Calculation of Affinities of Peptides for Proteins

Journal of Computational Chemistry

Volumn 25, Issue 3, 2004, Pages 393-411

  Donnini, Serena ^a   Juffer, André H ^a  

^a UNIVERSITY OF OULU   (Finland)

Author keywords

Continuum approach; Double decoupling method; Free energy calculation; LIE method; Molecular dynamics

Indexed keywords

APPROXIMATION THEORY; BIOLOGICAL MEMBRANES; CATALYSIS; CELLS; COMPLEXATION; COMPUTATIONAL METHODS; COMPUTER SIMULATION; CONFORMATIONS; ENTROPY; GIBBS FREE ENERGY; IONIC STRENGTH; MOLECULAR DYNAMICS; PERTURBATION TECHNIQUES; PH EFFECTS; POLARIZATION; POLYSACCHARIDES;

CONTINUUM APPROACHES; DOUBLE DECOUPLING METHODS; FREE ENERGY CALCULATIONS; LIE METHODS;

ENZYMES;

LIGAND; PEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; PROTEIN BINDING; THERMODYNAMICS;

ALGORITHMS; BINDING SITES; LIGANDS; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 0942266531     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10387     Document Type: Article

References (92)

1. Creighton, T. E. Proteins, Structure and Molecular Properties; Freeman and Company: New York, 1993.
2. Lodish, H.; Berk, A.; Zipursky, S. L.; Matsudaira, P.; Baltimore, D.; Darnell, J. Molecular Cell Biology; Freeman and Company: New York, 1999.
3. Veselovsky, A. V.; Ivanov, A. S. Curr Drug Targets Infect Disord 2003, 3, 33.
4. Norledge, B. V.; Lambeir, A. M.; Abagyan, R. A.; Rottmann, A.; Fernandez, A. M.; Filimonov, V. V.; Peter, M. G.; Wierenga, R. K. Proteins Struct Funct Genet 2001, 42, 383.
5. McCammon, J. A. Curr Opin Struct Biol 1996, 8, 245.
6. Wang, W.; Donini, O.; Reyes, C. M.; Kollman, P. A. Annu Rev Biophys Biomol Struct 2001, 30, 211.
7. Beveridge, D. L.; DiCapua, F. M. Annu Rev Biophys Chem 1989, 18, 431.
8. King, P. M. In Computer Simulation of Biomolecular Systems; van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A., Eds.; Kluwer Academic Publishers: Leiden, 1993, chap 12, vol. 2.
9. Ooi, T.; Oobatake, M.; Nemethy, G.; Scheraga, H. A. Proc Natl Acad Sci USA 1987, 84, 3086.
10. Janin, J. Prog Biophys Mol Biol 1995, 64, 145.
11. Juffer, A. H.; Eisenhaber, F.; Hubbard, S. J.; Walther, D.; Argos, P. Protein Sci 1995, 4, 2499.
12. Griffiths, D. J. Introduction to Electrodynamics; Prentice-Hall International, Inc: London, 1981.
13. Warwicker, J.; Watson, H. C. J Mol Biol 1982, 157, 671.
14. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins Struct Funct Genet 1986, 1, 47.
15. Warwicker, J. J. Theor Biol 1986, 121, 199.
16. Zauhar, R. J.; Morgan, R. S. J Mol Biol 1985, 186, 815.
17. Rashin, A. A. J Phys Chem 1990, 94, 1725.
18. Juffer, A. H.; Botta, E. F. F.; van Keulen, B. A. M.; van der Ploeg, A.; Berendsen, H. J. C. J Comp Phys 97, 1991, 144.
19. Chothia, C. Nature 1976, 248, 338.
20. Sharp, K. A.; Nicholls, A.; Fine, R. F.; Honig, B. Science 1991, 252, 106.
21. Pickett, S. D.; Sternberg, M. J. E. J Mol Biol 1993, 231, 825.
22. Froloff, N.; Windemuth, A.; Honig, B. Protein Sci 1997, 6, 1293.
23. Horton, N.; Lewis, M. Protein Sci 1992, 1, 169.
