Department   Undergraduate School  , School of Science and Technology
   Position   Associate Professor
Language English
Publication Date 2019/11
Type Academic Journal
Peer Review Peer reviewed
Invitation Invited paper
Title Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory
Contribution Type Co-authored (first author)
Journal Biophysics and Physicobiology
Journal TypeAnother Country
Publisher The Biophysical Society of Japan
Volume, Issue, Page 16,pp.407-429
Author and coauthor Yutaka Maruyama, Hiroshi Takano, Ayori Mitsutake
Details In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose 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.