Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors

Methods in Neurosciences

Volumn 25, Issue C, 1995, Pages 366-428

  Ballesteros, Juan A ^a   Weinstein, Harel ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77957055780     PISSN: 10439471     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1043-9471(05)80049-7     Document Type: Article

References (136)

1. Schertler, G.F., Villa, C., Henderson, R., Nature (London), 362, 1993, 770.
2. Colquhoun, D., Farrant, M., Nature (London), 366, 1993, 510.
3. Ward, W.H., Timms, D., Fersht, A.R., Trents Pharmacol. Sci., 11, 1990, 280.
4. Zhou, W., Flanagan, C., Ballesteros, J.A., Konvicka, K., Davidson, J.S., Weinstein, H., Millar, R.P., Sealfon, S.C., Mol. Pharmacol., 45, 1994, 165.
5. Suryanarayana, S., von Zastrow, M., Kobilka, B.K., J. Biol. Chem., 267, 1992, 21991.
6. Pittel, Z., Wess, J., Mol. Pharmacol., 45, 1994, 61.
7. Rao, V.R., Cohen, G.B., Oprian, D.D., Nature (London), 367, 1994, 639.
8. Zhang, D., Weinstein, H., J. Med. Chem., 36, 1993, 934.
9. Thornton, J.M., Flores, T.P., Jones, D.T., Swindells, M.B., Nature (London), 354, 1991, 105.
10. Lesk, A.M., Boswell, D.R., Curr. Opin. Struct. Biol., 2, 1992, 242.
11. Benner, S.A., Gerloff, D., Adv. Enzyme Regul., 31, 1991, 121.
12. Rost, B., Sander, C., J. Mol. Biol., 232, 1993, 584.
13. Brooks, C.L., Karplus, M., Pettitt, B.M., Proteins: A Theoretical Perspective of Dynamics, Structure, and their Thermodynamics. 1988, Wiley, San Diego, CA.
14. McCammon, J.A., Science, 238, 1987, 486.
15. van Gunsteren, W.F., Weiner, P.K., Computer Simulations of Biomolecular Systems. 1989, ESCOM, New York.
16. van Gunsteren, W.F., Brunne, R.M., Mark, A.E., van Helden, S.P., Bertran, J., (eds.) Molecular Aspects of Biotechnology: Computational Models and Theories, 1992, Kluwer Academic Publishers, Leiden, The Netherlands, 105.
17. Weinstein, H., Mehler, E.L., Bertran, J., (eds.) Molecular Aspects of Biotechnology: Computational Models and Theories, 1992, Kluwer Academic Publishers, Dordrecht, The Netherlands, 153.
18. Jahnig, F., Edholm, O., J. Mol. Biol., 226, 1992, 837.
19. Weinsterin, H., Bonati, L., Cosentino, U., Lasagni, M., Moro, G., Pitea, D., Schiraldi, A., (eds.) Trends in Ecological Physical Chemistry, 1992, Elsevier, Dordrecht, The Netherlands, 1.
20. Dahl, S.G., Edvardsen, O., Sylte, I., Proc. Natl. Acad. Sci. U.S.A., 88, 1991, 8111.
21. Findlay, J., Eliopoulos, E., Trends Pharmacol. Sci., 11, 1990, 492.
22. Hibert, M.F., Trumpp-Kallmeyer, S., Bruinvels, A., Hoflack, J., Mol. Pharmacol., 40, 1991, 8.
23. Huggins, J.P., Trumpp-Kallmeyer, S., Hilbert, M.F., Hoflack, J.M., Fanger, B.O., Jones, C.R., Eur. J. Pharmacol., 245, 1993, 203.
24. Livingstone, C.D., Strange, P.G., Naylor, L.H., Biochem. J., 287, 1992, 277.
25. Maloney-Huss, K., Lybrand, T.P., J. Mol. Biol., 225, 1992, 859.
26. Nordvall, G., Hacksell, U., J. Med. Chem., 36, 1993, 967.
27. Trumpp-Kallmeyer, S., Hoflack, J., Bruinvels, A., Hibert, M., J. Med. Chem., 35, 1992, 3448.
28. (in press)Trumpp-Kallmeyer, S., Hoflack, J., Hibert, M., Buck, S.H., (eds.) The Tachykinin Receptors, 1993, Humana Press, Milan, Italy.
29. Westkaemper, R.B., Glennon, R.A., Pharmacol. Biochem. Behav., 40, 1991, 1019.
30. in press Donnelly, D., Findlay, J.B.C., Blundell, T.L., Receptors & Channels. 1994.
