Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions

被引:56
作者
Cukuroglu, Engin [1 ,2 ]
Gursoy, Attila [1 ,2 ]
Nussinov, Ruth [3 ,4 ]
Keskin, Ozlem [1 ,2 ]
机构
[1] Koc Univ, Ctr Computat Biol & Bioinformat, Istanbul, Turkey
[2] Koc Univ, Coll Engn, Istanbul, Turkey
[3] NCI, Canc & Inflammat Program, Frederick Natl Lab Canc Res, Leidos Biomed Res Inc, Frederick, MD 21701 USA
[4] Tel Aviv Univ, Sackler Sch Med, Dept Human Genet & Mol Med, Sackler Inst Mol Med, IL-69978 Tel Aviv, Israel
来源
PLOS ONE | 2014年 / 9卷 / 01期
基金
美国国家卫生研究院;
关键词
HOT-SPOTS; BINDING-ENERGY; SEQUENCE; CLASSIFICATION; SIMILARITIES; DATABASE; SITES; ARCHITECTURES; PREFERENCES; VALIDATION;
D O I
10.1371/journal.pone.0086738
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Improvements in experimental techniques increasingly provide structural data relating to protein-protein interactions. Classification of structural details of protein-protein interactions can provide valuable insights for modeling and abstracting design principles. Here, we aim to cluster protein-protein interactions by their interface structures, and to exploit these clusters to obtain and study shared and distinct protein binding sites. We find that there are 22604 unique interface structures in the PDB. These unique interfaces, which provide a rich resource of structural data of protein-protein interactions, can be used for template-based docking. We test the specificity of these non-redundant unique interface structures by finding protein pairs which have multiple binding sites. We suggest that residues with more than 40% relative accessible surface area should be considered as surface residues in template-based docking studies. This comprehensive study of protein interface structures can serve as a resource for the community. The dataset can be accessed at http://prism.ccbb.ku.edu.tr/piface.
引用
收藏
页数:12
相关论文
共 71 条
[1]   Ten thousand interactions for the molecular biologist [J].
Aloy, P ;
Russell, RB .
NATURE BIOTECHNOLOGY, 2004, 22 (10) :1317-1321
[2]   InterPreTS: protein Interaction Prediction through Tertiary Structure [J].
Aloy, P ;
Russell, RB .
BIOINFORMATICS, 2003, 19 (01) :161-162
[3]   Interrogating protein interaction networks through structural biology [J].
Aloy, P ;
Russell, RB .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (09) :5896-5901
[4]   Data growth and its impact on the SCOP database: new developments [J].
Andreeva, Antonina ;
Howorth, Dave ;
Chandonia, John-Marc ;
Brenner, Steven E. ;
Hubbard, Tim J. P. ;
Chothia, Cyrus ;
Murzin, Alexey G. .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D419-D425
[5]  
[Anonymous], 2008, P 7 PYTHON SCI C
[6]  
[Anonymous], PROTEINS
[7]   Emergence of scaling in random networks [J].
Barabási, AL ;
Albert, R .
SCIENCE, 1999, 286 (5439) :509-512
[8]  
Bateman A, 2004, NUCLEIC ACIDS RES, V32, pD138, DOI [10.1093/nar/gkp985, 10.1093/nar/gkh121, 10.1093/nar/gkr1065]
[9]   PPIDD: An extraction and visualisation method of biological protein-protein interfaces [J].
Benoit, Vincent ;
Mucchielli-Giorgi, Marie-Helene ;
Dumont, Benoit ;
Durosay, Patrice ;
Reymond, Nancie ;
Delacroix, Herve .
BIOCHIMIE, 2008, 90 (04) :640-647
[10]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242