Conformation-Dependent Intermolecular Interaction Energies of the Triphosphate Anion with Divalent Metal Cations. Application to the ATP-Binding Site of a Binuclear Bacterial Enzyme. A Parallel Quantum Chemical and Polarizable Molecular Mechanics Investigation

Journal of Computational Chemistry

Volumn 25, Issue 2, 2004, Pages 160-168

  Gresh, Nohad ^a   Shi, Gen Bin ^b  

^a CNRS   (France)

^b VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

ATP, GTP; ATP binding enzymes; Conformation dependent interaction energies; Polarizable molecular mechanics; Quantum chemistry; Triphosphate anion

Indexed keywords

ADENOSINETRIPHOSPHATE; BACTERIA; BINDING ENERGY; CONFORMATIONS; HYDROLYSIS; MOLECULAR DYNAMICS; POLARIZATION; QUANTUM THEORY; X RAY CRYSTALLOGRAPHY;

INTERACTION ENERGIES; INTERMOLECULAR INTERACTIONS; POLARIZABLE MOLECULAR MECHANICS;

PHOSPHATES;

ADENOSINE TRIPHOSPHATE; BETA LACTAMASE; GUANOSINE TRIPHOSPHATE; THERMOLYSIN;

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

ADENOSINE TRIPHOSPHATE; BETA-LACTAMASES; BINDING SITES; GUANOSINE TRIPHOSPHATE; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; THERMODYNAMICS; THERMOLYSIN;

EID: 0347603170     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10312     Document Type: Article

References (49)

