Free energy calculations and ligand binding

Advances in Protein Chemistry

Volumn 66, Issue , 2003, Pages 123-158

  Brandsdal, Bjørn O ^a   Österberg, Fredrik ^a   Almlöf, Martin ^a   Feierberg, Isabella ^a   Luzhkov, Victor B ^a   Åqvist, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

APROTININ; CYTOCHROME P450; PLASMEPSIN II; TRYPSIN;

LIGAND BINDING; LINEAR ENERGY TRANSFER; LINEAR INTERACTION ENERGY APPROACH; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; REVIEW; THERMODYNAMICS;

EID: 0242696091     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0065-3233(03)66004-3     Document Type: Article

References (109)

1. Almlöf, M., Brandsdal, B. O., and Åqvist, J. (2003). To be published.
2. Alterman, M., Andersson, H. O., Garg, N., Ahlsen, G., Lovgren, S., Classon, B., Danielson, U. H., Kvarnstrom, I., Vrang, L., Unge, T., Samuelsson, B., and Hallberg, A. (1999). J. Med. Chem. 42, 3835-3844.
3. Alterman, M., Bjoersne, M., Muehlman, A., Classon, B., Kvarnstroem, I., Danielson, H., Markgren, P. O., Nillroth, U., Unge, T., Hallberg, A., and Samuelsson, B. (1998). J. Med. Chem. 41, 3782-3792.
4. Åqvist, J. (1990). J. Phys. Chem. 94, 8021-8024.
5. Åqvist, J. (1994). J. Phys. Chem. 98, 8253-8255.
6. Åqvist, J. (1996). J. Comp. Chem. 17, 1587-1597.
7. Åqvist, J., and Hansson, T. (1996). J. Phys. Chem. 100, 9512-9521.
8. Åqvist, J., Luzhkov, V. B., and Brandsdal, B. O. (2002). Acc. Chem. Res. 35, 358-365.
9. Åqvist, J., and Marelius, J. (2001). Comb. Chem. High. T. Ser. 4, 613-626.
10. Åqvist, J., Medina, C., and Samuelsson, J. E. (1994). Protein Eng. 7, 385-391.
11. Åqvist, J., and Mowbray, S. L. (1995). J. Biol. Chem. 270, 9978-9981.
12. Banba, S., and Brooks, C. L. (2000). J. Chem. Phys. 113, 3423-3433.
13. Bash, P. A., Singh, U. C., Brown, F. K., Langridge, R., and Kollman, P. A. (1987). Science 235, 574-576.
14. Bennett, C. H. (1976). J. Comp. Phys. 22, 245-268.
15. Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R., and van Gunsteren, W. F. (1994). Chem. Phys. Lett. 222, 529-539.
16. Beveridge, D. L., and DiCapua, F. M. (1989). Annu. Rev. Biophys. Biophys. Chem. 18, 431-492.
17. Boresch, S., and Karplus, M. (1999a). J. Phys. Chem. A 103, 103-118.
18. Boresch, S., and Karplus, M. (1999b). J. Phys. Chem. A 103, 119-136.
19. Brandsdal, B. O., Åqvist, J., and Smalås, A. O. (2001a). Protein Sci. 10, 1584-1595.
20. Brandsdal, B. O., Smalås, A. O., and Åqvist, J. (2001b). FEBS Lett. 499, 171-175.
21. Böhm, H. J. (1994). J. Comput. Aided. Mol. Des. 8, 243-256.
22. Carlson, H. A., and Jorgensen, W. L. (1995). J. Phys. Chem. 99, 10667-10673.
23. Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz Jr, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995). J. Am. Chem. Soc. 117, 5179-5197.
