title: Structural similarity and classification of protein interaction interfaces.
abstract: Interactions between proteins play a key role in many cellular processes. Studying protein-protein interactions that share similar interaction interfaces may shed light on their evolution and could be helpful in elucidating the mechanisms behind stability and dynamics of the protein complexes. When two complexes share structurally similar subunits, the similarity of the interaction interfaces can be found through a structural superposition of the subunits. However, an accurate detection of similarity between the protein complexes containing subunits of unrelated structure remains an open problem. Here, we present an alignment-free machine learning approach to measure interface similarity. The approach relies on the feature-based representation of protein interfaces and does not depend on the superposition of the interacting subunit pairs. Specifically, we develop an SVM classifier of similar and dissimilar interfaces and derive a feature-based interface similarity measure. Next, the similarity measure is applied to a set of 2,806×2,806 binary complex pairs to build a hierarchical classification of protein-protein interactions. Finally, we explore case studies of similar interfaces from each level of the hierarchy, considering cases when the subunits forming interactions are either homologous or structurally unrelated. The analysis has suggested that the positions of charged residues in the homologous interfaces are not necessarily conserved and may exhibit more complex conservation patterns.
authors: Informatics Institute and Department of Computer Science, University of Missouri, Columbia, Missouri, United States of America.
authors: Nan
authors: N
authors: Zhao
authors: Bin
authors: B
authors: Pang
authors: Chi-Ren
authors: CR
authors: Shyu
authors: Dmitry
authors: D
authors: Korkin
references: Methods Mol Biol. 2008;484:505-21
references: 18592198
references: BMC Bioinformatics. 2008 Jan 08;9:9
references: 18182098
references: Bioinformatics. 2000 Oct;16(10):906-14
references: 11120680
references: Biochemistry. 2004 Jun 29;43(25):7983-91
references: 15209493
references: J Mol Biol. 2005 Feb 4;345(5):1281-94
references: 15644221
references: Acta Crystallogr A. 2008 Jan;64(Pt 1):88-95
references: 18156675
references: J Mol Graph. 1995 Oct;13(5):323-30, 307-8
references: 8603061
references: J Mol Biol. 2003 Oct 3;332(5):989-98
references: 14499603
references: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D310-4
references: 16381874
references: Bioinformatics. 2005 May 1;21(9):1901-7
references: 15657096
references: Nat Rev Microbiol. 2009 Nov;7(11):787-97
references: 19806153
references: Bioinformatics. 2005 Jun 15;21(12):2850-5
references: 15855251
references: Comput Appl Biosci. 1993 Dec;9(6):745-56
references: 8143162
references: BMC Bioinformatics. 2010 May 27;11:286
references: 20507585
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W331-6
references: 15991339
references: Cell. 2006 Sep 8;126(5):869-80
references: 16959567
references: BMC Biol. 2007 Oct 09;5:43
references: 17925020
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D189-92
references: 14681391
references: Science. 1999 Oct 8;286(5438):291-5
references: 10514372
references: Bioinformatics. 2003 Jan;19(1):161-2
references: 12499311
references: Proteins. 2003 Jul 1;52(1):2-9
references: 12784359
references: J Mol Biol. 1996 Jul 26;260(4):604-20
references: 8759323
references: PLoS Comput Biol. 2006 Nov 17;2(11):e155
references: 17112313
references: Nature. 2001 Aug 16;412(6848):701-5
references: 11507631
references: J Mol Biol. 1997 Sep 12;272(1):121-32
references: 9299342
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D419-25
references: 18000004
references: Bioinformatics. 2007 Dec 15;23(24):3320-7
references: 17989092
references: Proteins. 2004 Jul 1;56(1):143-56
references: 15162494
references: Curr Opin Struct Biol. 2000 Apr;10(2):153-9
references: 10753808
references: J Comput Chem. 2002 Jan 15;23(1):15-27
references: 11913381
references: Structure. 1997 Aug 15;5(8):1093-108
references: 9309224
references: Biochemistry. 2005 May 10;44(18):7035-47
references: 15865448
references: Proteins. 2010 Jan;78(1):109-17
references: 19731379
references: Proteins. 2007 Dec 1;69(4):704-18
references: 17918726
references: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W363-7
references: 15980490
references: Parasitol Res. 1999 Oct;85(10):844-9
references: 10494812