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Volumn 78, Issue 10, 2010, Pages 2189-2201

FoldGPCR: Structure prediction protocol for the transmembrane domain of G proteincoupled receptors from class A

Author keywords

Class A GPCR; Implicit solvent; Ligand binding; Membrane protein; Simulated annealing; Structure prediction

Indexed keywords

BETA 2 ADRENERGIC RECEPTOR; CARAZOLOL; G PROTEIN COUPLED RECEPTOR; LIGAND; MEMBRANE PROTEIN; RHODOPSIN; BETA 2 ADRENERGIC RECEPTOR BLOCKING AGENT; BETA ADRENERGIC RECEPTOR BLOCKING AGENT; PROPANOLAMINE DERIVATIVE;

EID: 77955803232     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22731     Document Type: Article
Times cited : (27)

References (66)
  • 2
    • 0038024615 scopus 로고    scopus 로고
    • The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
    • Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 2003;63:1256-1272.
    • (2003) Mol. Pharmacol. , vol.63 , pp. 1256-1272
    • Fredriksson, R.1    Lagerstrom, M.C.2    Lundin, L.G.3    Schioth, H.B.4
  • 3
    • 36949011636 scopus 로고    scopus 로고
    • The G protein-coupled receptor subset of the rat genome
    • Gloriam DE, Fredriksson R, Schioth HB. The G protein-coupled receptor subset of the rat genome. BMC Genomics 2007;8:338.
    • (2007) BMC Genomics , vol.8 , pp. 338
    • Gloriam, D.E.1    Fredriksson, R.2    Schioth, H.B.3
  • 4
    • 27944458624 scopus 로고    scopus 로고
    • GPCR agonists and antagonists in the clinic
    • Tyndall JD, Sandilya R. GPCR agonists and antagonists in the clinic. Med Chem 2005;1:405-421.
    • (2005) Med. Chem. , vol.1 , pp. 405-421
    • Tyndall, J.D.1    Sandilya, R.2
  • 5
    • 0033771402 scopus 로고    scopus 로고
    • The superfamily of heptahelical receptors
    • Lefkowitz RJ. The superfamily of heptahelical receptors. Nat Cell Biol 2000;2: E133-136.
    • (2000) Nat. Cell. Biol. , vol.2
    • Lefkowitz, R.J.1
  • 6
    • 0037452868 scopus 로고    scopus 로고
    • Sequence analyses of G-protein-coupled receptors: Similarities to rhodopsin
    • Mirzadegan T, Benko G, Filipek S, Palczewski K. Sequence analyses of G-protein-coupled receptors: similarities to rhodopsin. Biochemistry 2003;42:2759-2767.
    • (2003) Biochemistry , vol.42 , pp. 2759-2767
    • Mirzadegan, T.1    Benko, G.2    Filipek, S.3    Palczewski, K.4
  • 7
    • 30144441512 scopus 로고    scopus 로고
    • A chemogenomic analysis of the transmembrane binding cavity of human G-proteincoupled receptors
    • Surgand JS, Rodrigo J, Kellenberger E, Rognan D. A chemogenomic analysis of the transmembrane binding cavity of human G-proteincoupled receptors. Proteins 2006;62:509-538.
    • (2006) Proteins , vol.62 , pp. 509-538
    • Surgand, J.S.1    Rodrigo, J.2    Kellenberger, E.3    Rognan, D.4
  • 9
    • 4344581120 scopus 로고    scopus 로고
    • The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure
    • 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;342:571-583.
    • (2004) J. Mol. Biol. , vol.342 , pp. 571-583
    • Okada, T.1    Sugihara, M.2    Bondar, A.N.3    Elstner, M.4    Entel, P.5    Buss, V.6
  • 15
    • 43749109187 scopus 로고    scopus 로고
    • Crystal structure of squid rhodopsin
    • Murakami M, Kouyama T. Crystal structure of squid rhodopsin. Nature 2008;453:363-367.
    • (2008) Nature , vol.453 , pp. 363-367
    • Murakami, M.1    Kouyama, T.2
  • 16
    • 47049130668 scopus 로고    scopus 로고
    • Crystal structure of the ligand-free G-protein-coupled receptor opsin
    • Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 2008;454:183-187.
    • (2008) Nature , vol.454 , pp. 183-187
    • Park, J.H.1    Scheerer, P.2    Hofmann, K.P.3    Choe, H.W.4    Ernst, O.P.5
  • 21
    • 0031565726 scopus 로고    scopus 로고
    • An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors
    • Baldwin JM, Schertler GF, Unger VM. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol 1997;272:144-164.
    • (1997) J. Mol. Biol. , vol.272 , pp. 144-164
    • Baldwin, J.M.1    Schertler, G.F.2    Unger, V.M.3
  • 22
    • 0032575763 scopus 로고    scopus 로고
    • Combined biophysical and biochemical information confirms arrangement of transmembrane helices visible from the three-dimensional map of frog rhodopsin
