title: Ligand- and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor.
abstract: We predicted the structural basis for pleiotropic signaling of the C-C chemokine type 5 (CCR5) G protein-coupled receptor (GPCR) by predicting the binding of several ligands to the lower-energy conformations of the CCR5 receptor and 11 mutants. For each case, we predicted the ∼ 20 most stable conformations for the receptor along with the binding sites for four anti-HIV ligands. We found that none of the ligands bind to the lowest-energy apo-receptor conformation. The three ligands with a similar pharmacophore (Maraviroc, PF-232798, and Aplaviroc) bind to a specific higher-energy receptor conformation whereas TAK-779 (with a different pharmacophore) binds to a different high-energy conformation. This result is in agreement with the very different binding-site profiles for these ligands obtained by us and others. The predicted Maraviroc binding site agrees with the recent structure of CCR5 receptor cocrystallized with Maraviroc. We performed 11 site-directed mutagenesis experiments to validate the predicted binding sites. Here, we independently predicted the lowest 10 mutant protein conformations for each of the 11 mutants and then docked the ligands to these lowest conformations. We found the predicted binding energies to be in excellent agreement with our mutagenesis experiments. These results show that, for GPCRs, each ligand can stabilize a different protein conformation, complicating the use of cocrystallized structures for ligand screening. Moreover, these results show that a single-point mutation in a GPCR can dramatically alter the available low-energy conformations, which in turn alters the binding site, potentially altering downstream signaling events. These studies validate the conformational selection paradigm for the pleiotropic function and structural plasticity of GPCRs.
authors.affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125; and wag@wag.caltech.edu abrolr@csmc.edu.
authors.forename: Ravinder
authors.initials: R
authors.lastname: Abrol
authors.affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125; and.
authors.forename: Bartosz
authors.initials: B
authors.lastname: Trzaskowski
authors.affiliation: Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125; and wag@wag.caltech.edu abrolr@csmc.edu.
authors.forename: William A
authors.initials: WA
authors.lastname: Goddard
authors.affiliation: PharmSelex Inc., Seattle, WA 98102.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Nesterov
authors.affiliation: PharmSelex Inc., Seattle, WA 98102.
authors.forename: Ivan
authors.initials: I
authors.lastname: Olave
authors.affiliation: PharmSelex Inc., Seattle, WA 98102.
authors.forename: Christopher
authors.initials: C
authors.lastname: Irons
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D003510:Cyclohexanes / Q000378:metabolism; D006801:Humans; D008024:Ligands; D000077592:Maraviroc; D008958:Models, Molecular; D050505:Mutant Proteins / Q000378:metabolism; D009154:Mutation / Q000235:genetics*; D017433:Protein Structure, Secondary; D019713:Receptors, CCR5 / Q000737:chemistry* / Q000235:genetics*; D040681:Structural Homology, Protein; D013816:Thermodynamics; D014230:Triazoles / Q000378:metabolism
chemical_list: D003510:Cyclohexanes; D008024:Ligands; D050505:Mutant Proteins; D019713:Receptors, CCR5; D014230:Triazoles; D000077592:Maraviroc
keywords: GEnSeMBLE; conformational ensemble; functional selectivity; ligand–protein binding prediction; protein structure prediction