclease (SNase), is calculated from the model calculations based on the Jumping-Among-Minima (JAM) model. In this model, the protein dynamics is described in terms of two types of motions: intra- and inter-substate motions. These results are compared in order to investigate the effects of solvent and anharmonicity on protein dynamics. From the comparison of the structure factors, we derive information on the nature of the dynamics in the low frequency region.
Keywords: Protein energy landscape, JAM model, Molecular dynamics simulation, Normal mode analysis
