Hydrogen bond energetics: A simulation and statistical analysis of N-methyl acetamide (NMA), water, and human lysozyme

Journal of Physical Chemistry B

Volumn 105, Issue 44, 2001, Pages 11000-11015

  Buck, Matthias ^a,b,c   Karplus, Martin ^a,b  

^a HARVARD UNIVERSITY   (United States)

^b UNIVERSITÉ DE STRASBOURG   (France)

^c MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LYSOZYME;

COMPUTER SIMULATION; CRYSTAL STRUCTURE; DIMERS; ELECTROSTATICS; HYDROGEN; HYDROGEN BONDS; POLYPEPTIDES; POTENTIAL ENERGY; PROTEINS; SOLVENTS; STATISTICAL METHODS; WATER;

MOLECULAR DYNAMICS;

EID: 0035829905     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp011042s     Document Type: Article

References (69)

1. Pauling, L.C. The Nature of the Chemical Bond. Cornell University Press, 1960.
2. Eisenberg, D.; Kauzmann, W. The Structure and Properties of Water. Oxford University Press: New York, 1960.
3. Franks, F.; Ed. Water: A comprehensive treatise. Plenum Press: New York, 1972.
4. Schuster, P.; Zundel, G.; Sandorfy, A. The Hydrogen Bond. Elsevier Pub. Co.: New York, 1979.
5. Glusker, J.P. Top. Curr. Chem. 1998, 198, 2-56.
6. Baker, E.N.; Hubbard, R.E. Prog. Biophys. Mol. Biol. 1984, 44, 97-179.
7. Mirsky, A.E.; Pauling, L. Proc. Natl. Acad. Sci. U.S.A. 1936, 22, 439-447.
8. Pauling, L.C.; Corey, R.B. Proc. R. Soc. London, Ser. B 1953, 141, 21-33.
9. Karplus, P.A.; Faerman, C. Curr. Opin. Struct. Biol. 1994, 4, 770-776.
10. Covell, D.G.; Wallquist, A. J. Mol. Biol. 1997, 269, 281-297.
11. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577-2637.
12. Jeffrey, G.A.; Saenger, W. Hydrogen Bonding in Proteins. Chapter 19 from Hydrogen Bonding in Biological Structures; Springer, New York, 1991.
13. Stickle, D.F.; Presta, L.G.; Dill, K.A.; Rose, G.D. J. Mol. Biol. 1992, 226, 1143-59.
14. McDonald, I.K.; Thornton, J.M. Hydrogen bonding in globular proteins and Atlas of side chain and mainchain hydrogen bonding in proteins. Material supplementary to McDonald and Thornton, 1994.
15. McDonald, I.K.; Thornton, J.M. J. Mol. Biol. 1994, 238, 777-793.
16. Bordo, D.; Argos, P. J. Mol. Biol. 1994, 243, 504-519.
17. Xu, D.; Tsai, C.-J.; Nussinov, R. Protein Eng. 1997, 10, 999-1012.
18. Saenger, W. Annu. Rev. Biophys. Biophys. Chem. 1987, 16, 93-114.
19. Teeter, M.M. Annu. Rev. Biophys. chem. 1991, 20, 577-600.
20. Levitt, M.; Park, B.H. Structure 1993, 1, 223-226.
21. Sidhu, K.S.; Goodfellow, J.M.; Turner, J.Z. J. Chem. Phys. 1999, 110, 7943-7950.
22. Thanki, N.; Thornton, J.M.; Goodfellow, J.M. J. Mol. Biol. 1991, 221, 669-691.
23. Hooft, R.W.W.; Sander, C.; Vriend, G. Proteins: Struct. Funct., Genet. 1996, 26, 363-376.
24. Mills, J.E.J.; Dean, P.M. J. Comput. Aided Mol. Design 1996, 10, 607-622.
25. Dingley, A.J.; Grzesiek, S. J. Am. Chem. Soc. 1998, 120, 8293-8297.
26. Cornilescu, G.; Ramirez, B.E.; Frank, M.K.; Clore, G.M.; Gronenborn, A.M.; Bax, A. J. Am. Chem. Soc. 1998, 121, 6275-6279.
27. Harris, T.K.; Mildvan, A.S. Proteins: Struct. Funct., Genet. 1999, 35, 275-282.
28. Brooks, B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
29. 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.; Lan, F.T.K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
30. Reiher, W.D. Theoretical studies of hydrogen bonding. Ph.D. Thesis, Harvard University, 1985.
