Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory
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- Maruyama Yutaka
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science
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- Takano Hiroshi
- Department of Physics, Faculty of Science and Technology, Keio University
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- Mitsutake Ayori
- Department of Physics, School of Science and Technology, Meiji University
説明
<p>Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using specialpurpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.</p>
収録刊行物
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- Biophysics and Physicobiology
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Biophysics and Physicobiology 16 (0), 407-429, 2019
一般社団法人 日本生物物理学会
