Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation

N. Karasawa, A. Mitsutake, Hiroshi Takano

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n]polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μs molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

Original languageEnglish
Article number062408
JournalPhysical Review E
Volume96
Issue number6
DOIs
Publication statusPublished - 2017 Dec 15

Fingerprint

Molecular Dynamics
molecular dynamics
proteins
Protein
atoms
Simulation
simulation
Principal Components
principal components analysis
complex systems
Principal Component Analysis
Complex Systems
estimates
Estimate
eggs
lysozyme
Dynamic Properties
Protein Structure
Relaxation Time
dynamic characteristics

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics

Cite this

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation. / Karasawa, N.; Mitsutake, A.; Takano, Hiroshi.

In: Physical Review E, Vol. 96, No. 6, 062408, 15.12.2017.

Research output: Contribution to journalArticle

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