title: Homology model-assisted elucidation of binding sites in GPCRs.
abstract: G protein-coupled receptors (GPCRs) are important mediators of cell signaling and a major family of drug targets. Despite recent breakthroughs, experimental elucidation of GPCR structures remains a formidable challenge. Homology modeling of 3D structures of GPCRs provides a practical tool for elucidating the structural determinants governing the interactions of these important receptors with their ligands. The working model of the binding site can then be used for virtual screening of additional ligands that may fit this site, for determining and comparing specificity profiles of related receptors, and for structure-based design of agonists and antagonists. The current review presents the protocol and enumerates the steps for modeling and validating the residues involved in ligand binding. The main stages include (a) modeling the receptor structure using an automated fragment-based approach, (b) predicting potential binding pockets, (c) docking known binders, (d) analyzing predicted interactions and comparing with positions that have been shown to bind ligands in other receptors, (e) validating the structural model by mutagenesis.
authors.affiliation: Institute of Biochemistry, Food Science, and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, Israel.
authors.forename: Anat
authors.initials: A
authors.lastname: Levit
authors.forename: Dov
authors.initials: D
authors.lastname: Barak
authors.forename: Maik
authors.initials: M
authors.lastname: Behrens
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Meyerhof
authors.forename: Masha Y
authors.initials: MY
authors.lastname: Niv
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016296:Mutagenesis / Q000235:genetics; D050505:Mutant Proteins / Q000737:chemistry; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry*; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D000098706:Taste Receptors, Type 2
chemical_list: D050505:Mutant Proteins; D043562:Receptors, G-Protein-Coupled; D000098706:Taste Receptors, Type 2