    • Herzyk P, Hubbard RE. Combined biophysical and biochemical information confirms arrangement of transmembrane helices visible from the three-dimensional map of frog rhodopsin. J Mol Biol 1998;281:741-754.
    • (1998) J. Mol. Biol. , vol.281 , pp. 741-754
    • Herzyk, P.1    Hubbard, R.E.2
  • 23
    • 0030998038 scopus 로고    scopus 로고
    • The transmembrane 7-alpha-bundle of rhodopsin: Distance geometry calculations with hydrogen bonding constraints
    • Pogozheva ID, Lomize AL, Mosberg HI. The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophys J 1997;72:1963-1985.
    • (1997) Biophys. J. , vol.72 , pp. 1963-1985
    • Pogozheva, I.D.1    Lomize, A.L.2    Mosberg, H.I.3
  • 25
    • 0037235663 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
    • Bissantz C, Bernard P, Hibert M, Rognan D. Protein-based virtual screening of chemical databases. II. Are homology models of G-Protein Coupled Receptors suitable targets? Proteins 2003;50:5-25.
    • (2003) Proteins , vol.50 , pp. 5-25
    • Bissantz, C.1    Bernard, P.2    Hibert, M.3    Rognan, D.4
  • 26
    • 33645793799 scopus 로고    scopus 로고
    • Structure modeling of all identified G protein-coupled receptors in the human genome
    • Zhang Y, Devries ME, Skolnick J. Structure modeling of all identified G protein-coupled receptors in the human genome. PLo S Comput Biol 2006;2: e13.
    • (2006) PLo S Comput. Biol. , vol.2
    • Zhang, Y.1    Devries, M.E.2    Skolnick, J.3
  • 29
    • 30344447955 scopus 로고    scopus 로고
    • Assessment of predictions submitted for the CASP6 comparative modeling category
    • Tress M, Ezkurdia I, Grana O, Lopez G, Valencia A. Assessment of predictions submitted for the CASP6 comparative modeling category. Proteins 2005;61 Suppl 7:27-45.
    • (2005) Proteins , vol.61 , Issue.7 SUPPL. , pp. 27-45
    • Tress, M.1    Ezkurdia, I.2    Grana, O.3    Lopez, G.4    Valencia, A.5
  • 30
    • 0037215651 scopus 로고    scopus 로고
    • Rhodopsin crystal: New template yielding realistic models of G-protein-coupled receptors?
    • Archer E, Maigret B, Escrieut C, Pradayrol L, Fourmy D. Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors? Trends Pharmacol Sci 2003;24:36-40.
    • (2003) Trends Pharmacol. Sci. , vol.24 , pp. 36-40
    • Archer, E.1    Maigret, B.2    Escrieut, C.3    Pradayrol, L.4    Fourmy, D.5
  • 32
    • 36749099341 scopus 로고    scopus 로고
    • Assessment of CASP7 predictions for template-based modeling targets
    • Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007;69 Suppl 8:38-56.
    • (2007) Proteins , vol.69 , Issue.8 SUPPL. , pp. 38-56
    • Kopp, J.1    Bordoli, L.2    Battey, J.N.3    Kiefer, F.4    Schwede, T.5
  • 33
    • 0242322528 scopus 로고    scopus 로고
    • An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins
    • Im W, Feig M, Brooks CL, III. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys J 2003;85:2900-2918.
    • (2003) Biophys. J. , vol.85 , pp. 2900-2918
    • Im, W.1    Feig, M.2    Brooks III, C.L.3
  • 34
    • 33846804141 scopus 로고    scopus 로고
    • Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations
    • Bu L, Im W, Brooks CL, III. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys J 2007;92:854-863.
    • (2007) Biophys. J. , vol.92 , pp. 854-863
    • Bu, L.1    Im, W.2    Brooks III, C.L.3
  • 35
    • 40549132223 scopus 로고    scopus 로고
    • Improved model building and assessment of the Calcium-sensing receptor transmembrane domain
    • Bu L, Michino M, Wolf RM, Brooks CL, III. Improved model building and assessment of the Calcium-sensing receptor transmembrane domain. Proteins 2008;71:215-226.
    • (2008) Proteins , vol.71 , pp. 215-226
    • Bu, L.1    Michino, M.2    Wolf, R.M.3    Brooks III, C.L.4
  • 36
    • 42949100258 scopus 로고    scopus 로고
    • De novo prediction of the structures of M. tuberculosis membrane proteins
    • Bu L, Brooks CL, III. De novo prediction of the structures of M. tuberculosis membrane proteins. J Am Chem Soc 2008;130:5384-5385.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 5384-5385
    • Bu, L.1    Brooks III, C.L.2
  • 37
    • 10344226224 scopus 로고    scopus 로고
    • Refinement of NMR structures using implicit solvent and advanced sampling techniques
