Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state

Biopolymers

Volumn 44, Issue 2, 1997, Pages 153-180

  Jen Jacobson, Linda ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Adaptation; Binding energy; Enzyme catalysis; Nonspecific binding; Protein DNA recognition; Sequence specific binding; Thermodynamics; Transition state

Indexed keywords

BINDING ENERGY; CATALYSIS; ENZYME INHIBITION; FREE ENERGY; SUBSTRATES;

SEQUENCE SPECIFIC BINDING;

DNA;

TRANSCRIPTION FACTOR;

CATALYSIS; DNA PROTEIN COMPLEX; ENZYME SUBSTRATE; HUMAN; NONHUMAN; PROTEIN DNA BINDING; REVIEW; STRUCTURE ANALYSIS; THERMODYNAMICS;

BASE SEQUENCE; BINDING SITES; DEOXYRIBONUCLEASE BAMHI; DEOXYRIBONUCLEASE ECORI; DNA; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 0030736323     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0282(1997)44:2<153::aid-bip4>3.3.co;2-v     Document Type: Article

References (36)

1. von Hippel, P. H. & McGhee, J. D. (1972) Ann. Rev. Biochem. 41, 231-300.
2. Lin, S.-Y. & Riggs, A. D. (1975) Cell 4, 107-111.
3. von Hippel, P. H. & Berg, O. G. (1986) Proc. Natl. Acad. Sci. USA 83, 1608-1612.
4. Record, M. T., Jr. & Spolar, R. S. (1990) in Nonspecific DNA-Protein Interactions, Revzin, A., Ed., CRC Press, Boca Raton, FL, pp. 33-69.
5. von Hippel, P. H. (1994) Science 263, 769-770.
6. Lesser, D. R., Kurpiewski, M. R. & Jen-Jacobson, L. (1990) Science 250, 776-786.
7. Engler, L. E., Welch, K. K. & Jen-Jacobson, L. (1997) J. Mol. Biol. 269, 82-101.
8. Siebenlist, U. & Gilbert, W. (1980) Proc. Natl. Acad. Sci. USA 77, 122-126.
9. Jen-Jacobson, L. (1995) Methods Enzymol. 259, 305-344.
10. Thielking, V., Alves, J., Fliess, A., Maass, G. & Pingoud, A. (1990) Biochemistry 29, 4682-4691.
11. Mossing, M. C. & Record, M. T., Jr. (1985) J. Mol. Biol. 186, 295-305.
12. Frank, D. E., Saecker, R. M., Bond, J. P., Capp, M. W., Todikov, O. V., Melcher, S. E., Levandoski, M. M. & Record, M. T., Jr. (1997) J. Mol. Biol. 267, 1186-1206.
13. Jen-Jacobson, L., Lesser, D. R. & Kurpiewski, M. R. (1991) in Nucleic Acids and Molecular Biology, Vol. 5, Eckstein, F. & Lilley, D. M. J., Eds., Springer-Verlag, Heidelberg, pp. 141-170.
14. Record, M. T., Jr., Lohman, T. M. & deHaseth, P. L. (1976) J. Mol. Biol. 107, 145-158.
15. Record, M. T., Jr., Ha, J.-H. & Fisher, M. A. (1991) Methods Enzymol. 208, 291-343.
16. Terry, B. J., Jack, W. E., Rubin, R. A. & Modrich, P. (1983) J. Biol. Chem. 258, 9820-9825.
17. Jen-Jacobson, L., Kurpiewski, M., Lesser, D., Grable, J., Boyer, H. W., Rosenberg, J. M. & Greene, P. J. (1983) J. Biol. Chem. 258, 14638-14646.
18. Senear, D. F. & Ackers, G. K. (1990) Biochemistry 29, 6568-6577.
19. Ha, J.-H., Spolar, R. S. & Record, M. T., Jr. (1989) J. Mol. Biol. 209, 801-816.
20. Takeda, Y., Ross, P. D. & Mudd, C. P. (1992) Proc. Natl. Acad. Sci. USA 89, 8180-8184.
21. Jin, L., Yang, J. & Carey, J. (1993) Biochemistry 32, 7302-7309.
22. Ladbury, J. E., Wright, J. G., Sturtevant, J. M. & Sigler, P. B. (1994) J. Mol. Biol. 218, 669-681.
23. Hyre, D.E. & Spicer, L. D. (1995) Biochemistry 34, 3212-3221.
24. Merabet, E. & Ackers, G. K. (1995) Biochemistry 34, 8554-8563.
25. Lundbäck, T. & Hard, T. (1996) Proc. Natl. Acad. Sci. USA 93, 4754-4759.
26. Petri, V., Hsieh, M. & Brenowitz, M. (1995) Biochemistry 34, 9977-9984.
27. Parsegian, V. A., Rand, R. P. & Rau, D. C. (1995) Methods Enzymol. 259, 43-94.
28. Garner, M. M. & Rau, D. C. (1995) EMBO J. 14, 1257-1263.
29. Sidorova, N. Y. & Rau, D. C. (1996) Proc. Natl. Acad. Sci. USA 93, 12272-12277.
30. Senear, D. F. & Batey, R. (1991) Biochemistry 30, 6677-6688.
31. von Hippel, P. H. (1979) in Biological Regulation and Development, Vol. 1, Goldberger, R. F., Ed., Plenum Press, N.Y., pp. 279-347.
32. Yang, S.-W. & Nash, H. A. (1995) EMBO J. 14, 6292-6300.
33. Seeman, N. C., Rosenberg, J. M. & Rich, A. (1976) Proc. Natl. Acad. Sci. USA 73, 804-808.
34. Rosenberg, J. M. & Greene, P. (1982) DNA 1, 117-124.
35. Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. (1988) Science 242, 899-907.
36. Harrison, S. C. & Aggarwal, A. K. (1990) Ann. Rev. Biochem. 59, 933-969.