BeAtMuSiC: prediction of changes in protein-protein binding affinity on mutations

被引:241
作者
Dehouck, Yves [1 ]
Kwasigroch, Jean Marc [1 ]
Rooman, Marianne [1 ]
Gilis, Dimitri [1 ]
机构
[1] ULB, Dept BioModelling BioInformat & BioProc, B-1050 Brussels, Belgium
关键词
HOT-SPOT RESIDUES; STATISTICAL POTENTIALS; STABILITY CHANGES; ENERGY; INTERFACES; RECOGNITION; DATABASE; DESIGN; SERVER; MUTAGENESIS;
D O I
10.1093/nar/gkt450
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The ability of proteins to establish highly selective interactions with a variety of (macro) molecular partners is a crucial prerequisite to the realization of their biological functions. The availability of computational tools to evaluate the impact of mutations on protein-protein binding can therefore be valuable in a wide range of industrial and biomedical applications, and help rationalize the consequences of non-synonymous single-nucleotide polymorphisms. BeAtMuSiC (http://babylone.ulb.ac.be/beatmusic) is a coarse-grained predictor of the changes in binding free energy induced by point mutations. It relies on a set of statistical potentials derived from known protein structures, and combines the effect of the mutation on the strength of the interactions at the interface, and on the overall stability of the complex. The BeAtMuSiC server requires as input the structure of the protein-protein complex, and gives the possibility to assess rapidly all possible mutations in a protein chain or at the interface, with predictive performances that are in line with the best current methodologies.
引用
收藏
页码:W333 / W339
页数:7
相关论文
共 52 条
[1]   PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces [J].
Assi, Salam A. ;
Tanaka, Tomoyuki ;
Rabbitts, Terence H. ;
Fernandez-Fuentes, Narcis .
NUCLEIC ACIDS RESEARCH, 2010, 38 (06) :e86.1-e86.11
[2]   The interface of protein-protein complexes: Analysis of contacts and prediction of interactions [J].
Bahadur, R. P. ;
Zacharias, M. .
CELLULAR AND MOLECULAR LIFE SCIENCES, 2008, 65 (7-8) :1059-1072
[3]   The diversity of physical forces and mechanisms in intermolecular interactions [J].
Berezovsky, Igor N. .
PHYSICAL BIOLOGY, 2011, 8 (03)
[4]   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
[5]   Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction [J].
Bradshaw, Richard T. ;
Patel, Bhavesh H. ;
Tate, Edward W. ;
Leatherbarrow, Robin J. ;
Gould, Ian R. .
PROTEIN ENGINEERING DESIGN & SELECTION, 2011, 24 (1-2) :197-207
[6]   Comprehensive in silico mutagenesis highlights functionally important residues in proteins [J].
Bromberg, Yana ;
Rost, Burkhard .
BIOINFORMATICS, 2008, 24 (16) :I207-I212
[7]   Dissecting protein-protein recognition sites [J].
Chakrabarti, P ;
Janin, J .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2002, 47 (03) :334-343
[8]   A feature-based approach to modeling proteinprotein interaction hot spots [J].
Cho, Kyu-il ;
Kim, Dongsup ;
Lee, Doheon .
NUCLEIC ACIDS RESEARCH, 2009, 37 (08) :2672-2687
[9]   A HOT-SPOT OF BINDING-ENERGY IN A HORMONE-RECEPTOR INTERFACE [J].
CLACKSON, T ;
WELLS, JA .
SCIENCE, 1995, 267 (5196) :383-386
[10]   KFC Server: interactive forecasting of protein interaction hot spots [J].
Darnell, Steven J. ;
LeGault, Laura ;
Mitchell, Julie C. .
NUCLEIC ACIDS RESEARCH, 2008, 36 :W265-W269