24. Vajda, S.; Weng, Z.; Rosenfeld, R.; DeLisi, C. Biochemistry 1994, 33, 13977.
25. Noskov, S. Y.; Lim, C. Biophys J 2001, 81, 737.
26. Bash, P. A.; Singh, C. U.; Brown, F. K.; Landridge, R.; Kollman, P. A. Science 1987, 235, 574.
27. Rao, B. G.; Tilton, R. F.; Singh, U. C. J Am Chem Soc 1992, 114, 4447.
28. Miyamoto, S.; Kollman, P. A.; Proteins Struct Funct Genet 1993, 16, 226.
29. Hermans, J.; Wang, L. J Am Chem Soc 1997, 119, 2707.
30. Helms, V.; Wade, R. C. J Am Chem Soc 1998, 120, 2710.
31. Dixit, S. B.; Chipot, S. J Phys Chem A 2001, 105, 9795.
32. Chau, P. L. Chem Phys Lett 2001, 334, 343.
33. Villa, A.; Mark, A. J Comp Chem 2002, 23, 548.
34. Helms, V.; Wade, R. C. J Comp Chem 1997, 18, 449.
35. Daura, X.; Hunenberger, P. H.; Mark, A. E.; Querol, E.; Aviles, F. X.; Gunsteren, W. F. J Am Chem Soc 1996, 118, 6285.
36. Juffer, A. H.; de Vlieg, J.; Argos, P. J Comp Chem 1996, 17, 1783.
37. Juffer, A. H.; Shepherd, C.; Vogel, H. J Chem Phys 2001, 114, 1892.
38. Aqvist, J.; Luzhkov, V. B.; Brandsdal, B. O. Ace Chem Res 2002, 35, 358.
39. Leach, A. R. Molecular Modelling Principles and Applications; Addison Wesley Longman Limited: Essex, 1996.
40. Juffer, A. H.; Argos, P; Vogel, H. J Phys Chem B 1997, 101, 7664.
41. Hill, T. L. An Introduction to Statistical Thermodynamics; Dover Publications, Inc: New York, 1986.
42. Hill, T. L. Statistical Thermodynamics; Dover Publications, Inc: New York, 1987.
43. McQuarrie, D. A. Statistical Mechanics; Harper and Row: New York, 1976.
44. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys J 1997, 72, 1047.
45. Smith, P. E.; van Gunsteren, W. F. J Phys Chem 1994, 98, 13735.
46. Kreyszig, E. Advanced Engineering Mathematics; John Wiley & Sons, Inc: New York, 1999.
47. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.; Weissig, H.; Shindyalov, I.; Bourne, P. Nucleic Acids Res 2000, 28, 235.
48. Abagyan, R.; Totrov, M.; Kuznetscov, D. J Comp Chem 1994, 15, 488.
49. Nemethy, G.; Gibson, K. D.; Palmer, K. A.; Yoon, C. N.; Paterlini, G.; Zagari, A.; Rumsey, S.; Scheraga, H. A. J Phys Chem 1992, 96, 6472.
50. Halgren, T. A. J Comp Chem 1995, 17, 490.
51. Totrov, M.; Abagyan, R. Biopolymers 2001, 60, 124.
52. Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. Comp Phys Commun 1995, 95, 43.
53. van der Spoel, D.; van Buuren, A. R.; Apol, E.; Meulenhoff, P. J.; Tieleman, D.; Sijbers, A. L. T.; Hess, B.; Feenstra, K. A.; Lindhal, E.; van Drunen, R.; Berendsen, H. J. C. Gromacs User Manual, Version 3.0; Nijenborg 4, 9747 AG: Groningen, The Netherlands. Internet: www.gromacs.org, 2001.
54. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; Reidel: Dordrecht, 1981; p. 331.
55. Smith, P. E.; van Gunsteren, W. F. J Chem Phys 1994, 100, 3169.
56. Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Geber, P. R.; van Gunsteren, W. F. Chem Phys Lett 1994, 222, 529.
57. Mordasini, T. Z.; McCammon, J. A. J Phys Chem B 2000, 104, 360.
58. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Nola, A. D. J Chem Phys 1984, 81, 3684.
