메뉴 건너뛰기




Volumn 106, Issue 34, 2009, Pages 14253-14258

Coarse-grained modeling of allosteric regulation in protein receptors

Author keywords

Agonism; Allostery; GPCR; Signal transduction

Indexed keywords

BETA 2 ADRENERGIC RECEPTOR; RHODOPSIN;

EID: 70149098505     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0901811106     Document Type: Article
Times cited : (39)

References (55)
  • 1
    • 78651189765 scopus 로고
    • On nature of allosteric transitions: A plausible model
    • Monod J, Wyman J, Changeux JP (1965) On nature of allosteric transitions: A plausible model. J Mol Biol 12:88-118.
    • (1965) J Mol Biol , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 2
    • 0013863816 scopus 로고
    • Comparison of experimental binding data and theoretical models in proteins containing subunits
    • Koshland DEJ, Némethy G, Filmer D (1966) Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5:365-368.
    • (1966) Biochemistry , vol.5 , pp. 365-368
    • Koshland, D.E.J.1    Némethy, G.2    Filmer, D.3
  • 4
    • 47649125643 scopus 로고    scopus 로고
    • Allosteric regulation and catalysis emerge via a common route
    • Goodey NM, Bencovic SJ (2008) Allosteric regulation and catalysis emerge via a common route. Nat Chem Biol 4:474-482.
    • (2008) Nat Chem Biol , vol.4 , pp. 474-482
    • Goodey, N.M.1    Bencovic, S.J.2
  • 5
    • 37249067732 scopus 로고    scopus 로고
    • The origin of protein interactions and allostery in colocalization
    • DOI 10.1038/nature06524, PII NATURE06524
    • Kuriyan J, Eisenberg D (2007) The origin of protein interactions and allostery in colocalization. Nature 450:983-990. (Pubitemid 350273628)
    • (2007) Nature , vol.450 , Issue.7172 , pp. 983-990
    • Kuriyan, J.1    Eisenberg, D.2
  • 7
    • 0346220393 scopus 로고    scopus 로고
    • The role of dynamics in allosteric regulation
    • Kern D, Zuiderweg ERP (2003) The role of dynamics in allosteric regulation. Curr Opin Struct Biol 13:748-757.
    • (2003) Curr Opin Struct Biol , vol.13 , pp. 748-757
    • Kern, D.1    Zuiderweg, E.R.P.2
  • 8
    • 17644402459 scopus 로고    scopus 로고
    • Transduction of receptor signals by β-arrestins
    • Lefkowitz RJ, Shehoy SK (2005) Transduction of receptor signals by β-arrestins. Science 308:512-517.
    • (2005) Science , vol.308 , pp. 512-517
    • Lefkowitz, R.J.1    Shehoy, S.K.2
  • 11
    • 49649084492 scopus 로고    scopus 로고
    • Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms
    • Okazaki K, Takada S (2008) Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms. Proc Natl Acad Sci USA 105:11182-11187.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 11182-11187
    • Okazaki, K.1    Takada, S.2
  • 12
    • 45849095234 scopus 로고    scopus 로고
    • How do proteins interact?
    • Boehr DD, Wright P (2008) How do proteins interact? Science 320:1429-1430.
    • (2008) Science , vol.320 , pp. 1429-1430
    • Boehr, D.D.1    Wright, P.2
  • 13
    • 13444261019 scopus 로고    scopus 로고
    • G protein-coupled receptors: A count of 1001 conformations
    • DOI 10.1111/j.1472-8206.2005.00319.x
    • Vauquelin G, Van Liefde I (2005) G protein-coupled receptors: a count of 1001 conformations. Fundam Clin Pharmacol 19:45-56. (Pubitemid 40204346)
    • (2005) Fundamental and Clinical Pharmacology , vol.19 , Issue.1 , pp. 45-56
    • Vauquelin, G.1    Van Liefde, I.2
  • 15
    • 48249141040 scopus 로고    scopus 로고
    • Allostery and cooperativity revisited
    • Cui Q, Karplus M (2008) Allostery and cooperativity revisited. Protein Sci 17:1-13.
    • (2008) Protein Sci , vol.17 , pp. 1-13
    • Cui, Q.1    Karplus, M.2
  • 19
    • 29244491983 scopus 로고    scopus 로고
    • Structural allostery and binding of the transferrin-receptor complex
    • DOI 10.1074/mcp.M500095-MCP200
