Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor

Journal of the American Chemical Society

Volumn 132, Issue 14, 2010, Pages 5205-5214

  Bhattacharya, Supriyo ^a   Vaidehi, Nagarajan ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION MECHANISMS; ACTIVATION PATHWAY; ACTIVE STATE; ADRENERGIC RECEPTORS; AROMATIC RESIDUES; BARRIER CROSSING; BOUND LIGANDS; CHEMICAL STRUCTURE; COARSE GRAINS; COARSE-GRAIN METHOD; CONFORMATIONAL TRANSITIONS; ENERGY MINIMIZATION; G-PROTEIN COUPLED RECEPTORS; MONTE CARLO ALGORITHMS; POTENTIAL ENERGY LANDSCAPES; SALBUTAMOL; STERIC HINDRANCES; TRANSMEMBRANE HELICES; VIRTUAL LIGAND SCREENING;

BINDING ENERGY; BINDING SITES; CHEMICAL REACTIONS; COMPUTATIONAL METHODS; CRYSTAL STRUCTURE; ENZYME INHIBITION; FLUORESCENCE SPECTROSCOPY; HYDROGEN BONDS; LIGANDS; POTENTIAL ENERGY; PROTEINS;

CONFORMATIONS;

ADRENALIN; BETA 2 ADRENERGIC RECEPTOR; BETA 2 ADRENERGIC RECEPTOR BLOCKING AGENT; BETA 2 ADRENERGIC RECEPTOR STIMULATING AGENT; CARAZOLOL; DOPAMINE; G PROTEIN COUPLED RECEPTOR; LIGAND; NORADRENALIN; SALBUTAMOL; TIMOLOL;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DRUG BINDING SITE; DRUG RECEPTOR BINDING; DRUG SCREENING; LIGAND BINDING; MONTE CARLO METHOD;

ADRENERGIC BETA-AGONISTS; ALBUTEROL; ALGORITHMS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DOPAMINE; LIGANDS; MODELS, MOLECULAR; MONTE CARLO METHOD; NOREPINEPHRINE; PROTEIN CONFORMATION; RECEPTORS, ADRENERGIC, BETA; SPECTROMETRY, FLUORESCENCE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77950823494     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja910700y     Document Type: Article

References (34)