59. van Gunsteren, W. F.; Berendsen, H. J. C Mol Sim 1988, 1, 173.
60. Miyamoto, S.; Kollman, P. A. J Comp Chem 1992, 13, 952.
61. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J Comp Chem 1997, 18, 1463.
62. Feenstra, K. A; Hess, B.; Berendsen, H. J. C. J Comp Chem 1999, 20, 786.
63. Straatsma, T. P.; McCammon, J. J Chem Phys 1991, 95, 1175.
64. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford Science Publication: Oxford, 1987.
65. Hess, B. J. Chem Phys 2002, 116, 209.
66. Straatsma, T. P.; Zacharias, M.; McCammon, J. A. In Computer Simulation of Biomolecular Systems; van Gunsteren, W. F., Weiner, P. K., Wilkinson, A., Eds.; Kluwer Academic Publishers: Leiden, 1993, chap 14, vol. 2.
67. Daura, X.; Gademann, K.; Juan, B.; Seebach, D.; van Gunsteren, W.; Mark, A. E. Angew Chem Int Ed 1999, 38, 236.
68. Williamson, M. A. Biochem J 1994, 297, 249.
69. Waksman, G.; Shoelson, S. E.; Pant, N.; Cowburn, D.; Kuriyan, J. Cell 1993, 72, 779.
70. Mikol, V.; Baumann, G.; Keller, T. H.; Manning, U.; Zurini, M. G. M. J Mol Biol 1995, 246, 344.
71. Schapira, M.; Totrov, M.; Abagyan, R. J Mol Recognit 1999, 12, 177.
72. Juffer, A. H.; Vogel, H. Protein Struct Funct Genet 2000, 41, 554.
73. Pitera, J. W.; van Gusteren, W. F. J Am Chem Soc 2001, 123, 3163.
74. Ben-Naim, A. J Phys Chem 1978, 82, 792.
75. Viguera, A. R.; Arrondo, J. L.; Musacchio, A.; Saraste, M.; Serrano, L. Biochemistry 1994, 33, 10925.
76. Pisabarro, M. T.; Serrano, L. Biochemistry 1996, 35, 10634.
77. Wierenga, R. K.; Noble, M. E.; Davenport, R. C. Biochemistry 1992, 38, 4389.
78. Rozovsky, S.; McDermott, A. E. J Mol Biol 2001, 310, 259.
79. Baptista, A. M.; Martel, P. J.; Petersen, S. B. Proteins Struct Funct Genet 1997, 27, 532.
80. Smith, D. E.; Haymet, A. J. J. J Chem Phys 1993, 98, 6445.
81. Renzoni, D. A.; Rugh, D. J. R.; Siligardi, G.; Das, P.; Morton, C. J.; Rossi, C.; Waterfiel, M. D.; Campbel, I. D.; Ladbury, J. E. Biochemistry 1996, 35, 1546.
82. Wittekind, M.; Mapelli, C.; Farme, B. T.; Suen, K.-L.; Goldfarb, V.; Tsao, J.; Lavoie, T.; Barbacid, M.; Meyers, C. A.; Mueller, L. Biochemistry 1994, 33, 13531.
83. Ladbury, J. E.; Lemmon, M. A.; Green, J.; Botfield, M. C.; Schlessinger, J. Proc Natl Acad Sci USA 1995, 92, 3199.
84. Henriques, D. A.; Ladbury, J. E.; Jackson, R. M. Protein Sci 2000, 9, 1975.
85. Aqvist, J.; Hansson, T. J Phys Chem 1996, 100, 9512.
86. Morton, A.; Baase, W. A.; Matthews, B. W. Biochemistry 1995, 34, 8564.
87. Wu, X.; Knudsen, B.; Feller, S. M.; Zheng, J.; Sali, A.; Cowburn, D.; Hanafusa, H.; Kuriyan, J. Structure 1995, 3, 215.
88. Lim, W. A.; Fox, R. O.; Richards, F. M. Protein Sci 1994, 3, 1261.
89. Zhou, Y.; Abagyan, R. Fold Des 1998, 3, 513.
90. Lee, C.; Leung, B.; Lemmon, M. A.; Zheng, J.; Cowbum, D.; Kuriyan, J.; Saksela, K. EMBO J 1995, 14, 5006.
91. Krystek, S.; Stouch, T.; Novotny, J. J Mol Biol 1993, 234, 661.
92. Sheriff, S.; Silverton, E. W.; Padlan, E. A.; Cohen, G. H.; Smithg-Gill, S. J.; Finzel, B. C.; Davies, D. R. Proc Natl Acad Sci USA 1987, 84, 8075.