Increased flexibility enhances misincorporation: Temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase

Journal of Biological Chemistry

Volumn 282, Issue 2, 2007, Pages 1397-1408

  Perlow Poehnelt, Rebecca A ^a,b   Likhterov, Ilya ^a,c   Wang, Lihua ^a   Scicchitano, David A ^a   Geacintov, Nicholas E ^a   Broyde, Suse ^a,d  

^a NEW YORK UNIVERSITY   (United States)

^b MERCK RESEARCH LABORATORIES   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

^d 1009 Silver Center ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BYPASS FIDELITY; CARCINOGEN; CONFORMATIONAL FLEXIBILITY;

CONFORMATIONS; DNA; METABOLITES; MOLECULAR DYNAMICS; MOLECULAR MODELING; THERMAL EFFECTS;

NUCLEOTIDES;

BENZO[A]PYRENE; CARCINOGEN; DNA; DNA POLYMERASE; GUANINE; NUCLEOTIDE; DNA DIRECTED DNA POLYMERASE BETA;

ARTICLE; COMPARATIVE STUDY; CONFORMATIONAL TRANSITION; DNA ADDUCT; KINETICS; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; SIMULATION; STRUCTURE ANALYSIS; SULFOLOBUS SOLFATARICUS; TEMPERATURE MEASUREMENT; TEMPERATURE SENSITIVITY; BASE MISPAIRING; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; HEAT; PROTEIN CONFORMATION;

CRENARCHAEOTA; SULFOLOBUS SOLFATARICUS;

BASE PAIR MISMATCH; BENZO(A)PYRENE; CARCINOGENS; DNA ADDUCTS; DNA POLYMERASE BETA; GUANINE; HEAT; KINETICS; MODELS, MOLECULAR; NUCLEOTIDES; PROTEIN CONFORMATION; SULFOLOBUS SOLFATARICUS;

EID: 33847724386     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M606769200     Document Type: Article

References (77)

