The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement

TitleThe utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement
Publication TypeJournal Article
Year of Publication2011
AuthorsBrylinski M, Lee SY, Zhou H, Skolnick J
JournalJ Struct Biol
Volume173
Issue3
Pagination558-69
Date Published2011 Mar
ISSN1095-8657
KeywordsAlgorithms, Binding Sites, Computer Simulation, Ligands, Models, Molecular, Protein Conformation, Proteins
Abstract

Exhaustive exploration of molecular interactions at the level of complete proteomes requires efficient and reliable computational approaches to protein function inference. Ligand docking and ranking techniques show considerable promise in their ability to quantify the interactions between proteins and small molecules. Despite the advances in the development of docking approaches and scoring functions, the genome-wide application of many ligand docking/screening algorithms is limited by the quality of the binding sites in theoretical receptor models constructed by protein structure prediction. In this study, we describe a new template-based method for the local refinement of ligand-binding regions in protein models using remotely related templates identified by threading. We designed a Support Vector Regression (SVR) model that selects correct binding site geometries in a large ensemble of multiple receptor conformations. The SVR model employs several scoring functions that impose geometrical restraints on the Cα positions, account for the specific chemical environment within a binding site and optimize the interactions with putative ligands. The SVR score is well correlated with the RMSD from the native structure; in 47% (70%) of the cases, the Pearson's correlation coefficient is >0.5 (>0.3). When applied to weakly homologous models, the average heavy atom, local RMSD from the native structure of the top-ranked (best of top five) binding site geometries is 3.1Å (2.9Å) for roughly half of the targets; this represents a 0.1 (0.3)Å average improvement over the original predicted structure. Focusing on the subset of strongly conserved residues, the average heavy atom RMSD is 2.6Å (2.3Å). Furthermore, we estimate the upper bound of template-based binding site refinement using only weakly related proteins to be ∼2.6Å RMSD. This value also corresponds to the plasticity of the ligand-binding regions in distant homologues. The Binding Site Refinement (BSR) approach is available to the scientific community as a web server that can be accessed at http://cssb.biology.gatech.edu/bsr/.

Alternate JournalJournal of Structural Biology
Full Text

iPaper

PreviewAttachmentSize
2011_jsb.pdf1.22 MB

© Michal Brylinski
This website is hosted at the CCT