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
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- 巻
- 77
- 号
- 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
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- 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
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- 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