Protein-protein docking by simulating the process of association subject to biochemical constraints

We present a computational procedure for modeling protein–protein association and predicting the structures of protein–protein complexes. The initial sampling stage is based on an efficient Brownian dynamics algorithm that mimics the physical process of diffusional association. Relevant biochemical...

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Podrobná bibliografie
Vydáno v:	Proteins, structure, function, and bioinformatics Ročník 71; číslo 4; s. 1955 - 1969
Hlavní autoři:	Motiejunas, Domantas, Gabdoulline, Razif, Wang, Ting, Feldman-Salit, Anna, Johann, Tim, Winn, Peter J., Wade, Rebecca C.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.06.2008
Témata:	Algorithms Amino Acid Sequence Animals Biochemical Phenomena Biochemistry Brownian dynamics clustering Computational Biology - methods Computer Simulation Crystallography, X-Ray Databases, Factual Diffusion encounter complex flexible refinement Fourier Analysis Humans Hydrogen Bonding Models, Biological molecular dynamics Molecular Sequence Data Osmolar Concentration Protein Conformation Protein Structure, Secondary Protein Structure, Tertiary protein-protein association protein-protein docking Proteins - chemistry Proteins - metabolism Static Electricity
ISSN:	0887-3585, 1097-0134, 1097-0134
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Popis
Shrnutí:	We present a computational procedure for modeling protein–protein association and predicting the structures of protein–protein complexes. The initial sampling stage is based on an efficient Brownian dynamics algorithm that mimics the physical process of diffusional association. Relevant biochemical data can be directly incorporated as distance constraints at this stage. The docked configurations are then grouped with a hierarchical clustering algorithm into ensembles that represent potential protein–protein encounter complexes. Flexible refinement of selected representative structures is done by molecular dynamics simulation. The protein–protein docking procedure was thoroughly tested on 10 structurally and functionally diverse protein–protein complexes. Starting from X‐ray crystal structures of the unbound proteins, in 9 out of 10 cases it yields structures of protein–protein complexes close to those determined experimentally with the percentage of correct contacts >30% and interface backbone RMSD <4 Å. Detailed examination of all the docking cases gives insights into important determinants of the performance of the computational approach in modeling protein–protein association and predicting of protein–protein complex structures. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Bibliografie:	BIOMS ark:/67375/WNG-XDKP2ZSF-W ArticleID:PROT21867 istex:E32464563977F50AC97791E3D3BFA6B0884CAB25 Klaus Tschira Foundation BIOMS, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany Genome Center, University of California, Davis, 451 East Health Science Drive, 95616 Davis CA, USA ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0887-3585 1097-0134 1097-0134
DOI:	10.1002/prot.21867