Papers

Peer-reviewed International journal
Oct 7, 2018

Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates

JOURNAL OF CHEMICAL PHYSICS
  • Fujisaki Hiroshi
  • ,
  • Moritsugu Kei
  • ,
  • Mitsutake Ayori
  • ,
  • Suetani Hiromichi

Volume
149
Number
13
First page
134112
Last page
134112
Language
English
Publishing type
Research paper (scientific journal)
DOI
10.1063/1.5049420

We simulate the nonequilibrium ensemble dynamics of a biomolecule using the weighted ensemble method, which was introduced in molecular dynamics simulations by Huber and Kim and further developed by Zuckerman and co-workers. As the order parameters to characterize its conformational change, we here use the coordinates derived from the diffusion map (DM) method, one of the manifold learning techniques. As a concrete example, we study the kinetic properties of a small peptide, chignolin in explicit water, and calculate the conformational change between the folded and misfolded states in a nonequilibrium way. We find that the transition time scales thus obtained are comparable to those using previously employed hydrogen-bond distances as the order parameters. Since the DM method only uses the 3D Cartesian coordinates of a peptide, this shows that the DM method can extract the important distance information of the peptide without relying on chemical intuition. The time scales are compared well with the previous results using different techniques, non-Markovian analysis and core-set milestoning for a single long trajectory. We also find that the most significant DM coordinate turns out to extract a dihedral angle of glycine, and the previously studied relaxation modes are well correlated with the most significant DM coordinates.

Link information
DOI
https://doi.org/10.1063/1.5049420
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/30292230
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000446815600015&DestApp=WOS_CPL
ID information
  • DOI : 10.1063/1.5049420
  • ISSN : 0021-9606
  • Pubmed ID : 30292230
  • Web of Science ID : WOS:000446815600015

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