Modeling active GPCR conformations

Methods in Enzymology

Volumn 522, Issue , 2013, Pages 21-35

  Taddese, Bruck ^a   Simpson, Lisa M ^a   Wall, Ian D ^b   Blaney, Frank E ^c   Reynolds, Christopher A ^a  

^a UNIVERSITY OF ESSEX   (United Kingdom)

^b GLAXOSMITHKLINE   (United Kingdom)

^c Memprot Consulting   (United Kingdom)

Author keywords

Activation; Agonist; GPCR; Homology modeling; Molecular dynamics; Restraints; Simulation

Indexed keywords

G PROTEIN COUPLED RECEPTOR; SODIUM;

ARTICLE; CHEMICAL BINDING; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTALLOGRAPHY; DIMERIZATION; ENZYME ACTIVATION; HUMAN; HYDRATION; LIGAND BINDING; MOLECULAR PROBE; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTON TRANSPORT; SIMULATION;

EID: 84873371131     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-407865-9.00002-9     Document Type: Chapter

References (68)

1. R. Abrol, J.K. Bray, and W.A. Goddard III Bihelix: Towards de novo structure prediction of an ensemble of G protein coupled receptor conformations Proteins 80 2012 505 518
2. F.H. Allen The Cambridge Structural Database: A quarter of a million crystal structures and rising Acta Crystallographica Section B 58 2002 380 388
3. J.M. Baldwin, G.F. Schertler, and V.M. Unger An alpha-carbon template for the transmembrane helices in the rhodopsin family of G protein-coupled receptors Journal of Molecular Biology 272 1997 144 164
4. C.I. Bayly, P. Cieplak, W.D. Cornell, and P.A. Kollman A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges - The RESP model The Journal of Physical Chemistry 97 1993 10269 10280
5. N. Bhogal, F.E. Blaney, P.M. Ingley, J. Rees, and J.B. Findlay Evidence for the proximity of the extreme N-terminus of the neurokinin-2 (NK2) tachykinin receptor to Cys167 in the putative fourth transmembrane helix Biochemistry 43 2004 3027 3038
6. B.R. Brooks, C.L. Brooks III, A.D. Mackerell Jr., L. Nilsson, R.J. Petrella, and B. Roux CHARMM: The biomolecular simulation program Journal of Computational Chemistry 30 2009 1545 1614
7. M. Buck, S. Bouguet-Bonnet, R.W. Pastor, and A.D. Mackerell Jr. Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme Biophysical Journal 90 2006 L36 L38
8. J. Carlsson, L. Yoo, Z.G. Gao, J.J. Irwin, B.K. Shoichet, and K.A. Jacobson Structure-based discovery of A2A adenosine receptor ligands Journal of Medicinal Chemistry 53 2010 3748 3755
9. A.H. Cheung, R.A. Dixon, W.S. Hill, I.S. Sigal, and C.D. Strader Separation of the structural requirements for agonist-promoted activation and sequestration of the beta-adrenergic receptor Molecular Pharmacology 37 1990 775 779
10. G.G. Chicchi, M.P. Graziano, G. Koch, P. Hey, K. Sullivan, and P.P. Vicario Alterations in receptor activation and divalent cation activation of agonist binding by deletion of intracellular domains of the glucagon receptor The Journal of Biological Chemistry 272 1997 7765 7769
11. C. de Graaf, and D. Rognan Selective structure-based virtual screening for full and partial agonists of the beta2 adrenergic receptor Journal of Medicinal Chemistry 51 2008 4978 4985
12. X. Deupi, and J. Standfuss Structural insights into agonist-induced activation of G protein-coupled receptors Current Opinion in Structural Biology 21 2011 541 551
13. R.O. Dror, D.H. Arlow, P. Maragakis, T.J. Mildorf, A.C. Pan, and H. Xu Activation mechanism of the beta2-adrenergic receptor Proceedings of the National Academy of Sciences of the United States of America 108 2011 18684 18689