    • Xu GZ, Liu RT, Zak O, Aisen P, Chance MR (2005) Structural allostery and binding of the transferrin center dot receptor complex. Mol Cell Proteomics 4:1959-1967. (Pubitemid 41830190)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.12 , pp. 1959-1967
    • Xu, G.1    Liu, R.2    Zak, O.3    Aisen, P.4    Chance, M.R.5
  • 20
    • 1642588255 scopus 로고    scopus 로고
    • Structures of mismatch replication errors observed in a DNA polymerase
    • Johnson SJ, Beese LS (2004) Structures of mismatch replication errors observed in a DNA polymerase. Cell 116:803-816.
    • (2004) Cell , vol.116 , pp. 803-816
    • Johnson, S.J.1    Beese, L.S.2
  • 21
    • 1542379652 scopus 로고    scopus 로고
    • Evolutionary Trace of G Protein-coupled Receptors Reveals Clusters of Residues That Determine Global and Class-specific Functions
    • DOI 10.1074/jbc.M312671200
    • Madabushi S, Gross AK, Philippi A, Meng EC, Lichtarge O (2004) Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J Biol Chem 279:8126-8132. (Pubitemid 38294703)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.9 , pp. 8126-8132
    • Madabushi, S.1    Gross, A.K.2    Philippi, A.3    Meng, E.C.4    Wensel, T.G.5    Lichtarge, O.6
  • 22
    • 63849294621 scopus 로고    scopus 로고
    • 2-adrenergic receptor reconciles structural and biochemical observations
    • 2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci USA 106:4689-4694.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 4689-4694
    • Dror, R.O.1
  • 23
    • 54449098286 scopus 로고    scopus 로고
    • Structural basis for ligand binding and specificity in adrenergic receptors: Implications for GPCR-targeted drug discovery
    • Huber T, Menon S, Sakmar TP (2008) Structural basis for ligand binding and specificity in adrenergic receptors: Implications for GPCR-targeted drug discovery. Biochem 47:11013-11023.
    • (2008) Biochem , vol.47 , pp. 11013-11023
    • Huber, T.1    Menon, S.2    Sakmar, T.P.3
  • 24
    • 40949130399 scopus 로고    scopus 로고
    • A novel switch region regulates H-ras membrane orientation and signal output
    • Abankwa D, et al. (2008) A novel switch region regulates H-ras membrane orientation and signal output. EMBO J 27:727-735.
    • (2008) EMBO J , vol.27 , pp. 727-735
    • Abankwa, D.1
  • 25
    • 34347370129 scopus 로고    scopus 로고
    • Dynamic models of G-protein coupled receptor dimers: Indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer
    • DOI 10.1007/s10822-006-9053-3
    • Filizola M, Wang SX, Weinstein H (2006) Dynamic models of G-protein coupled receptor dimers: Indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer. J Comput Aided Mol Des 20:405-416. (Pubitemid 44823879)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.7-8 , pp. 405-416
    • Filizola, M.1    Wang, S.X.2    Weinstein, H.3
  • 27
    • 10344261477 scopus 로고    scopus 로고
    • Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations
    • Faraldo-Comez JD, et al. (2004) Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins Struct Funct Genet 57:783-791.
    • (2004) Proteins Struct Funct Genet , vol.57 , pp. 783-791
    • Faraldo-Comez, J.D.1
  • 29
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • DOI 10.1016/j.jmb.2005.07.031, PII S0022283605008193
    • Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J Mol Biol 352:807-822. (Pubitemid 41267070)
    • (2005) Journal of Molecular Biology , vol.352 , Issue.4 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2
  • 31
    • 38349092279 scopus 로고    scopus 로고
    • Conformational transitions in adenylate kinase: Allosteric communication reduces misligation
    • Whitford PC, Gosavi S, Onuchic JN (2008) Conformational transitions in adenylate kinase: Allosteric communication reduces misligation. J Biol Chem 283:2042-2048.