1. Kokoska, R. J., Bebenek, K., Boudsocq, F., Woodgate, R., and Kunkel, T. A. (2002) J. Biol. Chem. 277, 19633-19638
2. Gonzalez, M., and Woodgate, R. (2002) Bioessays 24, 141-148
3. Frank, E. G., Sayer, J. M., Kroth, H., Ohashi, E., Ohmori, H., Jerina, D. M., and Woodgate, R. (2002) Nucleic Acids Res. 30, 5284-5292
4. Duvauchelle, J. B., Blanco, L., Fuchs, R. P., and Cordonnier, A. M. (2002) Nucleic Acids Res. 30, 2061-2067
5. Bresson, A., and Fuchs, R. P. (2002) EMBO J. 21, 3881-3887
6. Boudsocq, F., Ling, H., Yang, W., and Woodgate, R. (2002) DNA Repair 1, 343-358
7. Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2001) Cell 107, 91-102
8. Woodgate, R. (1999) Genes Dev. 13, 2191-2195
9. Steitz, T. A., and Yin, Y. W. (2004) Philos. Trans. R. Soc. Lond. B Biol. Sci. 359, 17-23
10. Boudsocq, F., Iwai, S., Hanaoka, F., and Woodgate, R. (2001) Nucleic Acids Res. 29, 4607-4616
11. Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N. E., and Patel, D. J. (2006) PLoS Biol. 4, e11
12. Doublié, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998) Nature 391, 251-258
13. Franklin, M. C., Wang, J., and Steitz, T. A. (2001) Cell 105, 657-667
14. Huang, H., Chopra, R., Verdine, G. L., and Harrison, S. C. (1998) Science 282, 1669-1675
15. Kiefer, J. R., Mao, C., Braman, J. C., and Beese, L. S. (1998) Nature 391, 304-307
16. Li, Y., Korolev, S., and Waksman, G. (1998) EMBO J. 17, 7514-7525
17. Rothwell, P. J., and Waksman, G. (2005) Adv. Protein Chem. 71, 401-440
18. Potapova, O., Chan, C., DeLucia, A. M., Helquist, S. A., Kool, E. T., Grindley, N. D., and Joyce, C. M. (2006) Biochemistry 45, 890-898
19. Doublié, S., and Ellenberger, T. (1998) Curr. Opin. Struct. Biol. 8, 704-712
20. Eom, S. H., Wang, J., and Steitz, T. A. (1996) Nature 382, 278-281
21. Kunkel, T. A., and Bebenek, K. (2000) Annu. Rev. Biochem. 69, 497-529
22. Sawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J., and Pelletier, H. (1997) Biochemistry 36, 11205-11215
23. Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., and Kraut, J. (1996) Biochemistry 35, 12742-12761
24. Morales, J. C., and Kool, E. T. (1999) J. Am. Chem. Soc. 121, 2323-2324
25. Morales, J. C., and Kool, E. T. (2000) Biochemistry 39, 12979-12988
26. Ling, H., Sayer, J. M., Plosky, B. S., Yagi, H., Boudsocq, F., Woodgate, R., Jerina, D. M., and Yang, W. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 2265-2269
27. Fiala, K. A., and Suo, Z. (2004) Biochemistry 43, 2106-2115
28. Perlow-Poehnelt, R. A., Likhterov, I., Scicchitano, D. A., Geacintov, N. E., and Broyde, S. (2004) J. Biol. Chem. 279, 36951-36961
29. Ling, H., Boudsocq, F., Plosky, B. S., Woodgate, R., and Yang, W. (2003) Nature 424, 1083-1087
30. Rechkoblit, O., Amin, S., and Geacintov, N. E. (1999) Biochemistry 38, 11834-11843
31. Lipinski, L. J., Ross, H. L., Zajc, B., Sayer, J. M., Jerina, D. M., and Dipple, A. (1998) Int. J. Oncol. 13, 269-273
32. Zhuang, P., Kolbanovskiy, A., Amin, S., and Geacintov, N. E. (2001) Biochemistry 40, 6660-6669
33. Alekseyev, Y. O., and Romano, L. J. (2000) Biochemistry 39, 10431-10438
34. Zang, H., Harris, T. M., and Guengerich, F. P. (2005) Chem. Res. Toxicol. 18, 389-400
35. Hsu, G. W., Huang, X., Luneva, N. P., Geacintov, N. E., and Beese, L. S. (2005) J. Biol. Chem. 280, 3764-3770
36. Meehan, T., and Straub, K. (1979) Nature 277, 410-412
37. Cheng, S. C., Hilton, B. D., Roman, J. M., and Dipple, A. (1989) Chem. Res. Toxicol. 2, 334-340
38. Geacintov, N. E., Cosman, M., Hingerty, B. E., Amin, S., Broyde, S., and Patel, D. J. (1997) Chem. Res. Toxicol. 10, 111-146
39. Shukla, R., Jelinsky, S., Liu, T., Geacintov, N. E., and Loechler, E. L. (1997) Biochemistry 36, 13263-13269
40. Rodriguez, H., and Loechler, E. L. (1995) Mutat. Res. 326, 29-37
41. Moriya, M., Spiegel, S., Fernandes, A., Amin, S., Liu, T., Geacintov, N., and Grollman, A. P. (1996) Biochemistry 35, 16646-16651
42. Jelinsky, S. A., Liu, T., Geacintov, N. E., and Loechler, E. L. (1995) Biochemistry 34, 13545-13553
