Energetics of sequence-specific protein - DNA association: Conformational stability of the DNA binding domain of integrase Tn916 and its cognate DNA duplex

Biochemistry

Volumn 42, Issue 12, 2003, Pages 3492-3502

  Milev, Stoyan ^a   Gorfe, Alemayehu A ^a   Karshikoff, Andrey ^b   Clubb, Robert T ^c   Bosshard, Hans Rudolf ^a   Jelesarov, Ilian ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b KAROLINSKA INSTITUTE   (Sweden)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION REACTIONS; BACTERIA; CALORIMETRY; CONFORMATIONS; MOLECULAR VIBRATIONS; PROTEINS; SPECIFIC HEAT; SPECTROSCOPIC ANALYSIS;

THERMAL MOTIONS;

DNA;

DOUBLE STRANDED DNA; INTEGRASE;

ARTICLE; CALORIMETRY; HEATING; MOLECULAR RECOGNITION; MOLECULAR STABILITY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; SPECTROSCOPY; THERMODYNAMICS;

BASE SEQUENCE; BINDING SITES; CIRCULAR DICHROISM; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; ENERGY METABOLISM; ESCHERICHIA COLI; INTEGRASES; PROTEIN CONFORMATION; PROTEIN DENATURATION; PROTEIN STRUCTURE, TERTIARY; SPECTROMETRY, FLUORESCENCE; THERMODYNAMICS;

BACTERIA (MICROORGANISMS);

EID: 0037378835     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi026936x     Document Type: Article

References (34)

1. Scott, J. R., and Churchward, G. G. (1995) Annu. Rev. Microbiol. 49, 367-397.
2. Landy, A. (1989) Annu. Rev. Biochem. 58, 913-949.
3. Wojciak, J. M., Connolly, K. M., and Clubb, R. T. (1999) Nat. Struct. Biol. 6, 366-373.
4. Connolly, K. M., Wojciak, J. M., and Clubb, R. T. (1998) Nat. Struct. Biol. 5, 546-550.
5. Miley, S., Gorfe, A. A., Karshikoff, A., Clubb, R. T., Bosshard, H. R., and Jelesarov, I. (2003) Biochemistry 42, 3481-3491.
6. Marky, L. A., and Breslauer, K. J. (1987) Biopolymers 26, 16011620.
7. Privalov, P. L., and Potekhin, S. A. (1986) Methods Enzymol. 131, 4-51.
8. Freire, E., and Biltonen, R. L. (1978) Biopolymers 17, 463-479.
9. Freire, E. (1995) Methods Enzymol. 259, 144-169.
10. Kholodenko, V., and Freire, E. (1991) Anal. Biochem. 270, 336-338.
11. Karshikoff, A., and Ladenstein, R. (1998) Protein Eng. 11, 867-872.
12. Makhatadze, G. I., Medvedkin, V. N., and Privalov, P. L. (1990) Biopolymers 30, 1001-1010.
13. Hubbard, S. J., and Thornton, J. M. (1993). NACCESS, Computer Program, Department of Biochemistry and Molecular Biology, University College, London.
14. Murphy, K. P., and Freire, E. (1992) Adv. Protein Chem. 43, 313-361.
15. Makhatadze, G. I., and Privalov, P. L. (1995) Adv. Protein Chem. 47, 307-425.
16. Spolar, R. S., Livingstone, J. R., and Record, M. T., Jr. (1992) Biochemistry 31, 3947-55.
17. Darden, T. A., York, D. M., and Pedersen, L. J. (1993) J. Chem. Phys. 98, 10089-10092.
18. MacKerell, J., A. D., Bashford, D., Bellott, M., Dunbrack, R. L., Jr., 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. M., C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, I., W. E.; Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. A.-a. (1998) J. Phys. Chem. B 102, 3586-3616.
19. Brooks, B. R., Bruccorleri, R. E., Olafson, B. D., David, J. S., Swaminathan, S., and Karplus, M. (1983) J. Comput. Chem. 4, 187-217.
20. Perczel, A., Park, K., and Fasman, G. D. (1992) Proteins: Struct. Funct. Genet. 13, 57-69.
21. Gomez, J., Hilser, V. J., Xie, D., and Freire, E. (1995) Proteins 22, 404-412.
22. Privalov, P. L., and Makhatadze, G. I. (1990) J. Mol. Biol. 213, 385-391.
23. Amend, J. P., and Helgeson, H. C. (2000) Biophys. Chem. 84, 105-136.
24. Holbrook, J, A., Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (1999) Biochemistry 38, 8409-8422.
25. Jelesarov, I., Crane-Robinson, C., and Privalov, P. L. (1999) J. Mol. Biol. 294, 981-995.
26. Chalikian, T. V., Volker, J., Plum, G. E., and Breslauer, K. J. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 7853-7858.
27. Klump, H. (1990) in Landolt Börnstein Neue Serie Group VII (Saenger, W., Ed.) pp 241-256, Biophysik Springer, Berlin.
28. Rouzina, I., and Bloomfield, V. A. (1999) Biophys. J. 77, 3242-3251.
29. Viguera, A. R., Martinez, J. C., Filimonov, V. V., Mateo, P. L., and Serrano, L. (1994) Biochemistry 33, 2142-2150.
30. Battiste, J. L., Li, R. H., and Woodward, C. (2002) Biochemistry 41, 2237-2245.
31. Zavodszky, P., Kardos, J., Svingor, and Petsko, G. A. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 7406-7411.
32. Schellman, J. A. (1978) Biopolymers 17, 1305-1322.
33. Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Protein Sci. 4, 2138-48.
34. Ladbury, J. E., Sturtevant, J. M., and Leontis, N. B. (1994) Biochemistry 33, 6828-6833.