title: Exploring allosteric coupling in the alpha-subunit of heterotrimeric G proteins using evolutionary and ensemble-based approaches.
abstract: BACKGROUND
  Allosteric coupling, which can be defined as propagation of a perturbation at one region of the protein molecule (such as ligand binding) to distant sites in the same molecule, constitutes the most general mechanism of regulation of protein function. However, unlike molecular details of ligand binding, structural elements involved in allosteric effects are difficult to diagnose. Here, we identified allosteric linkages in the alpha-subunits of heterotrimeric G proteins, which were evolved to transmit membrane receptor signals by allosteric mechanisms, by using two different approaches that utilize fundamentally different and independent information.
  
  
  RESULTS
  We analyzed: 1) correlated mutations in the family of G protein alpha-subunits, and 2) cooperativity of the native state ensemble of the Galphai1 or transducin. The combination of these approaches not only recovered already-known details such as the switch regions that change conformation upon nucleotide exchange, and those regions that are involved in receptor, effector or Gbetagamma interactions (indicating that the predictions of the analyses can be viewed with a measure of confidence), but also predicted new sites that are potentially involved in allosteric communication in the Galpha protein. A summary of the new sites found in the present analysis, which were not apparent in crystallographic data, is given along with known functional and structural information. Implications of the results are discussed.
  
  
  CONCLUSIONS
  A set of residues and/or structural elements that are potentially involved in allosteric communication in Galpha is presented. This information can be used as a guide to structural, spectroscopic, mutational, and theoretical studies on the allosteric network in Galpha proteins, which will provide a better understanding of G protein-mediated signal transduction.
authors.affiliation: Ankara University Faculty of Medicine, Department of Pharmacology and Clinical Pharmacology, Sihhiye 06100, Ankara, Turkey. kemalsayar@yahoo.com
authors.forename: Kemal
authors.initials: K
authors.lastname: Sayar
authors.forename: Ozlem
authors.initials: O
authors.lastname: Uğur
authors.forename: Tong
authors.initials: T
authors.lastname: Liu
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Hilser
authors.forename: Ongun
authors.initials: O
authors.lastname: Onaran
mesh_terms: D000494:Allosteric Regulation / Q000235:genetics / Q000502:physiology*; D000495:Allosteric Site / Q000235:genetics*; D000595:Amino Acid Sequence; D001483:Base Sequence; D003198:Computer Simulation; D019143:Evolution, Molecular; D044385:GTP-Binding Protein alpha Subunits / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D011485:Protein Binding; D016415:Sequence Alignment; D015398:Signal Transduction / Q000235:genetics*; D013816:Thermodynamics
chemical_list: D044385:GTP-Binding Protein alpha Subunits