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Original Research

Hydrophobicity profiles in G protein-coupled receptor transmembrane helical domains

Pages 123-133 | Published online: 01 Dec 2010

References

  • Hamm HE. The many faces of G protein signaling. J Biol Chem. 1998;273(2):669–672.
  • Ji TH, Grossmann M, Ji I. G protein-coupled receptors. I. Diversity ofreceptorligand interactions. J Biol Chem. 1998;273(28):17299–17302.
  • Gilman AG. G proteins: Transducers of receptor-generated signals. Annu Rev Biochem. 1987;56:615–649.
  • Engelhardt S, Rochais F. G proteins: More than transducers of receptor-generated signals? Circ Res. 2007;100(8):1109–1111.
  • Bjarnadottir TK, Gloriam DE, Hellstrand SH, Kristiansson H, Fredriksson R, Schioth HB. Comprehensive repertoire and phylogenetic analysis of the G protein-coupled receptors in human and mouse. Genomics. 2006;88(3):263–273.
  • Glusman G, Yanai I, Rubin I, Lancet D. The complete human olfactory subgenome. Genome Res. 2001;11(5):685–702.
  • Gilad Y, Lancet D. Population differences in the human functional olfactory repertoire. Mol Biol Evol. 2003;20(3):307–314.
  • Buck L, Axel R. A novel multigene family may encode odorant receptors: A molecular basis for odor recognition. Cell. 1991;65(1):175–187.
  • Palczewski K, Kumasaka T, Hori T, et al. Crystal structure of rhodopsin: A G protein-coupled receptor. Science. 2000;289(5480):739–745.
  • Stenkamp RE, Teller DC, Palczewski K. Crystal structure of rhodopsin: A G-protein-coupled receptor. Chembiochem. 2002;3(10):963–967.
  • Lai PC, Bahl G, Gremigni M, et al. An olfactory receptor pseudogene whose function emerged in humans: A case study in the evolution of structure-function in GPCRs. J Struct Funct Genomics. 2008;9(1–4):29–40.
  • Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V. The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol. 2004;342(2):571–583.
  • Rasmussen SG, Choi HJ, Rosenbaum DM, et al. Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature. 2007;450(7168):383–387.
  • Warne T, Serrano-Vega MJ, Baker JG, et al. Structure of a beta1 -adrenergic G-protein-coupled receptor. Nature. 2008;454(7203):486–491.
  • Hartmut M. Crystallization of membrane proteins. Trends Biochem Sci. 1983;8(2):56–59.
  • Sanchez R, Sali A. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol. 2000;143:97–129.
  • Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. 2007;Chapter 2:Unit 29.
  • Tebben AJ, Schnur DM. Beyond rhodopsin: G protein-coupled receptor structure and modeling incorporating the beta2-adrenergic and adenosine A(2A) crystal structures. Methods Mol Biol. 2010;672:359–386.
  • Singer MS. Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor. Chem Senses. 2000;25(2):155–165.
  • Lai PC, Singer MS, Crasto CJ. Structural activation pathways from dynamic olfactory receptor-odorant interactions. Chem Senses. 2005;30(9):781–792.
  • Cole C, Barber JD, Barton GJ. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 2008;36(Web Server issue):W197–W201.
  • Persson B, Argos P. Prediction of membrane protein topology utilizing multiple sequence alignments. J Protein Chem. 1997;16(5):453–457.
  • Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol. 2001;305(3):567–580.
  • Tusnady GE, Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 2001;17(9):849–850.
  • Vaidehi N, Floriano WB, Trabanino R, et al. Prediction of structure and function of G protein-coupled receptors. Proc Natl Acad Sci U S A. 2002;99(20):12622–12627.
  • Eisenberg D, Schwarz E, Komaromy M, Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J Mol Biol. 1984;179(1):125–142.
  • Eisenberg D. Three-dimensional structure of membrane and surface proteins. Annu Rev Biochem. 1984;53:595–623.
  • Donnelly D. Modelling alpha-helical transmembrane domains. Biochem Soc Trans. 1993;21(1):36–39.
  • Hanson MA, Stevens RC. Discovery of new GPCR biology: One receptor structure at a time. Structure. 2009;17(1):8–14.
  • Lagerstrom MC, Schioth HB. Structural diversity of G protein-coupled receptors and significance for drug discovery. Nat Rev Drug Discov. 2008;7(4):339–357.
  • Michino M, Abola E, Brooks CL 3rd, Dixon JS, Moult J, Stevens RC. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat Rev Drug Discov. 2009;8(6):455–463.
  • Chothia C. The nature of the accessible and buried surfaces in proteins. J Mol Biol. 1976;105(1):1–12.
