Accurate intraprotein electrostatics derived from first principles: An effective fragment potential method study of the proton affinities of lysine 55 and tyrosine 20 in turkey ovomucoid third domain

Journal of Physical Chemistry A

Volumn 105, Issue 15, 2001, Pages 3829-3837

  Minikis, Ryan M ^a   Kairys, Visvaldas ^a   Jensen, Jan H ^a,b  

^a E11 SSH   (United States)

^b UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTON TRANSFER;

AMINO ACIDS; ELECTRIC POTENTIAL; ELECTRONIC STRUCTURE; PROTEINS; PROTONS;

ELECTROSTATICS;

EID: 0035912426     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0032659     Document Type: Article

References (56)

1. (a) Sharp, K. A.; Honig, B.. Annu. Rev. Biophys. Biophys. Chem. 1990, 19, 301.
2. (b) Warshel, A.; Åqvist, J. Annu. Rev. Biophys. Biophys. Chem. 1991, 20, 267.
3. Bashford, D. Curr. Opin. Struct. Blol. 1991, 1, 175.
4. Gilson, M. K. Curr. Opin. Struct. Biol. 1995, 5, 216.
5. (e) Warshel, A.; Papazyan, A. Curr. Opin. Struct. Biol. 1998, 8, 211.
6. (f) Ullmann, G. M.; Knapp, E.-W. Ear. Biophys. J. 1999, 28, 533.
7. See for example: Rappe, A. K.;Casewit, C. J. Molecular Mechanics Across Chemistry; University Science Books: Sausalito, CA, 1997.
8. (a) Weiner, S. J.; Kollman, PA.; Case, D. A.; Singh, U. C.; Ohio. C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.
9. (b) Weiner, S. J.; Kollman, PA.; Nguyen, D. T.; Case, D. A. J. Comput. Chem 1986, 7, 230.
10. (a) Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J. J. Comput. Chem. 1983, 4, 187.
11. (b) Nilsson, L. Karplus, M. J. Comput. Chem. 7, 591.
12. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stole, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 2, 3586.
13. Van Gunsteren, W. F.; Berendsen, H. J. C. Angew. Chem., Int. Ed. Engl. 1990, 29, 992.
14. Wiberg, K. B.; Rablen, P. R. J. Comput. Chem. 1993,14, 1504-1518.
15. Sokalski, W. A.; Maruszewski, K.; Harihan, P. C.; Kaufman, J. J. Int. J. Quantum Chem. Quantum Biol. Symp. 1989, 16, 119.
16. Stone, A. J.; Price, S. L. J. Phys. Chem. 1988, 92, 3325.
17. (a) Faerman, C. H.; Price, S. L. J. Am. Chem. Soc. 1990,112,1990.
18. (b) Price, S. L.; Richards, N. G. J. /. Comput. Aided Mol. Des. 1991,5,41.
19. Hunter, C. A.; Singh, J.; Thomton, J. M. J. Mol. Biol. 1991, 218, 837.
20. Mitchel, J. B. O.; Nandi, C. L.; Thornton, J. M.; Price, S. L.; Singh, J.; Snarey, M. J. Chem. Soc., Faraday Trans. 1993, 89, 2619.
21. Dixon, R. W.; Kollman, P. A. J. Comput. Chem. 1997, 18, 1632.
22. (a) Buckingham, A. D.; Fowler, P. W. J. Chem. Phys. 1983, 79, 6426.
23. (b) Buckingham, A. D.; Fowler, P. W. Can. J. Chem. 1985,63,2018.
24. See for example the following reviews: (a) Price, S. L. J. Chem. Soc., Faraday Trans. 1996, 92, 2997.
25. (b) Engkvist, O.; Åstrand, P.-O.; Karlstrom, G. Chem. Rev. 2000, 700, 4087.
