InterProSurf: a web server for predicting interacting sites on protein surfaces

Bioinformatics (Oxford, England) - Tập 23 Số 24 - Trang 3397-3399 - 2007
Surendra S. Negi1, Catherine H. Schein1, Numan Oezguen1, Trevor D. Power1, Werner Braun1
1Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0857, USA

Tóm tắt

AbstractSummary: A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments.Availability: The InterProSurf web server is available at http://curie.utmb.edu/Contact:  [email protected]Supplementary information: Other test examples are available as Supplementary Material at Bioinformatics online.

Từ khóa


Tài liệu tham khảo

Bock, 2001, Predicting protein-protein interactions from primary structure, Bioinformatics, 17, 455, 10.1093/bioinformatics/17.5.455

Caffrey, 2004, Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?, Protein Sci, 13, 190, 10.1110/ps.03323604

DeLano, 2002, Unraveling hot spots in binding interfaces: progress and challenges, Curr. Opin. Struct. Biol, 12, 14, 10.1016/S0959-440X(02)00283-X

Dorig, 1993, The human Cd46 molecule is a receptor for measles-virus (Edmonston strain), Cell, 75, 295, 10.1016/0092-8674(93)80071-L

Gao, 2004, Structure-based method for analyzing protein-protein interfaces, J. Mol. Model, 10, 44, 10.1007/s00894-003-0168-3

Glaser, 2003, ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information, Bioinformatics, 19, 163, 10.1093/bioinformatics/19.1.163

Hoskins, 2006, An algorithm for predicting protein-protein interaction sites: abnormally exposed amino acid residues and secondary structure elements, Protein Sci, 15, 1017, 10.1110/ps.051589106

Innis, 2000, Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis, Protein Eng, 13, 839, 10.1093/protein/13.12.839

Janin, 2005, Assessing predictions of protein-protein interaction: the CAPRI experiment, Protein Sci, 14, 278, 10.1110/ps.041081905

Janin, 1990, The structure of protein-protein recognition sites, J. Bio. Chem, 265, 16027, 10.1016/S0021-9258(17)46181-3

Jones, 1996, Principles of protein-protein interactions, Proc. Natl Acad. Sci. USA, 93, 13, 10.1073/pnas.93.1.13

Jones, 1997, Analysis of protein-protein interaction sites using surface patches, J. Mol. Biol, 272, 121, 10.1006/jmbi.1997.1234

Lacy, 2005, A model of anthrax toxin lethal factor bound to protective antigen, Proc. Natl Acad. Sci. USA, 102, 16409, 10.1073/pnas.0508259102

Mendez, 2005, Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures, Proteins Struct. Funct. Bioinformatics, 60, 150, 10.1002/prot.20551

Miguel, 2004, Sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families, Bioinformatics, 20, 2380, 10.1093/bioinformatics/bth255

Negi, 2007, Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces, J. Mol. Model, 10.1007/s00894-007-0237-0

Negi, 2006, Determining functionally important amino acid residues of the E1 protein of Venezuelan equine encephalitis virus, J. Mol. Model, 12, 921, 10.1007/s00894-006-0101-7

Neuvirth, 2004, ProMate: a structure based prediction program to identify the location of protein-protein binding sites, J. Mol. Biol, 338, 181, 10.1016/j.jmb.2004.02.040

Pannifer, 2001, Crystal structure of the anthrax lethal factor, Nature, 414, 229, 10.1038/n35101998

Res, 2005, Character and evolution of protein-protein interfaces, Phys. Biol, 2, S36, 10.1088/1478-3975/2/2/S04

Schein, 2005, Molego-based definition of the architecture and specificity of metal-binding sites, Proteins Struct. Func. Bioinformatics, 58, 200, 10.1002/prot.20253

Tatsuo, 2000, SLAM (CDw150) is a cellular receptor for measles virus, Nature, 406, 893, 10.1038/35022579

Vongpunsawad, 2004, Selectively receptor-blind measles viruses: identification of residues necessary for SLAM- or CD46-induced fusion and their localization on a new hemagglutinin structural model, J. Virol, 78, 302, 10.1128/JVI.78.1.302-313.2004

Thông tin
Thông tin xuất bản

Bioinformatics (Oxford, England)

Tập 23 Số 24

3397-3399

Thông tin tác giả