    • Chen J, Im W, Brooks CL, III. Refinement of NMR structures using implicit solvent and advanced sampling techniques. J Am Chem Soc 2004;126:16038-16047.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 16038-16047
    • Chen, J.1    Im, W.2    Brooks III, C.L.3
  • 38
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen J, Brooks CL, III. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 2007;67:922-930.
    • (2007) Proteins , vol.67 , pp. 922-930
    • Chen, J.1    Brooks III, C.L.2
  • 39
    • 58149479285 scopus 로고    scopus 로고
    • Solvent dramatically affects protein structure refinement
    • Chopra G, Summa CM, Levitt M. Solvent dramatically affects protein structure refinement. Proc Natl Acad Sci USA 2008;105:20239-20244.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 20239-20244
    • Chopra, G.1    Summa, C.M.2    Levitt, M.3
  • 40
    • 38749131545 scopus 로고    scopus 로고
    • New G-protein-coupled receptor crystal structures: Insights and limitations
    • Kobilka B, Schertler GF. New G-protein-coupled receptor crystal structures: insights and limitations. Trends Pharmacol Sci 2008;29(2):79-83.
    • (2008) Trends Pharmacol. Sci. , vol.29 , Issue.2 , pp. 79-83
    • Kobilka, B.1    Schertler, G.F.2
  • 41
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 42
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with rosetta
    • Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004;55:656-677.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 46
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003;10:59-69.
    • (2003) Nat. Struct. Biol. , vol.10 , pp. 59-69
    • Suel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 47
    • 77957055780 scopus 로고
    • Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors
    • Ballesteros JA, Weinstein H. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. Methods Neurosci 1995;25:366-428.
    • (1995) Methods Neurosci. , vol.25 , pp. 366-428
    • Ballesteros, J.A.1    Weinstein, H.2
  • 49
    • 0035950051 scopus 로고    scopus 로고
    • Ligand-protein database: Linking protein-ligand complex structures to binding data
    • Roche O, Kiyama R, Brooks CL, III. Ligand-protein database: linking protein-ligand complex structures to binding data. J Med Chem 2001;44(22):3592-3598.
    • (2001) J. Med. Chem. , vol.44 , Issue.22 , pp. 3592-3598
    • Roche, O.1    Kiyama, R.2    Brooks III, C.L.3
  • 50
    • 16644374796 scopus 로고    scopus 로고
    • How does averaging affect protein structure comparison on the ensemble level?
    • Zagrovic B, Pande VS. How does averaging affect protein structure comparison on the ensemble level? Biophys J 2004;87:2240-2246.
    • (2004) Biophys. J. , vol.87 , pp. 2240-2246
    • Zagrovic, B.1    Pande, V.S.2
  • 51
    • 0001616080 scopus 로고    scopus 로고
    • Replica-exchange molecular dynamics method for protein folding
    • Sugita Y, Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 1999;314:141-151.
    • (1999) Chem. Phys. Lett. , vol.314 , pp. 141-151
    • Sugita, Y.1    Okamoto, Y.2
  • 52
    • 0034864528 scopus 로고    scopus 로고
    • Generalized-ensemble algorithms for molecular simulations of biopolymers
    • Mitsutake A, Sugita Y, Okamoto Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers 2001;60:96-123.
    • (2001) Biopolymers , vol.60 , pp. 96-123
    • Mitsutake, A.1    Sugita, Y.2    Okamoto, Y.3
  • 54
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gasphase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • Mackerell AD, Jr., Feig M, Brooks CL, III. Extending the treatment of backbone energetics in protein force fields: limitations of gasphase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004;25:1400-1415.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • Mackerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 55
    • 0141956090 scopus 로고    scopus 로고
    • Generalized born model with a simple smoothing function
    • Im W, Lee MS, Brooks CL, III. Generalized born model with a simple smoothing function. J Comput Chem 2003;24:1691-1702.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks III, C.L.3
  • 57
