論文

査読有り
2017年10月

Structural transition of solvated H-Ras/GTP revealed by molecular dynamics simulation and local network entropy

JOURNAL OF MOLECULAR GRAPHICS & MODELLING
  • Shota Matsunaga
  • ,
  • Yuta Hano
  • ,
  • Yuta Saito
  • ,
  • Kazuhiro J. Fujimoto
  • ,
  • Takashi Kumasaka
  • ,
  • Shigeyuki Matsumoto
  • ,
  • Tohru Kataoka
  • ,
  • Fumi Shima
  • ,
  • Shigenori Tanaka

77
開始ページ
51
終了ページ
63
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1016/j.jmgm.2017.07.028
出版者・発行元
ELSEVIER SCIENCE INC

The state transitions of solvated H-Ras protein with GTP were theoretically analyzed through molecular dynamics (MD) simulations. To accelerate the structural changes associated with the locations of two switch regions (I and II), the Parallel Cascade Selection MD (PaCS-MD) method was employed in this study. The interconversions between the State 1 and State 2 were thus studied in atomic details, leading to a reasonable agreement with experimental observations and consequent scenarios concerning the transition mechanism that would be essential for the development of Ras inhibitors as anti-cancer agents. Furthermore, the state-transition-based local network entropy (SNE) was calculated for the transition process from State 1 to State 2, by which the temporal evolution of information entropy associated with the dynamical behavior of hydrogen bond network composed of hydration water molecules was described. The calculated results of SNE thus proved to provide a good indicator to detect the dynamical state transition of solvated Ras protein system (and probably more general systems) from a viewpoint of nonequilibrium statistical thermodynamics. (C) 2017 Elsevier Inc. All rights reserved.

リンク情報
DOI
https://doi.org/10.1016/j.jmgm.2017.07.028
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/28837923
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000417659200006&DestApp=WOS_CPL
URL
http://europepmc.org/abstract/med/28837923
URL
http://orcid.org/0000-0001-9289-1557
ID情報
  • DOI : 10.1016/j.jmgm.2017.07.028
  • ISSN : 1093-3263
  • eISSN : 1873-4243
  • ORCIDのPut Code : 36351867
  • PubMed ID : 28837923
  • Web of Science ID : WOS:000417659200006

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