14. J.W. Essex, C.A. Reynolds, and W.G. Richards Theoretical determination of partition-coefficients Journal of the American Chemical Society 114 1992 3634 3639
15. F. Fanelli, and P.G. De Benedetti Update 1 of: Computational modeling approaches to structure-function analysis of G protein-coupled receptors Chemistry Review 111 2011 R438 R535
16. F. Fanelli, P.G. De Benedetti, F. Raimondi, and M. Seeber Computational modeling of intramolecular and intermolecular communication in GPCRs Current Protein & Peptide Science 10 2009 173 185
17. G.G. Ferenczy, P.J. Winn, and C.A. Reynolds Toward improved force fields. 2. Effective distributed multipoles Journal of Physical Chemistry A 101 1997 5446 5455
18. J.B. Findlay, and D.J. Pappin The opsin family of proteins The Biochemical Journal 238 1986 625 642
19. P. Ghanouni, Z. Gryczynski, J.J. Steenhuis, T.W. Lee, D.L. Farrens, and J.R. Lakowicz Functionally different agonists induce distinct conformations in the G protein coupling domain of the beta 2 adrenergic receptor The Journal of Biological Chemistry 276 2001 24433 24436
20. D.A. Goldfeld, K. Zhu, T. Beuming, and R.A. Friesner Successful prediction of the intra- and extracellular loops of four G protein-coupled receptors Proceedings of the National Academy of Sciences of the United States of America 108 2011 8275 8280
21. P.R. Gouldson, N.J. Kidley, R.P. Bywater, G. Psaroudakis, H.D. Brooks, and C. Diaz Toward the active conformations of rhodopsin and the beta2-adrenergic receptor Proteins 56 2004 67 84
22. A. Grossfield Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations Biochimica et Biophysica Acta 1808 2011 1868 1878
23. A. Grossfield, S.E. Feller, and M.C. Pitman Convergence of molecular dynamics simulations of membrane proteins Proteins 67 2007 31 40
24. Z. Huang, Y. Chen, S. Pratt, T.H. Chen, T. Bambino, and R.A. Nissenson The N-terminal region of the third intracellular loop of the parathyroid hormone (PTH)/PTH-related peptide receptor is critical for coupling to cAMP and inositol phosphate/Ca2 + signal transduction pathways The Journal of Biological Chemistry 271 1996 33382 33389
25. T. Huber, S. Menon, and T.P. Sakmar Structural basis for ligand binding and specificity in adrenergic receptors: Implications for GPCR-targeted drug discovery Biochemistry 47 2008 11013 11023
26. V. Isberg, T. Balle, T. Sander, F.S. Jorgensen, and D.E. Gloriam G protein- and agonist-bound serotonin 5-HT2A receptor model activated by steered molecular dynamics simulations Journal of Chemical Information and Modeling 51 2011 315 325
27. A.A. Ivanov, D. Barak, and K.A. Jacobson Evaluation of homology modeling of G protein-coupled receptors in light of the A(2A) adenosine receptor crystallographic structure Journal of Medicinal Chemistry 52 2009 3284 3292
28. M.P. Jacobson, D.L. Pincus, C.S. Rapp, T.J. Day, B. Honig, and D.E. Shaw A hierarchical approach to all-atom protein loop prediction Proteins 55 2004 351 367
29. G.A. Kaminski, R.A. Friesner, J. Tirado-Rives, and W.L. Jorgensen Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides The Journal of Physical Chemistry B 105 2001 6474 6487
30. V. Katritch, V. Cherezov, and R.C. Stevens Diversity and modularity of G protein-coupled receptor structures Trends in Pharmacological Sciences 33 2012 17 27
31. V. Katritch, V.P. Jaakola, J.R. Lane, J. Lin, A.P. Ijzerman, and M. Yeager Structure-based discovery of novel chemotypes for adenosine A(2A) receptor antagonists Journal of Medicinal Chemistry 53 2010 1799 1809