24. Dauber-Osguthorpe, P., Roberts, V. A., Osguthorpe, D. J., Wolff, J., Genest, M., and Hagler, A. T. (1988). Proteins 4, 31-47.
25. Doyle, D. A., Cabral, J. M., Pfuetzner, R. A., Kuo, A. L., Gulbis, J. M., Cohen, S. L., Chait, B. T., and MacKinnon, R. (1998). Science 280, 69-77.
26. Elber, R., and Karplus, M. (1990). J. Am. Chem. Soc. 112, 9161-9175.
27. Eldridge, M. D., Murray, C. W., Auton, T. R., Paolini, G. V., and Mee, R. P. (1997). J. Comput. Aided. Mol. Des. 11, 425-445.
28. Eriksson, M. A. L., Pitera, J., and Kollman, P. A. (1999). J. Med. Chem. 42, 868-881.
29. Ersmark, K., Feierberg, I., Bjelic, S., Hultén, J., Samuelsson, B., Åqvist, J., and Hallberg, A. (2003). Bioorg. Med. Chem. 11, 3723-3733.
30. Gerber, P. R., Mark, A. E., and van Gunsteren, W. F. (1993). J. Comput. Aided. Mol. Des. 7, 305-323.
31. Gilson, M. K. and Honig, B. (1988). Proteins 4, 7-18.
32. Gohlke, H., Hendlich, M., and Klebe, G. (2000). J. Mol. Biol. 295, 337-356.
33. Graffner-Nordberg, M., Kolmodin, K., Åqvist, J., Queener, S. F., and Hallberg, A. (2001). J. Med. Chem. 44, 2391-2402.
34. Halperin, I., Ma, B., Wolfson, H., and Nussinov, R. (2002). Proteins 47, 409-433.
35. Hansson, T., and Åqvist, J. (1995). Protein Eng. 8, 1137-1144.
36. Hansson, T., Marelius, J., and Åqvist, J. (1998). J. Comput. Aided. Mol. Des. 12, 27-35.
37. Hermans, J., and Wang, L. (1997). J. Am. Chem. Soc. 119, 2707-2714.
38. Honig, B., and Nicholls, A. (1995). Science 268, 1144-1149.
39. Hultén, J., Bonham, N. M., Nillroth, U., Hansson, T., Zuccarello, G., Bouzide, A., Åqvist, J., Classon, B., Danielson, U. H., Karlen, A., Kvarnstrom, I., Samuelsson, B., and Hallberg, A. (1997). J. Med. Chem. 40, 885-897.
40. Huo, S. H., Wang, J. M., Cieplak, P., Kollman, P. A., and Kuntz, I. D. (2002). J. Med. Chem. 45, 1412-1419.
41. Hwang, J. K., and Warshel, A. (1987). Biochemistry 26, 2669-2673.
42. Jain, A. N. (1996). J. Comput. Aided. Mol. Des. 10, 427-440.
43. Jayaram, B., and Beveridge, D. L. (1990). J. Phys. Chem. 94, 7288-7293.
44. Jones-Hertzog, D. K., and Jorgensen, W. L. (1997). J. Med. Chem. 40, 1539-1549.
45. Jorgensen, W. L., Maxwell, D. S., and TiradoRives, J. (1996). J. Am. Chem. Soc. 118, 11225-11236.
46. King, G., and Barford, R. A. (1993). J. Phys. Chem. 97, 8798-8802.
47. King, G., and Warshel, A. (1989). J. Chem. Phys. 91, 3647-3661.
48. Kirkwood, J. G. (1935). J. Chem. Phys. 3, 300-313.
49. Kollman, P. (1993). Chem. Rev. 93, 2395-2417.
50. Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., and Cheatham, T. E. (2000). Acc. Chem. Res. 33, 889-897.
51. Kong, X. J., and Brooks, C. L. (1996). J. Chem. Phys. 105, 2414-2423.