43. Shen, X., Sayer, J. M., Kroth, H., Ponten, I., O'Donnell, M., Woodgate, R., Jerina, D. M., and Goodman, M. F. (2002) J. Biol. Chem. 277, 5265-5274
44. Fernandes, A., Liu, T., Amin, S., Geacintov, N. E., Grollman, A. P., and Moriya, M. (1998) Biochemistry 37, 10164-10172
45. Rechkoblit, O., Zhang, Y., Guo, D., Wang, Z., Amin, S., Krzeminsky, J., Louneva, N., and Geacintov, N. E. (2002) J. Biol. Chem. 277, 30488-30494
46. Simhadri, S., Kramata, P., Zajc, B., Sayer, J. M., Jerina, D. M., Hinkle, D. C., and Wei, C. S. (2002) Mutat. Res. 508, 137-145
47. Zhao, B., Wang, J., Geacintov, N. E., and Wang, Z. (2006) Nucleic Acids Res. 34, 417-425
48. Avkin, S., Goldsmith, M., Velasco-Miguel, S., Geacintov, N. E., Friedberg, E. C., and Livneh, Z. (2004) J. Biol. Chem. 279, 53298-53305
49. Seo, K. Y., Nagalingam, A., Tiffany, M., and Loechler, E. L. (2005) Mutagenesis 20, 441-448
50. Hanrahan, C. J., Bacolod, M. D., Vyas, R. R., Liu, T., Geacintov, N. E., Loechler, E. L., and Basu, A. K. (1997) Chem. Res. Toxicol. 10, 369-377
51. Shukla, R., Geacintov, N. E., and Loechler, E. L. (1999) Carcinogenesis 20, 261-268
52. Rodriguez, H., and Loechler, E. L. (1993) Carcinogenesis 14, 373-383
53. Shibutani, S., Bodepudi, V., Johnson, F., and Grollman, A. P. (1993) Biochemistry 32, 4615-4621
54. Lenne-Samuel, N., Janel-Bintz, R., Kolbanovskiy, A., Geacintov, N. E., and Fuchs, R. P. (2000) Mol. Microb. 38, 299-307
55. Zhang, Y., Yuan, F., Wu, X., Wang, M., Rechkoblit, O., Taylor, J. S., Geacintov, N. E., and Wang, Z. (2000) Nucleic Acids Res. 28, 4138-4146
56. Napolitano, R., Janel-Bintz, R., Wagner, J., and Fuchs, R. P. (2000) EMBO J. 19, 6259-6265
57. Seo, K. Y., Nagalingam, A., Miri, S., Yin, J., Chandani, S., Kolbanovskiy, A., Shastry, A., and Loechler, E. L. (2006) DNA Repair 5, 515-522
58. Chandani, S., and Loechler, E. L. (2006) J. Mol. Graph. Model., in press
59. Geacintov, N. E., Cosman, M., Mao, B., Alfano, A., Ibanez, V., and Harvey, R. G. (1991) Carcinogenesis 12, 2099-2108
60. Huang, X., Kolbanovskiy, A., Wu, X., Zhang, Y., Wang, Z., Zhuang, P., Amin, S., and Geacintov, N. E. (2003) Biochemistry 42, 2456-2466
61. Pirogov, N., Shafirovich, V., Kolbanovskiy, A., Solntsev, K., Courtney, S. A., Amin, S., and Geacintov, N. E. (1998) Chem. Res. Toxicol. 11, 381-388
62. Mao, B., Xu, J., Li, B., Margulis, L. A., Smirnov, S., Ya, N. Q., Courtney, S. H., and Geacintov, N. E. (1995) Carcinogenesis 16, 357-365
63. Perlow, R. A., and Broyde, S. (2001) J. Mol. Biol. 309, 519-536
64. Perlow, R. A., and Broyde, S. (2002) J. Mol. Biol. 322, 291-309
65. Perlow, R. A., and Broyde, S. (2003) J. Mol. Biol. 327, 797-818
66. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242
67. Nair, D. T., Johnson, R. E., Prakash, S., Prakash, L., and Aggarwal, A. K. (2004) Nature 430, 377-380
68. Xie, X. M., Geacintov, N. E., and Broyde, S. (1999) Biochemistry 38, 2956-2968
69. Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., III, DeBolt, S., Ferguson, D. M., Seibel, G. L., and Kollman, P. A. (1995) Comp. Phys. Commun. 91, 1-41
70. Shibutani, S., Margulis, L. A., Geacintov, N. E., and Grollman, A. P. (1993) Biochemistry 32, 7531-7541
71. Chiapperino, D., Kroth, H., Kramarczuk, I. H., Sayer, J. M., Masutani, C., Hanaoka, F., Jerina, D. M., and Cheh, A. M. (2002) J. Biol. Chem. 277, 11765-11771
72. Kokoska, R. J., McCulloch, S. D., and Kunkel, T. A. (2003) J. Biol. Chem. 278, 50537-50545
73. Cosman, M., de los Santos, C., Fiala, R., Hingerty, B. E., Singh, S. B., Ibanez, V., Margulis, L. A., Live, D., Geacintov, N. E., Broyde, S., and Patel, D. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 1914-1918
74. Johnson, K. A. (1995) Methods Enzymol. 249, 38-61
75. Joyce, C. M., and Benkovic, S. J. (2004) Biochemistry 43, 14317-14324
76. Fiala, K. A., and Suo, Z. (2004) Biochemistry 43, 2116-2125
77. Cosman, M., Hingerty, B. E., Geacintov, N. E., Broyde, S., and Patel, D. J. (1995) Biochemistry 34, 15334-15350