1. Swaminath, G., Xiang, Y., Lee, T. W., Steenhuis, J., Parnot, C., and Kobilka, B. K. J. Biol. Chem. 2004, 279, 686-691
2. Swaminath, G., Deupi, X., Lee, T. W., Zhu, W., Thian, F. S., Kobilka, T. S., and Kobilka, B. K. J. Biol. Chem. 2005, 280, 22165-22171
3. Kobilka, B. K. and Deupi, X. Trends Pharmacol. Sci. 2007, 28, 397-406
4. Yao, X., Parnot, C., Deupi, X., Ratnala, V. R. P., Swaminath, G., Farrens, D., and Kobilka, B. K. Nat. Chem. Biol. 2006, 2, 417-422
5. Galés, C., Rebols, R. V., Hogue, M., Trieu, P., Brelt, A., Hébert, T. E., and Bouvier, M. Nat. Methods 2005, 2, 177-184
6. Leduc, M., Breton, B., Galés, C., Le Gouill, C., Bouvier, M., Chemtob, S., and Heveker, N. J. Pharmacol. Exp. Ther. 2009, 331, 297-307
7. Galandrin, S., Oligny-Longpré, G., and Bouvier, M. Trends Pharmacol. Sci. 2007, 28, 423-30
8. Vilardaga, J. P., Bunemann, M., Krasel, C., Castro, M., and Lohse, M. Nat. Biotechnol. 2003, 21, 807-812
9. Schneider, E. H., Schnell, D., Strasser, A., Dove, S., and Seifert, R. J. Pharmacol. Exp. Ther. 2010, doi: 10.1124/jpet.109.163220.
10. Mailman, R. B. Trends Pharmacol. Sci. 2007, 28, 390-393
11. Cherezov, V., Rosenbaum, D. M., Hanson, M. A., Rasmussen, G. F., Thian, F. S., Kobilka, T. S., Choi, H.-J., Kuhn, P., Weis, W. I., Kobilka, B. K., and Stevens, R. C. Science 2007, 318, 1258-1265
12. Hanson, M. A., Cherezov, V., Roth, C. B., Griffith, M. T., Jaakola, V.-P., Chien, E. Y. T., Velasquez, J., Kuhn, P., and Stevens, R. C. Structure 2008, 16, 897-905
13. Bhattacharya, S., Hall, S. E., Li, H., and Vaidehi, N. Biophys. J. 2008, 94, 2027-2042
14. Bhattacharya, S., Hall, S. E., and Vaidehi, N. J. Mol. Biol. 2008, 382, 539-555
15. Ng, K. K., Cherney, M. M., Vazquez, A. L., Machin, A., Alonso, J. M., Parra, F., and James, M. N. J. Biol. Chem. 2002, 277, 1381-1387
16. Liapakis, G., Chan, W. C., Papadokostaki, M., and Javitch, J. A. Mol. Pharmacol. 2004, 65, 1181-1190
17. Carmine, R. D., Ambrosio, C., Sbraccia, M., Cotecchia, S., Ijzerman, A. P., and Costa, T. Br. J. Pharmacol. 2002, 135, 1715-1722
18. Strader, C. D., Sigal, I. S., Candelore, M. R., Hill, W. S., and Dixon, R. A. J. Biol. Chem. 1988, 263, 10267-10271
19. Liapakis, G., Ballesteros, J. A., Papachristou, S., Chan, W. C., Chen, X., and Javitch, J. A. J. Biol. Chem. 2000, 275, 37779-37788
20. Wieland, K., Zuurmond, H. M., Krasel, C., IJzerman, A. P., and Lohse, M. J. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 9276-9281
21. Ballesteros, J. A. and Weinstein, H. Methods Neurosci. 1995, 25, 366-428
22. Kikkawa, H., Kurose, H., Isogaya, M., Sato, Y., and Nagao, T. Br. J. Pharmacol. 1997, 121, 1059-1064
23. Farrens, D. L., Altenbach, C., Yang, K., Hubbell, W. L., and Khorana, H. G. Science 1996, 274, 768-770
24. Schwartz, T. W., Frimurer, T. M., Holst, B., Rosenkilde, M. M., and Elling, C. E. Annu. Rev. Pharmacol. Toxicol. 2006, 46, 481-519
25. Huber, T., Menon, S., and Sakmar, T. P. Biochemistry 2008, 47, 11013-11023
26. Ballesteros, J. A., Jensen, A. D., Liapakis, G., Rasmussen, G. F., Shi, L., Gether, U., and Javitch, J. A. J. Biol. Chem. 2001, 276, 29171-29177
27. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C. A., Motoshima, H., Fox, B. A., Trong, I. L., Teller, D. C., Okada, T., Stenkamp, R. E., Yamamoto, M., and Miyano, M. Science 2000, 289, 739-745
28. Park, J. H., Scheerer, P., Hofmann, K. P., Choe, H.-W., and Ernst, O. P. Nature 2008, 454, 183-187
29. Li, J., Huang, P., Chen, C., de Riel, J. K., Weinstein, H., and Liu-Chen, L. Y. Biochemistry 2001, 40, 12039-12050
30. Kam, V. W. T. and Goddard, W. A., III. J. Chem. Theory Comput. 2008, 4, 2160-2169
31. Dror, R. O., Arlow, D. H., Borhani, D. W., Jensen, M. O., Piana, S., and Shaw, D. E. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 4689-4694
32. Lohse, M. J., Hoffmann, C., Nikolaev, V. O., Vilardaga, J. P., and BuÌnemann, M. Adv. Protein Chem. 2007, 74, 167-188
33. Kosztin, D., Izrailev, S., and Schulten, K. Biophys. J. 1999, 76, 188-197
34. Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., and Mainz, D. T. J. Med. Chem. 2006, 49, 6177-6196