52. Krowarsch, D., Dadlez, M., Buczek, O., Krokoszynska, I., Smalås, A. O., and Otlewski, J. (1999). J. Mol. Biol. 289, 175-186.
53. Kuhn, B., and Kollman, P. A. (2000a). J. Am. Chem. Soc. 122, 3909-3916.
54. Kuhn, B., and Kollman, P. A. (2000b). J. Med. Chem. 43, 3786-3791.
55. Kumar, S., Bouzida, D., Swendsen, R. H., Kollman, P. A., and Rosenberg, J. M. (1992). J. Comp. Chem. 13, 1011-1021.
56. Lamb, M. L., and Jorgensen, W. L. (1997). Curr. Opin. Chem. Biol. 1, 449-457.
57. Lamb, M. L., Tirado-Rives, J., and Jorgensen, W. L. (1999). Bioorg. Med. Chem. 7, 851-860.
58. Lee, F. S., Chu, Z. T., Bolger, M. B., and Warshel, A. (1992). Prot. Eng. 5, 215-228.
59. Lee, F. S., and Warshel, A. (1992). J. Chem. Phys, 97, 3100-3107.
60. Levy, R. M., Belhadj, M., and Kitchen, D. B. (1991). J. Chem. Phys. 95, 3627-3633.
61. Liu, H. Y., Mark, A. E., and van Gunsteren, W. F. (1996). J. Phys. Chem. 100, 9485-9494.
62. Ljungberg, K. B., Marelius, J., Musil, D., Svensson, P., Norden, B., and Åqvist, J. (2001). Eur. J. Pharm. Sci. 12, 441-446.
63. Luzhkov, V. B., and Åqvist, J. (2001). FEBS Lett. 495, 191-196.
64. Luzhkov, V. B., Österberg, F., Acharya, P., Chattopadhyaya, J., and Åqvist, J. (2002). Phys. Chem. Chem. Phys. 4, 4640-4647.
65. Luzhkov, V. B., Österberg, F., and Åqvist, J. (2003). To be published.
66. Marelius, J., Graffner-Nordberg, M., Hansson, T., Hallberg, A., and Åqvist, J. (1998a). J. Comput. Aided. Mol. Des. 12, 119-131.
67. Marelius, J., Kolmodin, K., Feierberg, I., and Åqvist, J. (1998b). J. Mol. Graphics Model. 16, 213-225, 261.
68. Marelius, J., Ljungberg, K. B., and Åqvist, J. (2001). Eur. J. Pharm. Sci. 14, 87-95.
69. Massova, I., and Kollman, P. A. (1999). J. Am. Chem. Soc. 121, 8133-8143.
70. McDonald, N. A., Carlson, H. A., and Jorgensen, W. L. (1997). J. Phys. Org. Chem. 10, 563-576.
71. Meuser, D., Splitt, H., Wagner, R., and Schrempf, H. (1999). FEBS Lett. 462, 447-452.
72. Mezei, M. (1987). J. Chem. Phys. 86, 7084-7088.
73. Mezei, M., Swaminathan, S., and Beveridge, D. L. (1978). J. Am. Chem. Soc. 100, 3255-3256.
74. Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. (1998). J. Comp. Chem. 19, 1639-1662.
75. Muegge, I., and Martin, Y. C. (1999). J. Med. Chem. 42, 791-804.
76. Naudin, C., Bonhomme, F., Bruneel, J. L., Ducasse, L., Grondin, J., Lasségues, J. C., and Servant, L. (2000). J. Raman Spectrosc. 31, 979-985.
77. Oostenbrink, B. C., Pitera, J. W., van Lipzig, M. M. H., Meerman, J. H. N., and van Gunsteren, W. F. (2000). J. Med. Chem. 43, 4594-4605.
78. Paulsen, M. D., and Ornstein, R. L. (1996). Protein Eng, 9, 567-571.
79. Pearlman, D. A., and Kollman, P. A. (1991). J. Chem. Phys. 94, 4532-4545.