    • (2008) J Biol Chem , vol.283 , pp. 2042-2048
    • Whitford, P.C.1    Gosavi, S.2    Onuchic, J.N.3
  • 32
    • 34848852941 scopus 로고    scopus 로고
    • Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations
    • DOI 10.1529/biophysj.107.105270
    • Zheng W, Brooks BR, Thirumalai D (2007) Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophys J 93:2289-2299. (Pubitemid 47511128)
    • (2007) Biophysical Journal , vol.93 , Issue.7 , pp. 2289-2299
    • Zheng, W.1    Brooks, B.R.2    Thirumalai, D.3
  • 33
    • 34248586875 scopus 로고    scopus 로고
    • Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model
    • DOI 10.1002/prot.21326
    • Zheng W, Liao JC, Brooks BR, Doniach S (2007) Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins Struct Funct Genet 67:886-896. (Pubitemid 46753936)
    • (2007) Proteins: Structure, Function and Genetics , vol.67 , Issue.4 , pp. 886-896
    • Zheng, W.1    Liao, J.-C.2    Brooks, B.R.3    Doniach, S.4
  • 34
    • 41449115497 scopus 로고    scopus 로고
    • Fast dynamics perturbation analysis for prediction of protein functional sites
    • Ming D, Cohn JD, Wall ME (2008) Fast dynamics perturbation analysis for prediction of protein functional sites. BMC Struct Biol 8:5.
    • (2008) BMC Struct Biol , vol.8 , pp. 5
    • Ming, D.1    Cohn, J.D.2    Wall, M.E.3
  • 35
    • 41049092674 scopus 로고    scopus 로고
    • Coupling between global dynamics and signal transduction pathways: A mechanism of allostery for chaperonin GroEL
    • Chennubhotla C, Yang Z, Bahar I (2008) Coupling between global dynamics and signal transduction pathways: A mechanism of allostery for chaperonin GroEL. Mol Biosystems 4:287-292.
    • (2008) Mol Biosystems , vol.4 , pp. 287-292
    • Chennubhotla, C.1    Yang, Z.2    Bahar, I.3
  • 36
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • Süel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 10:59-69.
    • (2003) Nat Struct Biol , vol.10 , pp. 59-69
    • Süel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 37
    • 9944263528 scopus 로고    scopus 로고
    • Searching for new allosteric sites in enzymes
    • Hardy JA, Wells JA (2004) Searching for new allosteric sites in enzymes. Curr Opin Struct Biol 14:706-715.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 706-715
    • Hardy, J.A.1    Wells, J.A.2
  • 38
    • 33745461893 scopus 로고    scopus 로고
    • Residues crucial for maintaining short paths in network communication mediate signaling in proteins
    • DOI 10.1038/msb4100063, PII M4100063, msb4100063
    • del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Molecular Syst Biol 2:1-12. (Pubitemid 43948162)
    • (2006) Molecular Systems Biology , vol.2
    • Del Sol, A.1    Fujihashi, H.2    Amoros, D.3    Nussinov, R.4
  • 39
    • 4344581120 scopus 로고    scopus 로고
    • The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure
    • DOI 10.1016/j.jmb.2004.07.044, PII S0022283604008733
    • Okada T, et al. (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol 342:571-583. (Pubitemid 39149759)
    • (2004) Journal of Molecular Biology , vol.342 , Issue.2 , pp. 571-583
    • Okada, T.1    Sugihara, M.2    Bondar, A.-N.3    Elstner, M.4    Entel, P.5    Buss, V.6
  • 40
    • 0034784920 scopus 로고    scopus 로고
    • Rhodopsin: Structural basis of molecular physiology
    • Menon ST, Han M, Sakmar TP (2001) Rhodopsin: Structural basis of molecular physiology. Physiol Rev 81:1659-1688. (Pubitemid 32947780)
    • (2001) Physiological Reviews , vol.81 , Issue.4 , pp. 1659-1688
    • Menon, S.T.1    Han, M.2    Sakmar, T.P.3
  • 41
    • 36448995359 scopus 로고    scopus 로고
    • 2-adrenergic G protein-coupled receptor
    • 2-adrenergic G protein-coupled receptor. Science 318:1258-1265.
    • (2007) Science , vol.318 , pp. 1258-1265