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB tool set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • Feig M, Karanicolas J, Brooks CL, III. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 2004;22:377-395.
    • (2004) J. Mol. Graph Model , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 58
    • 4644273133 scopus 로고    scopus 로고
    • An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data
    • Fleishman SJ, Harrington S, Friesner RA, Honig B, Ben-Tal N. An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data. Biophys J 2004;87:3448-3459.
    • (2004) Biophys. J. , vol.87 , pp. 3448-3459
    • Fleishman, S.J.1    Harrington, S.2    Friesner, R.A.3    Honig, B.4    Ben-Tal, N.5
  • 59
    • 84860183160 scopus 로고    scopus 로고
    • Predicting structurally conserved contacts for homologous proteins using sequence conservation filters
    • Michino M, Brooks CL, III. Predicting structurally conserved contacts for homologous proteins using sequence conservation filters. Proteins 2009;77:448-453.
    • (2009) Proteins , vol.77 , pp. 448-453
    • Michino, M.1    Brooks III, C.L.2
  • 60
    • 0036169280 scopus 로고    scopus 로고
    • The binding site of aminergic G protein-coupled receptors: The transmembrane segments and second extracellular loop
    • Shi L, Javitch JA. The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop. Annu Rev Pharmacol Toxicol 2002;42:437-467.
    • (2002) Annu. Rev. Pharmacol. Toxicol. , vol.42 , pp. 437-467
    • Shi, L.1    Javitch, J.A.2
  • 61
    • 33947356279 scopus 로고    scopus 로고
    • G protein coupled receptor structure and activation
    • Kobilka BK. G protein coupled receptor structure and activation. Biochim Biophys Acta 2007;1768:794-807.
    • (2007) Biochim. Biophys. Acta , vol.1768 , pp. 794-807
    • Kobilka, B.K.1
  • 62
    • 44049086134 scopus 로고    scopus 로고
    • Ligand-stabilized conformational states of human beta (2) adrenergic receptor: Insight into G-protein-coupled receptor activation
    • Bhattacharya S, Hall SE, Li H, Vaidehi N. Ligand-stabilized conformational states of human beta (2) adrenergic receptor: insight into G-protein-coupled receptor activation. Biophys J 2008;94:2027-2042.
    • (2008) Biophys. J. , vol.94 , pp. 2027-2042
    • Bhattacharya, S.1    Hall, S.E.2    Li, H.3    Vaidehi, N.4
  • 63
    • 16644386061 scopus 로고    scopus 로고
    • Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins
    • Zhang Y, Skolnick J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J 2004;87:2647-2655.
    • (2004) Biophys. J. , vol.87 , pp. 2647-2655
    • Zhang, Y.1    Skolnick, J.2
  • 64
    • 27644450114 scopus 로고    scopus 로고
    • The N-terminal juxtamembrane segment of the V1a vasopressin receptor provides two independent epitopes required for high-affinity agonist binding and signaling
    • Hawtin SR, Wesley VJ, Simms J, Argent CC, Latif K, Wheatley M. The N-terminal juxtamembrane segment of the V1a vasopressin receptor provides two independent epitopes required for high-affinity agonist binding and signaling. Mol Endocrinol 2005;19:2871-2881.
    • (2005) Mol. Endocrinol. , vol.19 , pp. 2871-2881
    • Hawtin, S.R.1    Wesley, V.J.2    Simms, J.3    Argent, C.C.4    Latif, K.5    Wheatley, M.6
  • 65
    • 34047253035 scopus 로고    scopus 로고
    • Differential helical orientations among related G protein-coupled receptors provide a novel mechanism for selectivity. Studies with salvinorin A and the kappa-opioid receptor
    • Vortherms TA, Mosier PD, Westkaemper RB, Roth BL. Differential helical orientations among related G protein-coupled receptors provide a novel mechanism for selectivity. Studies with salvinorin A and the kappa-opioid receptor. J Biol Chem 2007;282:3146-3156.
    • (2007) J. Biol. Chem. , vol.282 , pp. 3146-3156
    • Vortherms, T.A.1    Mosier, P.D.2    Westkaemper, R.B.3    Roth, B.L.4
  • 66
    • 0029907599 scopus 로고    scopus 로고
    • Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin
    • Farrens DL, Altenbach C, Yang K, Hubbell WL, Khorana HG. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 1996;274:768-770.
    • (1996) Science , vol.274 , pp. 768-770
    • Farrens, D.L.1    Altenbach, C.2    Yang, K.3    Hubbell, W.L.4    Khorana, H.G.5


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