26. (a) Jensen, J. H.; Day, P. N.; Gordon, M. S.; Basch, H.; Cohen, D.; Garmer, D. R.; Kraus, M.; Stevens, W. J. In Modeling the Hydrogen . Bond; ACS Symposium Series 569; Smith, D. A., Ed.; American Chemical Society: Washington, DC, 1994; Chapter 9.
27. (b) Day, P. N.; Jensen, J. H.; Gördon, M. S.; Webb, S. P.; Stevens, W. J.; Kraus, M.; Garmer, D.; Basch, H.; Cohen, D. J. Chem. Phys. 1996, 705, 1968.
28. Gordon, M. S.; Freitag, M.; Bandyopadhyay, P.; Jensen, J. H.; Kairys, V.; Stevens, W. J. J. Phys. Chem. A 2001, 705, 293.
29. Stone, A. J. Chem. Phys. Lett., 1981, 83, 233.
30. Garmer, D, R.; Stevens, W. J.. Phys. Chem. 1989, 93, 8263.
31. Bader, R. F. W. Atom in Molecules. A Quantum Theory Clarendon-Press: Oxford, 1994.
32. Koch, U.; Stone, A. J J. Chem. Soc., Faraday Trans. 1996, 92, 1701.
33. Price, S. L.; Stone, A. J J. Chem. Soc., Faraday Trans. 1992, 88, 1755.
34. Malta, C. F.; Bader, R. F. W. Proteins: Struct. Func, Genet. 2000, 40, 310.
35. We note that once transferable mMEPs are available for protein residues, they can easily be used in conjunction with the EFP method.
36. Kairys, V.; Jensen, J. H. J. Phys. Chem. A 2000, 104, 6656.
37. see for example (a) Zhang, Y.; Lee, T.-S.; Yang, W. J. Chem. Phys. 1999, 770, 46.
38. (b) Murphy, R. B.; Philipp, D. M.; Friesner, R. A. Chem. Phys. Lett. 2000,327,113.
39. Hoogstraten, C. G.; Choe, S.; Westler, W. M.; Markley, J. L. Protein Sei. 1995, 4, 2289.
40. Hehre, W. J.; Ditchfield, R.; Pople, J. A. /. Chem. Phys.1972,56, 2257.
41. King, H. F.; Stanton, R. E.; King, H.; Wyatt, R. E.; Parr R. G. J. Chem. Phys. 1967, 47, 1936.
42. Stevens, W. J.; Fink, W. H. Chem. Phys. Lett. 1987, 139, 15.
43. Bagus, P. S.; Hermann, K.; Bauschlicher, C. W., Jr. J. Chem. Phys. 1984, 50, 4378.
44. (a) Boys, S. F. Quantum Science of Atoms, Molecules and Solids, Lowdin, P. O. Ed.; Academic Press: New York, 1966.
45. (b) Edmiston, C.; Ruedenberg, K. Rev. Mod. Phys. 1963, 35, 457.
46. 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. J. Comput. Chem. 1993, 14, 1347.
47. Webb, S. P. Ph.D. Thesis, Iowa State University, 1998.
48. Yamaguchi, Y.; Masamura, Y.; Goddard, J. D.; Schaefer, H. F. A New Dimension, A New Dimension to Quantum Chemistry; Oxford University Press: Oxford, 1994.
49. Jeziorski, B.; Moszynski, R.; Ratkiewicz, A.; Rybak, S.; Szalewiez, K.; Williams, H. L. In Methods and techniques in computational chemistry; dementi, E, Ed.; Cagliari, 1993; Metecc-94 Vol B, Chapter 3.
50. Day, P. N.; Pachter, R.; Gordon, M. S.; Merrill, G. N. J. Client. ' Phys. 2000,112, 2063-2073.
51. Gordon, M. S. and co-workers, work in progress.
52. (a) Bandyopadhyay, P.; Gordon, M. S. J. Chem. Phys. 2000,113, 1104.
53. (b) Bandyopadhyay, P.; Gordon, M. S., work in progress.
54. Barone, V.; Cossi, M.; Tomasi, J. J. Chem. Phys. 1997, 707,3210.
55. da Suva, C. O.; da Suva, E. C.; Nascimento, M. A. C. J. Phys. Chem. A 2000, 103, 11194.
56. Antosiewicz, A.; McCammon, J. A.; Gilson, M. K. Biochemistry 1996, 35, 7819.