31. Ijzerman, A.P., Van, G.P.J., Jacobson, K.A., Drug Des. Discov., 9, 1992, 49.
32. Lewell, X.Q., Drug Des. Discov., 9, 1992, 29.
33. Yamamoto, Y., Kamiya, K., Terao, S., J. Med. Chem., 36, 1993, 820.
34. Cronet, P., Sander, C., Vriend, G., Protein Eng., 6, 1993, 59.
35. Smolyar, A., Osman, R., Mol. Pharmacol., 44, 1993, 882.
36. Humblet, C., Mirzadegan, T., Annu. Rep. Med. Chem., 27, 1992, 291.
37. Findlay, J.B.C., Donnelly, D., Dickey, B., Birnbaumer, L., (eds.) GTPases in Biology II, 1994, Springer-Verlag, New York, 17–32.
38. (in press)Hoflack, J., Trumpp-Kallmeyer, S., Hibert, M., Kubinyi, H., (eds.) 3D QSAR and Drug Design: Theory, Methods, and Applications, 1993, ESCOM, Heidelberg.
39. Kontoyianni, M., Lybrand, T.P., Perspect. Drug. Discov Des., 1, 1993, 291.
40. Baldwin, J.M., EMBO J., 12, 1993, 1693.
41. Donnelly, D., Johnson, M.S., Blundell, T.L., Saunders, J., FEBS Lett., 251, 1989, 109.
42. Chan, S.C., Wong, A.K., Chiu, D.K., Bull. Math. Biol., 54, 1992, 563.
43. Link, R., Daunt, D., Barsh, G., Chruscinski, A., Kobilka, B., Mol. Pharmacol., 42, 1992, 16.
44. Oksenberg, D., Marsters, S.A., O'Dowd, B.F., Havlik, S., Peroutka, S.J., Ashkenazi, A., Nature (London), 360, 1992, 161.
45. Kao, H.T., Adham, N., Olsen, M.A., Weinshank, R.L., Branchek, T.A., Hartig, P.R., FEBS Lett., 307, 1992, 324.
46. Dayhoff, M.O., Barker, W.C., Hunt, L.T., Hirs, C., Timashe'ff, S., (eds.) Methods in Enzymology, 1983, Academic Press, New York, 524.
47. Altschul, S.F., J. Mol. Biol., 219, 1991, 555.
48. Overington, J., Donnelly, D., Johnson, M.S., Sali, A., Blundell, T.L., Protein Sci., 1, 1992, 216.
49. Donnelly, D., Overington, J.P., Ruffle, S.V., Nugent, J.H.A., Blundell, T.L., Protein Sci., 2, 1993, 55.
50. Pascarella, S., Argos, P., J. Mol. Biol., 224, 1992, 461.
51. Svensson, B., Vass, I., Styring, S., Z. Naturforsch. C: Biosci., 46, 1991, 765.
52. Rees, D.C., Komiya, H., Yeates, T.O., Allen, J.P., Feher, G., Annu. Rev. Biochem., 58, 1989, 607.
53. Overington, J., Johnson, M.S., Sali, A., Blundell, T.L., Proc. R. Soc. London, Ser. B, 241, 1990, 132.
54. Zhang, D., Weinstein, H., FEBS Lett., 337, 1994, 207.
55. Findlay, J.B., Barclay, P.L., Brett, M., Davison, M., Pappin, D.J., Thompson, P., Vision Res., 24, 1984, 1501.
56. Kyte, J., Doolittle, R.F., J. Mol. Biol., 157, 1982, 105.
57. Deisenhofer, J., Michel, H., EMBO J., 8, 1989, 2149.
58. Degli Esposti, M., Crimi, M., Venturoli, G., Eur. J. Biochem., 190, 1990, 207.
59. Edelman, J., White, S.H., J. Mol. Biol., 210, 1989, 195.
60. Edelman, J., J. Mol. Biol., 232, 1993, 165.
61. Ballesteros, J.A., Weinstein, H., Biophys. J., 62, 1992, 107.
62. Henderson, R., Baldwin, J.M., Ceska, T.A., Zemlin, F., Beckmann, E., Downing, K.H., J. Mol. Biol., 213, 1990, 899.
63. Deisenhofer, J., Michel, H., Yeates, T.O., Komiya, H., Rees, D.C., Allen, J.P., Feher, G., Proc. Natl. Acad. Sci. U.S.A., 84, 1987, 6438.
