Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of human lysozyme

Toshiki Nagai, Ayori Mitsutake, Hiroshi Takano

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

Original languageEnglish
Article number023803
JournalJournal of the Physical Society of Japan
Volume82
Issue number2
DOIs
Publication statusPublished - 2013 Feb

Fingerprint

lysozyme
molecular dynamics
atoms
simulation
proteins
principal components analysis
degrees of freedom
relaxation time
aqueous solutions

Keywords

  • Molecular dynamics
  • Principal component analysis
  • Protein
  • Relaxation mode analysis
  • Simulation

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of human lysozyme. / Nagai, Toshiki; Mitsutake, Ayori; Takano, Hiroshi.

In: Journal of the Physical Society of Japan, Vol. 82, No. 2, 023803, 02.2013.

Research output: Contribution to journalArticle

@article{6753b9512ed1428598ba7153d956b1bc,
title = "Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of human lysozyme",
abstract = "A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.",
keywords = "Molecular dynamics, Principal component analysis, Protein, Relaxation mode analysis, Simulation",
author = "Toshiki Nagai and Ayori Mitsutake and Hiroshi Takano",
year = "2013",
month = "2",
doi = "10.7566/JPSJ.82.023803",
language = "English",
volume = "82",
journal = "Journal of the Physical Society of Japan",
issn = "0031-9015",
publisher = "Physical Society of Japan",
number = "2",

}

TY - JOUR

T1 - Principal component relaxation mode analysis of an all-atom molecular dynamics simulation of human lysozyme

AU - Nagai, Toshiki

AU - Mitsutake, Ayori

AU - Takano, Hiroshi

PY - 2013/2

Y1 - 2013/2

N2 - A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

AB - A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

KW - Molecular dynamics

KW - Principal component analysis

KW - Protein

KW - Relaxation mode analysis

KW - Simulation

UR - http://www.scopus.com/inward/record.url?scp=84874169983&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84874169983&partnerID=8YFLogxK

U2 - 10.7566/JPSJ.82.023803

DO - 10.7566/JPSJ.82.023803

M3 - Article

VL - 82

JO - Journal of the Physical Society of Japan

JF - Journal of the Physical Society of Japan

SN - 0031-9015

IS - 2

M1 - 023803

ER -