    • Cherezov, V.1
  • 42
    • 36448978229 scopus 로고    scopus 로고
    • 2-adrenergic receptor function
    • 2-adrenergic receptor function. Science 318:1266-1273.
    • (2007) Science , vol.318 , pp. 1266-1273
    • Rosenbaum, D.M.1
  • 43
    • 34548476934 scopus 로고    scopus 로고
    • Critical role for the second extracellular loop in the binding of both orthosteric and allosteric G protein-coupled receptor ligands
    • Avlani VA, et al. (2007) Critical role for the second extracellular loop in the binding of both orthosteric and allosteric G protein-coupled receptor ligands. J Biol Chem 282:25677-25686.
    • (2007) J Biol Chem , vol.282 , pp. 25677-25686
    • Avlani, V.A.1
  • 44
    • 12944249776 scopus 로고
    • Discussion of solution for best rotation to relate two sets of vectors
    • Kabsch W (1978) Discussion of solution for best rotation to relate two sets of vectors. Acta Crystallogr Sect A 34:827-828.
    • (1978) Acta Crystallogr Sect A , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 47
    • 48249126790 scopus 로고    scopus 로고
    • Distinct conformational changes in β-arrestin report biased agonism at seven-transmembrane receptors
    • Shukla AK, et al. (2008) Distinct conformational changes in β-arrestin report biased agonism at seven-transmembrane receptors. Proc Natl Acad Sci USA 105:9988-9993.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 9988-9993
    • Shukla, A.K.1
  • 48
    • 34447624153 scopus 로고    scopus 로고
    • Collateral efficacy in drug discovery: Taking advantage of the good (allosteric) nature of 7TM receptors
    • Kenakin T (2007) Collateral efficacy in drug discovery: taking advantage of the good (allosteric) nature of 7TM receptors. Trends in Pharm Sci 28:407-415.
    • (2007) Trends in Pharm Sci , vol.28 , pp. 407-415
    • Kenakin, T.1
  • 49
    • 44649172481 scopus 로고    scopus 로고
    • 2-adrenergic receptor
    • 2- adrenergic receptor. Structure 16:897-905.
    • (2008) Structure , vol.16 , pp. 897-905
    • Hanson, M.A.1
  • 50
    • 1642365068 scopus 로고    scopus 로고
    • New advances in normal mode analysis of supermolecular complexes and applications to structural refinement
    • Ma J (2004) New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Protein Pept Sci 5:119-123.
    • (2004) Curr Protein Pept Sci , vol.5 , pp. 119-123
    • Ma, J.1
  • 51
    • 41949089470 scopus 로고    scopus 로고
    • β-arrestin-biased agonism at the β2-adrenergic receptor
    • Drake MT, et al. (2008) β-arrestin-biased agonism at the β2-adrenergic receptor. J Biol Chem 283:5669-5676.
    • (2008) J Biol Chem , vol.283 , pp. 5669-5676
    • Drake, M.T.1
  • 52
    • 34447620659 scopus 로고    scopus 로고
    • Modulating G-protein-coupled receptors: From traditional pharmacology to allosterics
    • Gilchrist A (2007) Modulating G-protein-coupled receptors: from traditional pharmacology to allosterics. Trends in Pharm Sci 28:431-437.
    • (2007) Trends in Pharm Sci , vol.28 , pp. 431-437
    • Gilchrist, A.1
  • 53
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for high-hanging fruit in drug discovery at protein-protein interfaces
    • Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450:1001-1009.
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 54
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion MM (1997) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905-1908.
    • (1997) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 55
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • DOI 10.1006/jmbi.1996.0758
    • Bahar I, Jernigan RL (1997) Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 266:195-214. (Pubitemid 27170528)
    • (1997) Journal of Molecular Biology , vol.266 , Issue.1 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.