64. Deber, C.M., Hughes, D.W., Fraser, P.E., Pawagi, A.B., Moscarello, M.A., Arch. Biochem. Biophys., 245, 1986, 455.
65. Roux, M., Neumann, J.M., Hodges, R.S., Devaux, P.F., Bloom, M., Biochemistry, 28, 1989, 2313.
66. Yeagle, P.L., Biophys. J., 37, 1982, 227.
67. Henry, G.D., Sykes, B.D., Biochem. Cell Biol., 68, 1990, 318.
68. Gallusser, A., Kuhn, A., EMBO J., 9, 1990, 2723.
69. Eisenberg, D., Weiss, R.M., Terwilliger, T.C., Proc. Natl. Acad. Sci. U.S.A., 81, 1984, 140.
70. Rees, D.C., DeAnatonio, L., Eisenberg, D., Science, 245, 1989, 510.
71. Komiya, H., Yeates, T.O., Rees, D.C., Allen, J.P., Feher, G., Proc. Natl. Acad. Sci. U.S.A., 85, 1988, 9012.
72. Donnelly, D., Cogdell, R.J., Protein Eng., 6, 1993, 629.
73. Sankararamakrishnan, R., Vishveshwara, S., Int. J. Pept. Protein Res., 39, 1992, 356.
74. Williams, K.A., Deber, C.M., Biochemistry, 30, 1991, 8919.
75. MacArthur, M.W., Thornton, J.M., J. Mol. Biol., 218, 1991, 397.
76. Strehlow, K.G., Robertson, A.D., Baldwin, R.I., Biochemistry, 30, 1991, 5810.
77. Juretic, D., Lee, B., Trinajstic, N., Williams, R.W., Biopolymers, 33, 1993, 255.
78. in press Granatir, C.A., Parodi, L.A., Maggiora, G.M., Protein Sci., 1994.
79. Gray, T.M., Matthews, B.W., J. Mol. Biol., 175, 1984, 75.
80. McGregor, M.J., Islam, S.A., Sternberg, M.J., J. Mol. Biol., 198, 1987, 295.
81. Piela, L., Nemethy, G., Scheraga, H.A., Biopolymers, 26, 1987, 1273.
82. Ponder, J.W., Richards, F.M., J. Mol. Biol., 193, 1987, 775.
83. Dunbrack, R.L.J., Karplus, M., J. Mol. Biol., 230, 1993, 543.
84. Barlow, D.J., Thornton, J.M., J. Mol. Biol., 201, 1988, 601.
85. Woolfson, D.N., Williams, D.H., FEBS Lett., 277, 1990, 185.
86. Bazzo, R., Tappin, M.J., Pastore, A., Harvey, T.S., Carver, J.A., Campbell, I.D., Eur. J. Biochem., 173, 1988, 139.
87. Pastore, A., Harvey, T.S., Dempsey, C.E., Campbell, I.D., Eur. Biophys. J., 16, 1989, 363.
88. Yun, R.H., Anderson, A., Hermans, J., Proteins, 10, 1991, 219.
89. Sankararamakrishnan, R., Vishveshwara, S., Proteins: Struct. Funct. Genet., 15, 1993, 26.
90. Piela, L., Nemethy, G., Scheraga, H.A., Biopolymers, 26, 1987, 1587.
91. Woolfson, D.N., Mortishire, S.R.J., Williams, D.H., Biochem. Biophys. Res. Commun., 175, 1991, 733.
92. Sansom, M.S., Protein Eng., 5, 1992, 53.
93. Ballesteros, J.A., Weinstein, H., Biophys. J., 62, 1992, 110.
94. Sankararamakrishnan, R., Vishveshwara, S., Biopolymers, 30, 1990, 287.
95. Fasman, G.D., Prediction of Protein Structure and the Principles of Protein Conformation. 1989, Plenum, New York.
96. Summers, N.L., Karplus, M., Langone, J., (eds.) Methods in Enzymology, 1991, Academic Press, New York, 156.
97. Hilbert, M., Bohm, G., Jaenicke, R., Proteins: Struct., Funct. Genet., 17, 1993, 138.
98. Eisenberg, D., Schwarz, E., Komaromy, M., Wall, R., J. Mol. Biol., 179, 1984, 125.
99. Weiss, M.S., Abele, U., Weckesser, J., Welte, W., Schiltz, E., Schulz, G.E., Science, 254, 1991, 1627.
100. Cowan, S.W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R.A., Jansonius, J.N., Rosenbusch, J.P., Nature (London), 358, 1992, 727.
