title: Dynamics of bovine opsin bound to G-protein fragments.
abstract: G protein-coupled receptors (GPCRs) are a large class of membrane proteins that mediate communication of the cell with the outer environment. Upon activation by an agonist, GPCRs undergo large-scale conformational changes that enable binding of the G protein to the receptor. A key open question concerns the mechanism of the long-distance coupling between the agonist-binding site and the cytoplasmic site where G protein binds. Here we address this question by exploring the molecular dynamics of bovine opsin bound to three different fragments of G-proteins. We find that an extended network of hydrogen bonds connects the agonist retinal binding site to the G protein binding site via conserved amino acid residues. The dynamics of the hydrogen-bonding network inside opsin couples to interactions at the G protein binding site.
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan. Electronic address: sugihara-minoru@aist.go.jp.
authors.forename: Minoru
authors.initials: M
authors.lastname: Sugihara
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Koto-ku, Tokyo 135-0064, Japan; Department of Chemistry and Life Science, Aoyama Gakuin University, Sagamihara, Kanagawa 252-5258, Japan.
authors.forename: Makiko
authors.initials: M
authors.lastname: Suwa
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin-Dahlem 14195, Germany. Electronic address: nbondar@zedat.fu-berlin.de.
authors.forename: Ana-Nicoleta
authors.initials: AN
authors.lastname: Bondar
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D019204:GTP-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D055355:Opsins / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D043562:Receptors, G-Protein-Coupled / Q000819:agonists / Q000737:chemistry / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D055355:Opsins; D043562:Receptors, G-Protein-Coupled; D019204:GTP-Binding Proteins
keywords: G protein; G protein-coupled receptors; Protein dynamics; Rhodopsin