論文

査読有り
2009年2月

Development of new indices to evaluate protein-protein interfaces: Assembling space volume, assembling space distance, and global shape descriptor

Journal of Molecular Graphics and Modelling
  • Maeda
  • ,
  • MH
  • ,
  • Kinoshita K

担当区分
筆頭著者, 責任著者
27
6
開始ページ
706
終了ページ
711
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1016/j.jmgm.2008.11.002
出版者・発行元
ELSEVIER SCIENCE INC

Protein-protein interaction is fundamental to initiate the cellular functions of proteins, and thus structural analyses of protein interfaces are the first step to understand their functions at the molecular level. Although shape complementarities have been used to evaluate the fitness of interfaces, the conventional method did not distinguish between two main components of complementarity, the well-fitting of the surface shapes and the size of the gap regions between the pair of molecules, and could not evaluate the global shape of the interfaces. Therefore, we now propose three new indices to describe protein interfaces: assembling space volume (ASV), assembling space distance (AS-distance), and global shape descriptor (GS). The ASV is calculated using Delaunay tessellation, and the AS-distance is calculated as the ratio of ASV to delta-ASA (accessible surface area). The GS is calculated as the ratio of the volume of Delaunay tetrahedra with a long edge to that of all tetrahedra in the assembling space. To evaluate the feasibility of the three indices, we applied our method to homo-dimer proteins, and performed systematic comparisons with SURFNET by Laskowski and shape complementarity by Lawrence and Colman. As a result, our indices behave differently from the existing ones, and shed light on new features of protein-protein interfaces, as general trends of AS-distances for all protein interfaces. (C) 2008 Elsevier Inc. All rights reserved.

Web of Science ® 被引用回数 : 4

リンク情報
DOI
https://doi.org/10.1016/j.jmgm.2008.11.002
CiNii Articles
http://ci.nii.ac.jp/naid/80020113644
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/19110457
Web of Science
https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=JSTA_CEL&SrcApp=J_Gate_JST&DestLinkType=FullRecord&KeyUT=WOS:000263987400006&DestApp=WOS_CPL

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