80. Pitera, J., and Kollman, P. (1998). J. Am. Chem. Soc. 120, 7557-7567.
81. Pitera, J. W., and van Gunsteren, W. F. (2002). Mol. Simul. 28, 45-65.
82. Postma, J. P. M., Berendsen, H. J. C., and Haak, J. R. (1982). Faraday Symp. Chem. Soc. 17, 55-67.
83. Radmer, R. J., and Kollman, P. A. (1998). J. Comput. Aided. Mol. Des. 12, 215-227.
84. Schäfer, H., van Gunsteren, W. F., and Mark, A. E. (1999). J. Comp. Chem. 20, 1604-1617.
85. Schechter, I., and Berger, A. (1967). Biochem. Biophys. Res. Commun. 27, 157-162.
86. Silva, A. M., Lee, A. Y., Gulnik, S. V., Majer, P., Collins, J., Bhat, T. N., Collins, P. J., Cachau, R. E., Luker, K. E., Gluzman, I. Y., Francis, S. E., Oksman, A., Goldberg, D. E., and Erickson, J. W. (1996). Proc. Natl. Acad. Sci., USA 93, 10034-10039.
87. Sitkoff, D., Sharp, K. A., and Honig, B. (1994). J. Phys. Chem. 98, 1978-1988.
88. Smith, P. E., and van Gunsteren, W. F. (1994). J. Chem. Phys. 100, 577-585.
89. Srinivasan, J., Cheatham, T. E., Cieplak, P., Kollman, P. A., and Case, D. A. (1998). J. Am. Chem. Soc. 120, 9401-9409.
90. Still, W. C., Tempczyk, A., Hawley, R. C., and Hendrickson, T. (1990). J. Am. Chem. Soc. 112, 6127-6129.
91. Straatsma, T. P., and McCammon, J. A. (1992). Annu. Rev. Phys. Chem. 43, 407-435.
92. Tembe, B. L., and McCammon, J. A. (1984). Computers & Chemistry 8, 281-283.
93. Tidor, B. (1993). J. Phys. Chem. 97, 1069-1073.
94. Torrie, G. M., and Valleau, J. P. (1974). Chem. Phys. Lett. 28, 578-581.
95. Torrie, G. M., and Valleau, J. P. (1977). J. Comp. Phys. 23, 187-199.
96. van Gunsteren, W. F., and Berendsen, H. J. C. (1987). "Groningen Molecular Simulation (GROMOS) Library Manual." Biomos, B. V., Groningen, The Netherlands.
97. van Gunsteren, W. F. (1988). Prot. Eng. 2, 5-13.
98. Wall, I. D., Leach, A. R., Salt, D. W., Ford, M. G., and Essex, J. W. (1999). J. Med. Chem. 42, 5142-5152.
99. Wang, J., Dixon, R., and Kollman, P. A. (1999). Proteins 34, 69-81.
100. Wang, J. M., Morin, P., Wang, W., and Kollman, P. A. (2001). J. Am. Chem. Soc. 123, 5221-5230.
101. Wang, W., Wang, J., and Kollman, P. A. (1999). Proteins 34, 395-402.
102. Warshel, A. (1982). J. Phys. Chem. 86, 2218-2224.
103. Warshel, A. (1984). Pontif. Acad. Sci. Scr. Varia. 55, 60-81.
104. Warwicker, J., and Watson, H. C. (1982). J. Mol. Biol. 157, 671-679.
105. Werbovetz, K. A. (2000). Curr. Med. Chem. 7, 835-860.
106. Wong, C. F., and McCammon, J. A. (1986).J. Am. Chem. Soc. 108, 3830-3832.
107. Zacharias, M., Straatsma, T. P., and McCammon, J. A. (1994). J. Chem. Phys. 100, 9025-9031.
108. Zhou, R., Friesner, R. A., Ghosh, A., Rizzo, R. C., Jorgensen, W. L., and Levy, R. M. (2001). J. Phys. Chem. B 105, 10388-10397.
109. Zwanzig, R. W. (1954). J. Chem. Phys. 22, 1420-1426.