32. V. Katritch, K.A. Reynolds, V. Cherezov, M.A. Hanson, C.B. Roth, and M. Yeager Analysis of full and partial agonists binding to beta2-adrenergic receptor suggests a role of transmembrane helix V in agonist-specific conformational changes Journal of Molecular Recognition 22 2009 307 318
33. V. Katritch, M. Rueda, P.C. Lam, M. Yeager, and R. Abagyan GPCR 3D homology models for ligand screening: Lessons learned from blind predictions of adenosine A2a receptor complex Proteins 78 2010 197 211
34. B.K. Kobilka, and X. Deupi Conformational complexity of G protein-coupled receptors Trends in Pharmacological Sciences 28 2007 397 406
35. J.A. Lemkul, W.J. Allen, and D.R. Bevan Practical considerations for building GROMOS-compatible small-molecule topologies Journal of Chemical Information and Modeling 50 2010 2221 2235
36. E.L. Mehler, S.A. Hassan, S. Kortagere, and H. Weinstein Ab initio computational modeling of loops in G protein-coupled receptors: Lessons from the crystal structure of rhodopsin Proteins 64 2006 673 690
37. B. Mertz, A.V. Struts, S.E. Feller, and M.F. Brown Molecular simulations and solid-state NMR investigate dynamical structure in rhodopsin activation Biochimica et Biophysica Acta 1818 2012 241 251
38. M. Neri, S. Vanni, I. Tavernelli, and U. Rothlisberger Role of aggregation in rhodopsin signal transduction Biochemistry 49 2010 4827 4832
39. M.J. Niesen, S. Bhattacharya, and N. Vaidehi The role of conformational ensembles in ligand recognition in G protein coupled receptors Journal of the American Chemical Society 133 2011 13197 13204
40. K. Palczewski, T. Kumasaka, T. Hori, C.A. Behnke, H. Motoshima, and B.A. Fox Crystal structure of rhodopsin: A G protein-coupled receptor Science 289 2000 739 745
41. M.C. Peeters, G.J. van Westen, Q. Li, and A.P. Ijzerman Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation Trends in Pharmacological Sciences 32 2011 35 42
42. X. Periole, T. Huber, S.J. Marrink, and T.P. Sakmar G protein-coupled receptors self-assemble in dynamics simulations of model bilayers Journal of the American Chemical Society 129 2007 10126 10132
43. D. Provasi, M.C. Artacho, A. Negri, J.C. Mobarec, and M. Filizola Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques PLoS Computational Biology 7 2011 e1002193
44. S.G. Rasmussen, H.J. Choi, D.M. Rosenbaum, T.S. Kobilka, F.S. Thian, and P.C. Edwards Crystal structure of the human beta2 adrenergic G protein-coupled receptor Nature 450 2007 383 387
45. S.G. Rasmussen, B.T. Devree, Y. Zou, A.C. Kruse, K.Y. Chung, and T.S. Kobilka Crystal structure of the beta2 adrenergic receptor-Gs protein complex Nature 477 2011 549 555
46. C.A. Reynolds Theoretical electrode-potentials and conformational energies of benzoquinones and naphthoquinones in aqueous-solution Journal of the American Chemical Society 112 1990 7545 7551
47. C.A. Reynolds, J.W. Essex, and W.G. Richards Atomic charges for variable molecular-conformations Journal of the American Chemical Society 114 1992 9075 9079
48. C.A. Reynolds, J.W. Essex, and W.G. Richards Errors in free-energy perturbation calculations due to neglecting the conformational variation of atomic charges Chemical Physics Letters 199 1992 257 260
49. K.A. Reynolds, V. Katritch, and R. Abagyan Identifying conformational changes of the beta(2) adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators Journal of Computer-Aided Molecular Design 23 2009 273 288
