Energy analysis of chemistry for correct insertion by DNA polymerase β

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 36, 2006, Pages 13294-13299

  Lin, Ping ^a   Pedersen, Lars C ^b   Batra, Vinod K ^b   Beard, William A ^b   Wilson, Samuel H ^b   Pedersen, Lee G ^a,b  

^a The University of North Carolina at Chapel Hill   (United States)

^b NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

Molecular mechanics; Quantum mechanics; Reaction mechanism

Indexed keywords

ASPARTIC ACID; DEOXYRIBOSE; DNA DIRECTED DNA POLYMERASE BETA; NUCLEOSIDE;

ARTICLE; CATALYSIS; CHEMISTRY; DECOMPOSITION; ENERGY TRANSFER; ENZYME ACTIVE SITE; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTON TRANSPORT; QUANTUM MECHANICS; REACTION ANALYSIS; X RAY CRYSTALLOGRAPHY;

BINDING SITES; CATALYSIS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DNA POLYMERASE BETA; ELECTROSTATICS; ENERGY METABOLISM; HUMANS; HYDROGEN BONDING; KINETICS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; PROTONS; QUANTUM THEORY; THERMODYNAMICS;

EID: 33748620054     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0606006103     Document Type: Article

References (75)

1. Kunkel, T. A. & Bebenek, R. (2000) Annu. Rev. Biochem. 69, 497-529.
2. Beard, W. A. & Wilson, S. H. (2006) Chem. Rev. 106, 361-382.
3. Sawaya, M. R., Pelletier, H., Kumar, A., Wilson, S. H. & Kraut, J. (1994) Science 264, 1930-1935.
4. Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H. & Kraut, J. (1994) Science 264, 1891-903.
5. Sawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J. & Pelletier, H. (1997) Biochemistry 36, 11205-11215.
6. Krahn, J. M., Beard, W. A., Miller, H., Grollman, A. P. & Wilson, S. H. (2003) Structure (London) 11, 121-127.
7. Krahn, J. M., Beard, W. A. & Wilson, S. H. (2004) Structure (London) 12, 1823-1832.
8. Batra, V. K., Beard, W. A., Shock, D. D., Pedersen, L. C. & Wilson, S. H. (2005) Structure (London) 13, 1225-1233.
9. Bose-Basu, B., DeRose, E. F., Kirby, T. W., Mueller, G. A., Beard, W. A., Wilson, S. H. & London, R. E. (2004) Biochemistry 43, 8911-8922.
10. Kirby, T. W., DeRose, E. F., Beard, W. A., Wilson, S. H. & London, R. E. (2005) Biochemistry 44, 15230-15237.
11. Kim, S. J., Beard, W. A., Harvey, J., Shock, D. D., Knutson, J. R. & Wilson, S. H. (2003) J. Biol Chem. 278, 5072-5081.
12. Abashkin, Y. G., Erickson, J. W. & Burt, S. K. (2001) J. Phys. Chem. B. 105, 287-292.
13. Florian, J., Goodman, M. F. & Warshel, A. (2002) J. Phys. Chem. B. 106, 5739-5753.
14. Florian, J., Goodman, M. F. & Warshel, A. (2003) Biopolymers 68, 286-299.
15. Rittenhouse, R. C., Apostoluk, W. K., Miller, J. H. & Straatsma, T. P. (2003) Proteins Struct. Funct. Genet. 53, 667-682.
16. Yang, G. W., Franklin, M., Li, J., Lin, T. C. & Konigsberg, W. (2002) Biochemistry 41, 2526-2534.
17. Yang, L. J., Arora, K., Beard, W. A., Wilson, S. H. & Schlick, T. (2004) J. Am. Chem. Soc. 126, 8441-8453.