1. Sack, S.; Muller, J.; Marx, A.; Thormahlen, M.; Mandelkow, E.-M.; Brady, S. T.; Mandelkow, E. Biochemistry 1997, 36, 16155.
2. (a) Bourne, H. R.; Sanders, D. A.; McCormick, F. Nature 1990, 348, 125;
3. (b) Tong, L.; de Vos, A. M.; Milburn, M. V.; Kim, S.-H. J Mol Biol 1991, 217, 503;
4. (c) Scheffzek, K.; Ahmadian, M. R.; Kabsch, W.; Wiesmuller, L.; Lautwein, A.; Schmitz, F.; Wittinghofer, A. Science 1997, 277, 333.
5. (a) Lev, S.; Moreno, H.; Martinez, R.; Canoll, P.; Peles, E.; Musacchio, J. M.; Plowman, G. D.; Rudy, B.; Schlessinger, J. Nature 1995, 376, 737;
6. (b) Hatada, M. H.; Lu, X.; Laird, E. R.; Green, J.; Morgenstern, J. P.; Lou, M.; Marr, C. S.; Phillips, T. B.; Ram, M. K.; Theriault, K.; Zoller, M. J. ; Karas, J. L. Nature 1995, 377, 32;
7. (c) Johnson, L. N.; Noble, M. E.; Owen, D. J. Cell 1996, 85, 149.
8. (a) Fry, D. W.; Kraker, A. J.; McMichael, A.; Ambroso, L. A.; Nelson, J. M.; Leopold, W. R.; Connors, R. W.; Bridges, A. J. Science 1994, 265, 1093;
9. (b) Levitzki, A.; Gazit, A. Science 1995, 267, 1782;
10. (c) Mohammadi, M.; McMahon, G.; Su, L.; Tang, C.; Hirth, P.; Yeh, B. K.; Hubbard, S. R.; Schlessinger, J. Science 1997, 276, 955;
11. (d) Tong, L.; Pav, S.; White, D. M.; Rogers, S.; Crane, K. M.; Cywin, C. L.; Brown, M. L.; Pargellis, C. A. Nat Struct Biol 1997, 4, 311;
12. (e) Schindler, T.; Bornmann, W.; Pellicena, P.; Miller, T. W.; Clarkson, B.; Kuriyan, J. Science 2000, 289, 8;
13. (f) Zwick, E.; Bange, J.; Ullrich, A. Trends Mol Med 2002, 8, 17;
14. (g) Pargellis, C.; Tong, L.; Churchill, L.; Cirillo, P. F.; Gilmore, T.; Graham, A. G.; Grob, P. M.; Hickey, E. R.; Moss, N.; Pav, S.; Regan, J. Nat Struct Biol 2002, 9, 268;
15. (h) Shi, G.; Blaszczyk, J.; Ji, X.; Yan, H. J Med Chem 2001, 44, 1364.
16. (a) Gresh, N.; Claverie, P.; Pullman, A. Int J Quantum Chem 1986, 29, 101;
17. (b) Gresh, N. J Comput Chem 1995, 16, 856.
18. (a) Garmer, D R.; Gresh, N.; Roques, B. P. Proteins Struct Funct Genet 1998, 31, 42;
19. (b) Tiraboschi, G.; Roques, B. P.; Gresh, N. J Comput Chem 1999, 20, 1379;
20. (c) Tiraboschi, G.; Gresh, N.; Giessner-Prettre, C.; Pedersen, L. G.; Deerfield, D. W. J Comput Chem 2000, 21, 1011.
21. (a) Masella, M.; Gresh, N.; Flament, J. P. J Chem Soc Faraday Trans 1998, 94, 2745;
22. (b) Guo, H.; Gresh, N.; Roques, B. P.; Salahub, D. R. J Phys Chem B 2000, 104, 9746.
23. (a) Faerman, C. H.; Price, S. L. J Am Chem Soc 1990, 112, 4915;
24. (b) Price, S. L.; Faerman, C. H.; Murray, C. W. J Comput Chem 1991, 12, 1187;
25. (c) Price, S. L.; Stone, A. J. J Chem Soc Faraday Trans 1992, 88, 1755.
26. (a) Rogalewicz, F.; Ohanessian, G.; Gresh, N. J Comput Chem 2000, 21, 963;
27. (b) Tiraboschi, G.; Fournié-Zaluski, M. C.; Roques, B. P.; Gresh, N. J Comput Chem 2001, 22, 103;
28. (c) Antony, J.; Gresh, N.; Hemmingsen, L.; Olsen, L.; Schofield, C.; Bauer, R. J Comput Chem 2002, 23, 1281.
29. (a) Garmer, D. R.; Gresh, N. J Am Chem Soc 1994, 116, 3556;
30. (b) Gresh, N.; Garmer, D. R. J Comput Chem 1996, 17, 1481.
31. Shiota, T. Biosynthesis of Folate from Pterin Precursor. Chemistry and Biochemistry of Folates, John Wiley & Sons; New York, 1984, p. 121.
32. Biaszcyk, J.; Shi, G.-B.; Yan, H.; Ji, X. Structure 2000, 8, 1049.
33. Stevens, W. J.; Basch, H.; Krauss, M. J Chem Phys 1984, 81, 6026.
34. Stevens, W. J.; Fink, W. Chem Phys Lett 1987, 139, 15.
35. Pople, J. A.; Binkley, J. S.; Seeger, R. Int J Quantum Chem 1976, 10, 1.
36. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus, T. L.; Dupuis, M.; Montgomery, J. A., Jr. J Comput Chem 1993, 14, 1347.
37. (a) Lee, C.; Yang, W.; Parr, R. G. Phys Rev 1988, B37, 785;
38. (b) Becke, A. J Chem Phys 1993, 98, 5648.
39. Hay, P. J.; Wadt, W. R. J Chem Phys 1985, 82, 299.
40. Jaguar 4.1, Schrodinger Inc., Portland, Oregon, 2000.
41. Vigné-Maeder, F.; Claverie, P. J Chem Phys 1988, 88, 4934.
42. Garmer, D. R.; Stevens, W. J. J Phys Chem 1989, 93, 8263.
43. Gresh, N.; Roques, B. P. Biopolymers 1997, 47, 145.
44. Evangelakis, G.; Rizos, J.; Lagaris, I.; Demetropoulos, G. N. Comput Phys Commun 1987, 46, 401.
45. Gresh, N.; Sponer, J. J Phys Chem B 1999, 103, 11415.
46. Krauss, M.; Gresh, N.; Antony, J. J Phys Chem B 2003, 107, 1215.
47. Dougherty, D. A. Science 1996, 274, 163.
48. Hobza, P.; Sponer, J. Chem Rev 1999, 99, 3247.
49. Langlet, J.; Claverie, P.; Caillet, J.; Pullman, A. J Phys Chem 1988, 92, 1631.