論文

査読有り
2014年3月

Specific Non-Local Interactions Are Not Necessary for Recovering Native Protein Dynamics

PLOS ONE
  • Bhaskar Dasgupta
  • ,
  • Kota Kasahara
  • ,
  • Narutoshi Kamiya
  • ,
  • Haruki Nakamura
  • ,
  • Akira R. Kinjo

9
3
開始ページ
e91347
終了ページ
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1371/journal.pone.0091347
出版者・発行元
PUBLIC LIBRARY SCIENCE

The elastic network model (ENM) is a widely used method to study native protein dynamics by normal mode analysis (NMA). In ENM we need information about all pairwise distances, and the distance between contacting atoms is restrained to the native value. Therefore ENM requires O(N-2) information to realize its dynamics for a protein consisting of N amino acid residues. To see if (or to what extent) such a large amount of specific structural information is required to realize native protein dynamics, here we introduce a novel model based on only O(N) restraints. This model, named the ` contact number diffusion' model (CND), includes specific distance restraints for only local (along the amino acid sequence) atom pairs, and semi-specific non-local restraints imposed on each atom, rather than atom pairs. The semi-specific non-local restraints are defined in terms of the non-local contact numbers of atoms. The CND model exhibits the dynamic characteristics comparable to ENM and more correlated with the explicit-solvent molecular dynamics simulation than ENM. Moreover, unrealistic surface fluctuations often observed in ENM were suppressed in CND. On the other hand, in some ligand-bound structures CND showed larger fluctuations of buried protein atoms interacting with the ligand compared to ENM. In addition, fluctuations from CND and ENM show comparable correlations with the experimental B-factor. Although there are some indications of the importance of some specific non-local interactions, the semi-specific non-local interactions are mostly sufficient for reproducing the native protein dynamics.

リンク情報
DOI
https://doi.org/10.1371/journal.pone.0091347
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/24625758
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000332851300075&DestApp=WOS_CPL
ID情報
  • DOI : 10.1371/journal.pone.0091347
  • ISSN : 1932-6203
  • PubMed ID : 24625758
  • Web of Science ID : WOS:000332851300075

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