18. Yang, L. J., Beard, W. A., Wilson, S. H., Broyde, S. & Schlick, T. (2004) Biophys. J. 86, 3392-3408.
19. Yang, L. J., Beard, W. A., Wilson, S. H., Broyde, S. & Schlick, T. (2002) J. Mol. Biol. 317, 651-671.
20. Arora, K. & Schlick, T. (2004) Biophys. J. 87, 3088-3099.
21. Arora, K., Beard, W. A., Wilson, S. H. & Schlick, T. (2005) Biochemistry 44, 13328-13341.
22. Arora, K. & Schlick, T. (2005) J. Phys. Chem. B. 109, 5358-5367.
23. Radhakrishnan, R. & Schlick, T. (2004) Proc. Natl. Acad. Sci. USA 101, 5970-5975.
24. Batra, V. K., Beard, W. A., Shock, D. D., Krahn, J. M., Pedersen, L. C. & Wilson, S. H. (2006) Structure (London) 14, 757-766.
25. Brautigam, C. A. & Steitz, T. A. (1998) Curr. Opin. Struct. Biol. 8, 54-63.
26. Beard, W. A., Shock, D. D., Vande Berg, B. J. & Wilson, S. H. (2002) J. Biol. Chem. 277, 47393-47398.
27. Fersht, A. (1985) Enzyme Structure and Mechanism (Freeman, New York).
28. Vande Berg, B. J., Beard, W. A. & Wilson, S. H. (2001) J. Biol. Chem. 276, 3408-3416.
29. Joyce, C. M. & Benkovic, S. J. (2004) Biochemistry 43, 14317-14324.
30. Warshel, A. (2003) Annu. Rev. Biophys. Biomol. Struct. 32, 425-443.
31. Gao, J. L. & Truhlar, D. G. (2002) Annu. Rev. Phys. Chem. 53, 467-505.
32. Gogonea, V., Suarez, D., van der Vaart, A. & Merz, K. W. (2001) Curr. Opin. Struct. Biol. 11, 217-223.
33. Garcia-Viloca, M., Gao, J., Karplus, M. & Truhlar, D. G. (2004) Science 303, 186-195.
34. Friesner, R. A. & Guallar, V. (2005) Annu. Rev. Phys. Chem. 56, 389-427.
35. Vreven, T., Morokuma, K., Farkas, O., Schlegel, H. B. & Frisch, M. J. (2003) J. Comput. Chem. 24, 760-769.
36. Dapprich, S., Komaromi, I., Byun, K. S., Morokuma, K. & Frisch, M. J. (1999) J. Mol. Struct. 462, 1-21.
37. Florian, J., Goodman, M. F. & Warshel, A. (2003) J. Am. Chem. Soc. 125, 8163-8177.
38. Florian, J., Goodman, M. F. & Warshel, A. (2005) Proc. Natl. Acad. Sci. USA 102, 6819-6824.
39. Mildvan, A. S. (1997) Proteins Struct. Funct. Genet. 29, 401-416.
40. Dejaegere, A., Lim, C. & Karplus, M. (1991) J. Am. Chem. Soc. 113, 4353-4355.
41. Uchimaru, T., Tanabe, K., Nishikawa, S. & Taira, K. (1991) J. Am. Chem. Soc. 113, 4351-4353.
42. Lahiri, S. D., Zhang, G. F., Dunaway-Mariano, D. & Allen, K. N. (2003) Science 299, 2067-2071.
43. Lahiri, S. D., Zhang, G. F., Dunaway-Mariano, D. & Allen, K. N. (2002) Biochemistry 41, 8351-8359.
44. Tremblay, L. W., Zhang, G. F., Dai, J. Y., Dunaway-Mariano, D. & Allen, K. N. (2005) J. Am. Chem. Soc. 127, 5298-5299.
45. Egloff, M. P., Cohen, P. T. W., Reinemer, P. & Barford, D. (1995) J. Mol. Biol. 254, 942-959.
46. Steitz, T. A. & Steitz, J. A. (1993) Proc. Natl. Acad. Sci. USA 90, 6498-6502.
47. Kim, E. E. & Wyckoff, H. W. (1991) J. Mol. Biol. 218, 449-464.
48. Chaidaroglow, A., Brezinski, D. J., Middleton, S. A. & Kantrowitz, E. R. (1988) Biochemistry 27, 8338-8343.
49. Butlerransohoff, J. E., Kendall, D. A. & Kaiser, E. T. (1988) Proc. Natl. Acad. Sci. USA 85, 4276-4278.