50. T.D. Romo, A. Grossfield, and M.C. Pitman Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics Biophysical Journal 98 2010 76 84
51. D.M. Rosenbaum, C. Zhang, J.A. Lyons, R. Holl, D. Aragao, and D.H. Arlow Structure and function of an irreversible agonist-beta(2) adrenoceptor complex Nature 469 2011 236 240
52. R.C. Rubenstein, S.K. Wong, and E.M. Ross The hydrophobic tryptic core of the beta-adrenergic receptor retains Gs regulatory activity in response to agonists and thiols The Journal of Biological Chemistry 262 1987 16655 16662
53. P. Scheerer, J.H. Park, P.W. Hildebrand, Y.J. Kim, N. Krauss, and H.W. Choe Crystal structure of opsin in its G protein-interacting conformation Nature 455 2008 497 502
54. J. Selent, F. Sanz, M. Pastor, and F.G. De Induced effects of sodium ions on dopaminergic G protein coupled receptors PLoS Computational Biology 6 2010
55. L.M. Simpson, B. Taddese, I.D. Wall, and C.A. Reynolds Bioinformatics and molecular modelling approaches to GPCR oligomerization Current Opinion in Pharmacology 10 2010 30 37
56. L.M. Simpson, I.D. Wall, F.E. Blaney, and C.A. Reynolds Modeling GPCR active state conformations: The beta(2)-adrenergic receptor Proteins 79 2011 1441 1457
57. P.J. Stansfeld, and M.S. Sansom Molecular simulation approaches to membrane proteins Structure 19 2011 1562 1572
58. B. Taddese, L.M. Simpson, I.D. Wall, F.E. Blaney, N.J. Kidley, and H.S.X. Clark GPCR dynamics: Dimerization and activation models compared to experiment Biochemical Society Transactions 40 2012 394 399
59. E.S. Tan, E.S. Groban, M.P. Jacobson, and T.S. Scanlan Toward deciphering the code to aminergic G protein-coupled receptor drug design Chemistry and Biology 15 2008 343 353
60. D.P. Tieleman Methods and parameters for membrane simulations M.S.P. Sansom, P.C. Biggin, Molecular simulations and biomembrane: From biophysics to function 2010 RSC Cambridge 1 25
61. S. Vanni, M. Neri, I. Tavernelli, and U. Rothlisberger Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors Biochemistry 48 2009 4789 4797
62. S. Vohra, S.V. Chintapalli, C.J. Illingworth, P.J. Reeves, P.M. Mullineaux, and H.S. Clark Computational studies of Family A and Family B GPCRs Biochemical Society Transactions 35 2007 749 754
63. S. Vohra, B. Taddese, A.C. Conner, D.R. Poyner, D.L. Hay, J. Barwell, P.J. Reeves, G.J. Upton, and C.A. Reynolds Similarity between class A and class B G-protein-coupled receptors exemplified through calcitonin gene-related peptide receptor modelling and mutagenesis studies J R.Soc Interface 10 79 2013 20120846
64. S.J. Weiner, P.A. Kollman, D.T. Nguyen, and D.A. Case An all atom force-field for simulations of proteins and nucleic-acids Journal of Computational Chemistry 7 1986 230 252
65. P.J. Winn, G.G. Ferenczy, and C.A. Reynolds Toward improved force fields. 1. Multipole-derived atomic charges Journal of Physical Chemistry A 101 1997 5437 5445
66. F. Xu, H. Wu, V. Katritch, G.W. Han, K.A. Jacobson, and Z.G. Gao Structure of an agonist-bound human A2A adenosine receptor Science 332 2011 322 327
67. T. Yarnitzky, A. Levit, and M.Y. Niv Homology modeling of G protein-coupled receptors with X-ray structures on the rise Current Opinion in Drug Discovery & Development 13 2010 317 325
68. K. Zhu, D.L. Pincus, S. Zhao, and R.A. Friesner Long loop prediction using the protein local optimization program Proteins 65 2006 438 452