  • Janin J. Surface and inside volumes in globular proteins. Nature. 1979;277(5696):491–492.
  • von Heijne G, Blomberg C. Trans-membrane translocation of proteins. The direct transfer model. Eur J Biochem. 1979;97(1):175–181.
  • von Heijne G. Membrane proteins: The amino acid composition of membrane-penetrating segments. Eur J Biochem. 1981;120(2):275–278.
  • Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982;157(1):105–132.
  • Argos P, Rao JK, Hargrave PA. Structural prediction of membrane-bound proteins. Eur J Biochem. 1982;128(2–3):565–575.
  • Nozaki Y, Tanford C. The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J Biol Chem. 1971;246(7):2211–2217.
  • Segrest JP, Feldmann RJ. Membrane proteins: Amino acid sequence and membrane penetration. J Mol Biol. 1974;87(4):853–858.
  • Wolfenden R, Andersson L, Cullis PM, Southgate CC. Affinities of amino acid side chains for solvent water. Biochemistry. 1981;20(4):849–855.
  • Tikhonova IG, Fourmy D. The family of G protein-coupled receptors: An example of membrane proteins. Methods Mol Biol. 2010;654:441–444.
  • Trabanino RJ, Hall SE, Vaidehi N, Floriano WB, Kam VW, Goddard WA 3rd. First principles predictions of the structure and function of g-protein-coupled receptors: Validation for bovine rhodopsin. Biophys J. 2004;86(4):1904–1921.
  • Kalani MY, Vaidehi N, Hall SE, et al. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. Proc Natl Acad Sci U S A. 2004;101(11):3815–3820.
  • Hummel P, Vaidehi N, Floriano WB, Hall SE, Goddard WA 3rd. Test of the binding threshold hypothesis for olfactory receptors: Explanation of the differential binding of ketones to the mouse and human orthologs of olfactory receptor 912–993. Protein Sci. 2005;14(3):703–710.
  • Hall SE, Floriano WB, Vaidehi N, Goddard WA 3rd. Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparison of predicted odor recognition profiles with experiment. Chem Senses. 2004;29(7):595–616.
  • Freddolino PL, Kalani MY, Vaidehi N, et al. Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists. Proc Natl Acad Sci U S A. 2004;101(9):2736–2741.
  • Floriano WB, Vaidehi N, Zamanakos G, Goddard WA 3rd. Hier VLS hierarchical docking protocol for virtual ligand screening of large-molecule databases. J Med Chem. 2004;47(1):56–71.
  • Floriano WB, Vaidehi N, Goddard WA 3rd, Singer MS, Shepherd GM. Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci U S A. 2000;97(20):10712–10716.
  • Floriano WB, Vaidehi N, Goddard WA 3rd. Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors. Chem Senses. 2004;29(4):269–290.
  • Floriano WB, Hall S, Vaidehi N, Kim U, Drayna D, Goddard WA 3rd. Modeling the human PTC bitter-taste receptor interactions with bitter tastants. J Mol Model. 2006;12(6):931–941.
  • Araneda RC, Kini AD, Firestein S. The molecular receptive range of an odorant receptor. Nat Neurosci. 2000;3(12):1248–1255.
  • Ladds G, Goddard A, Davey J. Functional analysis of heterologous GPCR signalling pathways in yeast. Trends Biotechnol. 2005;23(7):367–373.
  • Owens SL, Fitzke FW, Inglehearn CF, et al. Ocular manifestations in autosomal dominant retinitis pigmentosa with a Lys-296-Glu rhodopsin mutation at the retinal binding site. Br J Ophthalmol. 1994;78(5):353–358.
  • Decaillot FM, Befort K, Filliol D, Yue S, Walker P, Kieffer BL. Opioid receptor random mutagenesis reveals a mechanism for G protein-coupled receptor activation. Nat Struct Biol. 2003;10(8):629–636.
  • Matsumoto H, Yoshizawa T. Rhodopsin regeneration is accelerated via noncovalent 11-cis retinal-opsin complex – a role of retinal binding pocket of opsin. Photochem Photobiol. 2008;84(4):985–989.
  • Strader CD, Sigal IS, Register RB, Candelore MR, Rands E, Dixon RA. Identification of residues required for ligand binding to the beta-adrenergic receptor. Proc Natl Acad Sci U S A. 1987;84(13):4384–4388.
  • Mersmann HJ, McNeel RL. Ligand binding to the porcine adipose tissue beta-adrenergic receptor. J Anim Sci. 1992;70(3):787–797.
  • Jaakola VP, Griffith MT, Hanson MA, et al. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science. 2008;322(59052)A:1211–1217.
  • Mustafi D, Palczewski K. Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors. Mol Pharmacol. 2009;75(1):1–12.
  • Malnic B, Hirono J, Sato T, Buck LB. Combinatorial receptor codes for odors. Cell. 1999;96(5):713–723.