50. Besler, B. H., Merz, K. M. & Kollman, P. A. (1990) J. Comput. Chem. 11, 431-439.
51. Cisneros, G. A., Liu, H. Y., Zhang, Y. K. & Yang, W. T. (2003) J. Am. Chem. Soc. 125, 10384-10393.
52. Liu, H. Y., Zhang, Y. K. & Yang, W. T. (2000) J. Am. Chem. Soc. 122, 6560-6570.
53. Kraynov, V. S., Showalter, A. K., Liu, J., Zhong, X. J. & Tsai, M. D. (2000) Biochemistry 39, 16008-16015.
54. Date, T., Yamamoto, S., Tanihara, K., Nishimoto, Y., Liu, N. & Matsukage, A. (1990) Biochemistry 29, 5027-5034.
55. Garcia-Diaz, M., Bebenek, K., Krahn, J. M., Blanco, L., Kunkel, T. A. & Pedersen, L. C. (2004) Mol. Cell. 13, 561-572.
56. Menge, K. L., Hostomsky, Z., Nodes, B. R., Hudson, G. O., Rahmati, S., Moomaw, E. W., Almassy, R. J. & Hostomska, Z. (1995) Biochemistry 34, 15934-15942.
57. Li, S. X., Vaccaro, J. A. & Sweasy, J. B. (1999) Biochemistry 38, 4800-4808.
58. Kraynov, V. S., Werneburg, B. G., Zhong, X. J., Lee, H., Ahn, J. W. & Tsai, M. D. (1997) Biochem. J. 323, 103-111.
59. Beard, W. A., Osheroff, W. P., Prasad, R., Sawaya, M. R., Jaju, M., Wood, T. G., Kraut, J., Kunkel, T. A. & Wilson, S. H. (1996) J. Biol. Chem. 271, 12141-12144.
60. Dalal, S., Kosa, J. L. & Sweasy, J. B. (2004) J. Biol. Chem. 279, 577-584.
61. Kosa, J. L. & Sweasy, J. B. (1999) J. Biol. Chem. 274, 35866-35872.
62. Maitra, M., Gudzelak, A., Li, S. X., Matsumoto, Y., Eckert, K. A., Jager, J. & Sweasy, J. B. (2002) J. Biol. Chem. 277, 35550-35560.
63. Shah, A. M., Conn, D. A., Li, S. X., Capaldi, A., Jager, J. & Sweasy, J. B. (2001) Biochemistry 40, 11372-11381.
64. Beard, W. A. & Wilson, S. H. (2003) Structure (London) 11, 489-496.
65. Arndt, J. W., Gong, W. M., Zhong, X. J., Showalter, A. K., Liu, J., Dunlap, C. A., Lin, Z., Paxson, C., Tsai, M. D. & Chan, M. K. (2001) Biochemistry 40, 5368-5375.
66. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Debolt, S., Ferguson, D., Seibel, G. & Kollman, P. (1995) Comput. Phys. Commun. 91, 1-41.
67. Case, D. A., Darden, T. A., Cheatham, I. T. E., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, K. M., Wang, B., Pearlman, D. A., et al. (2004) AMBER8 (Univ. of California, San Francisco).
68. Sigel, H. & Griesser, R. (2005) Chem. Soc. Rev. 34, 875-900.
69. Wang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. (2004) J. Comput. Chem. 25, 1157-1174.
70. Cornell, W. D., Cieplak, P., Bayly, C. I. & Kollman, P. A. (1993) J. Am. Chem. Soc. 115, 9620-9631.
71. Sagui, C. & Darden, T. A. (1999) Annu. Rev. Biophys. Biomol. Struct. 28, 155-179.
72. Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H. & Pedersen, L. G. (1995) J. Chem. Phys. 103, 8577-8593.
73. Darden, T., York, D. & Pedersen, L. (1993) J. Chem. Phys. 98, 10089-10092.
74. Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., Montgomery, J. A., Jr., Vreven, T., Kudin, K. N., Burant, J. C., et al. (2004) Gaussian 03 (Gaussian, Wallingford, CT), Revision C.02.
75. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.