101. Wong, S.K., Slaughter, C., Ruoho, A.E., Ross, E.M., J. Biol. Chem., 263, 1988, 7925.
102. Dohlman, H.G., Caron, M.G., Strader, C.D., Amlaiky, N., Lefkowitz, R.J., Biochemistry, 27, 1988, 1813.
103. Davison, M.D., Findlay, J.B., Biochem. J., 236, 1986, 389.
104. Davison, M.D., Findlay, J.B., Biochem. J., 234, 1986, 413.
105. Pardo, L., Ballesteros, J.A., Osman, R., Weinstein, H., Proc. Natl. Acad. Sci. U.S.A., 89, 1992, 4009.
106. Hoflack, J., Trumpp-Kallmeyer, S., Hibert, M., Trends Pharmacol. Sci., 15, 1994, 7.
107. Henderson, R., Schertler, G.F., Philos. Trans. R. Soc. London, Ser. B, 326, 1990, 379.
108. Taylor, E.W., Agarwal, A., FEBS Lett., 325, 1993, 161.
109. Chothia, C., Lesk, A.M., EMBO J., 5, 1986, 823.
110. Kontoyianni, M., Lybrand, T.P., Med. Chem. Res., 3, 1993, 407.
111. Jahnig, F., Edholm, O., Z. Phys. B, 78, 1990, 137.
112. Oprian, D.D., J. Bioenerg. Biomembr., 24, 1992, 211.
113. Gantz, I., DelValle, J., Wang, L.D., Tashiro, T., Munzert, G., Guo, Y.J., Konda, Y., Yamada, T., J. Biol. Chem., 267, 1992, 20840.
114. Ho, B.Y., Karschin, A., Branchek, T., Davidson, N., Lester, H.A., FEBS Lett., 312, 1992, 259.
115. Mansour, A., Meng, F., Meador, W.J.H., Taylor, L.P., Civelli, O., Akil, H., Eur. J. Pharmacol., 227, 1992, 205.
116. Pollock, N.J., Manelli, A.M., Hutchins, C.W., Steffey, M.E., MacKenzie, R.G., Frail, D.E., J. Biol. Chem., 267, 1992, 17780.
117. Strader, C.D., Candelore, M.R., Hill, W.S., Signal, I.S., Dixon, R.A., J. Biol. Chem., 264, 1989, 13572.
118. Altschuh, D., Lesk, A.M., Bloomer, A.C., Klug, A., J. Mol. Biol., 193, 1987, 693.
119. Altschuh, D., Vernet, T., Berti, P., Moras, D., Nagai, K., Protein Eng., 2, 1988, 193.
120. Pastor, N., Pinero, D., Valdes, A.M., Soberon, X., Mol. Microbiol., 4, 1990, 1957.
121. Gregoret, L.M., Cohen, F.E., J. Mol. Biol., 211, 1990, 959.
122. Chothia, C., Levitt, M., Richardson, D., J. Mol. Biol., 145, 1981, 215.
123. Hibert, M.F., Trumpp-Kallmeyer, S., Hoflack, J., Bruinvels, A., Trends Pharmacol. Sci., 14, 1993, 7.
124. Fong, T.M., Huang, R.R., Strader, C.D., J. Biol. Chem., 267, 1992, 25664.
125. Cheung, A.H., Huang, R.R., Strader, C.D., Mol. Pharmacol., 41, 1992, 1061.
126. Raymond, J.R., Hnatowich, M., Lefkowitz, R.J., Caron, M.G., Hypertension (Dallas), 15, 1990, 119.
127. Savarese, T.M., Wang, C.D., Fraser, C.M., J. Biol. Chem., 267, 1992, 11439.
128. Savarese, T.M., Fraser, C.M., Biochem. J., 283, 1992, 1.
129. Weinstein, H., Green, J.P., (eds.) Quantum Chemistry in Biomedical Sciences, Ann. N.Y. Acad. Sci., 367, 1981.
130. Hirst, D.M., A Computational Approach to Chemistry. 1990, Blackwell, San Diego, CA.
131. Clementi, E., Modern Techniques in Computaional Chemistry: MOTECC-91. 1991, ESCOM, London.
132. Hoflack, J., Hibert, M.F., S., T.-K., Bidart, J.M., Drug Des. Discov., 10, 1993, 157.
133. Zhang, D., Weinstein, H., Med. Chem. Res., 3, 1993, 357.
134. Edvardsen, O., Sylte, I., Dahl, S.G., Brain Res. Mol. Brain Res., 14, 1992, 166.
135. Luo, X., Zhang, D., Weinstein, H., Protein Sci., 2(Suppl. 1), 1993, 158.
136. in press Luo, X., Zhang, D., Weinstein, H., Protein Eng., 7, 1994.