31. Mitchell, J.B.O.; Price, S.L. J. Phys. Lett. 1991, 180, 517-523.
32. Brooks, C.L.; Karplus, M.; Pettitt, B.M. Proteins: A theoretical perspective of dynamics, structure and thermodynamics. Adv. Chem. Phys. LXXI; Wiley & Sons: N. Y., 1988.
33. Brooks, C.L.; Karplus, M. J. Chem. Phys. 1983, 79, 6312-6325.
34. Loncharich, R.J.; Brooks, B.R. Proteins: Struct. Funct., Genet. 1989, 6, 32-45.
35. MacKerell, A.D.; Karplus, M. J. Phys. Chem. 1991, 95, 10559-10560.
36. Guo, H.; Karplus, M.J. Phys. Chem. 1992, 96, 7273-7287.
37. Gelin, B.R.; Karplus, M. J. Am. Chem. Soc. 1975, 97, 6996-7006.
38. Rychaert, J.-P.; Ciccotti, G.; Berendsen, H.J.C. J. Comput. Phys. 1977, 23, 327-341.
39. Hoover, W.G. Phys. Rev. A 1985, 31, 1695-1697.
40. Nose, S. J. Chem. Phys. 1984, 81, 511-519.
41. Brünger, A.; Brooks, C.L.; Karplus, M. Chem. Phys. Lett. 1984, 105; 495-500.
42. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; DiNola, A.; Haak, J.R. J. Chem. Phys. 1984, 81, 3684-3690.
43. Allan; M.P.; Tildesley, D.J. Computer simulations in liquids, pp 181-185. Oxford University Press: New York, 1987.
44. McQuarrie, D.A. Statistical Mechanics, Harper Collins Pub. Macmillan Press: London, 1976.
45. Artymiuk, P.J.; Blake, C.C.F. J. Mol. Biol. 1981, 152, 737-762.
46. Brünger, A.T.; Karplus, M. Proteins: Struct. Funct., Genet. 1988, 4, 148-156.
47. Adalsteinsson, H.; Maulitz, A.H.; Bruice, T.C. J. Am. Chem. Soc. 1996, 118, 7689-7693.
48. Guo, H.; Karplus, M. J. Phys. Chem. 1994, 98, 7104-7105.
49. Gao, J.; Freindorf, M. J. Phys. Chem A 1997, 101, 3182-3188.
50. Dixon, D.A.; Dobbs, K.D.; Valentini, J.J. J. Phys. Chem. 1994, 98, 13435-13439.
51. Lazaridis, T.; Archontis, G.; Karplus, M. Adv. Protein Chem. 1995, 47, 262-344.
52. Ben-Tal, N.; Sitkoff, D.; Topol, I.A.; Yang, A.-S.; Burt, S.K.; Honig, B. J. Phys. Chem. B 1997, 101, 450-457.
53. Grzybowski, B.A.; Ishchenko, A.V.; DeWitte, R.S.; Whitesides, G.M.; Shaknovich, E.I. J. Phys. Chem. B 2000, 104, 7293-7298.
54. Markham, L.M.; Hudson, B.S. J. Phys. Chem. 1996, 100, 2731-2737.
55. Baudry, J.; Smith, J.C. J. Mol. Struct. (Theochem.) 1994, 308, 103-113.
56. Demetropoulos, I.N.; Gerothanassis, I.P.; Vakka, C.; Kakavas, C. J. Chem. Soc. (Faraday Trans.) 1996, 92, 921-931.
57. Buck, M.; Karplus, M. J. Am. Chem. Soc. 1999, 121, 9645-9658.
58. Jorgensen, W.L. J. Am. Chem. Soc. 1989, 111, 3770-3771.
59. Hermans, J.; Wang, L.J. Am. Chem. Soc. 1997, 119, 2707-2714.
60. Apaya, R.P.; Bondi, M.; Price, S.L. J. Comput. Aided Mol. Design 1997, 11, 479-490.
61. Nielsen, J.E.; Andersen, K.V.; Honig, B.; Hooft, R.W.W.; Klebe, G.; Vriend, G.; Wade, R.C. Protein Eng. 1999, 12, 657-662.
62. Oliva, M.T.; Moult, J. Protein Eng. 1999, 12, 727-735.
63. Jorgensen, W.L.; Chandrasekhar, J.; Madura, J.D.; Impey, R.W.; Klein, M.L. J. Chem. Phys. 1983, 79, 926-935.
64. Yu, H.-A.; Pettitt, M.; Karplus, M. J. Am. Chem. Soc. 1991, 113, 2425-2434.
65. Rossky, P.J.; Karplus, M. J. Am. Chem. Soc. 1979, 101, 1913-1937.
66. Sippl, M.J. J. Mol. Biol. 1996, 260, 644-648.
67. Lazaridis, T. J. Phys. Chem. B 1998, 102, 3542-3550.
68. Weeks, J.D.; Chandler, D.; Andersen, H.C. J. Chem. Phys. 1971, 54, 5237-5244.
69. Lazaridis, T.; Karplus, M. J. Chem. Phys. 1996, 105, 4294-4315.