Thermodynamic Parameters of Specific and Nonspecific Protein-DNA Binding

Supramolecular Chemistry

Volumn 12, Issue 2, 2000, Pages 143-160

  Jen Jacobson, Linda ^a   Engler, Lisa E ^a   Ames, Jennifer T ^a   Kurpiewski, Michael R ^a   Grigorescu, Arabela ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

Enthalpy entropy compensation; Heat capacity change; Nonspecific protein DNA complexes; Specific protein DNA complexes; Thermodynamics

Indexed keywords

EID: 0034556938     PISSN: 10610278     EISSN: None     Source Type: Journal    
DOI: 10.1080/10610270008027446     Document Type: Article

References (62)

1. Jen-Jacobson, L. (1997). Biopoly. 44, 153.
2. Otwinowski, Z., Schevitz, R.W., Zhang, R.G., Lawson, C.L., Joachimiak, A., Marmostein, R.Q., Luisi, B.F., and Sigler, P. (1988). Nature. 335, 321.
3. Harrison, S.C. and Aggarwal, A.K. (1990). Annu. Rev. Biochem, 59, 933.
4. Lesser, D.R., Kurpiewski, M.R., and Jen-Jacobson, L. (1990). Science. 250, 776.
5. Kim, Y., Choi, J., Grable, J.C., Greene, P., Hager, P., and Rosenberg, J.M. (1994). In: Structural Biology: The State of the Art. Proc. of the Eighth Conversation, SUNY, Albany, R. Sarma and M. Sarma, (Eds). Adenine Press: New York. p. 225.
6. Dickerson, R.E. (1998). Nucl. Acids. Res. 26, 1906.
7. Engler, L.E. (1998). Ph.D. Thesis, University of Pittsburgh, Pittsburgh, PA.
8. Dickerson, R.E. (1998). In: Structure, Motion, Interaction and Expression of Biological Macromolecules, Proceedings of Tenth Conversation in Biomolecular Stereodynamics, R.H. Sarma and M.H. Sarma, (Eds). Academic Press: Schenectady, N.Y.
9. Rosenberg, J.M. (1991). Curr. Op. Struct. Biol. 1, 104.
10. Newman, M., Strzelecka, T., Domer, L.F., Schildkraut, I., and Aggarwal, A.K. (1995). Science. 269, 656.
11. Record, M.T., Jr, Ha, J.H., and Fisher, M.A. (1991). Meth Enzymol. 208, 291.
12. Spolar, R.S. and Record, M.T., Jr. (1994). Science, 263, 777.
13. Jayaram, B., McConnell, K.J., Dixit, S.B., and Beveridge, D.L. (1999). J. Comp. Phys., 151, 333.
14. Riggs, A.D., Suzuki, H., and Cohn, M. (1970). J. Mol. Biol. 48, 67.
15. Lin, S.-Y. and Riggs, A.D. (1972). J. Mol. Biol. 72, 671.
16. Ha, J.H., Spolar, R.S., and Record, M.T., Jr. (1989). J Mol Biol. 209, 801.
17. Ladbury, J.E., Wright, J.G., Sturtevant, J.M., and Sigler, P.B. (1994). J. Mol. Biol. 218, 669.
18. Hyre, D.E. and Spicer, L.D. (1995). Biochemistry. 34, 3212.
19. Merabet, E. and Ackers, G.K. (1995). Biochemistry. 34, 8554.
20. Petri, V., Hsieh, M., and Brenowitz, M. (1995). Biochemistry. 34, 9977.
21. Berger, C., Jelesarov, I., and Bosshard, H.R. (1996). Biochemistry. 35, 14984.
22. Frank, D.E., Saecker, R.M., Bond, J.P., Capp, M.W., Tsodikov, O.V., Melcher, S.E., Levandoski, M.M., and Record, M.T., Jr. (1997). J. Mol. Biol. 267, 1186.
23. Winkler, F.K., Banner, D.W., Oefner, C, Tsernoglou, D., Brown, R.S., Heathman, S.P., Bryan, R.K., Martin, P.D., Petratos, K., and Wilson, K.S. (1993). The EMBO Journal. 12, 1781.
24. Luisi, B., Xu, W.X., Otwinowski, Z., Freedman, L.P., Yamamoto, K.R., and Sigler, P.B. (1991). Nature. 352, 497.
25. Jen-Jacobson, L. (1995). Meth. Enzymol. 259, 305.
26. Takeda, Y., Ross, P.D., and Mudd, C.P. (1992). Proc. Natl. Acad. Sci. USA. 89, 8180.
27. Cao, D., Engler, L.E., and Jen-Jacobson, L. unpublished results.
28. Duan, Y., Wilkosz, P., and Rosenberg, J.M. (1996). J. Mol. Biol. 264, 546.
29. Kozlov, A.G. and Lohman, T.M. (1998). J. Mol. Biol. 278, 999.
30. Sturtevant, J.M. (1977). Proc. Natl. Acad. Sci. USA. 74, 2236.
31. Spolar, R.S., Livingstone, J.R., and Record, M.T., Jr (1992). Biochemistry. 31, 3947.
32. Murphy, K.P. and Freire, E. (1992). Adv. Prof. Chem. 43, 313.
33. Makhatadze, G.I. and Privalov, P.L. (1995). Adv. Prot. Chem. 47, 307.
34. Lundbäck, T., Cairns, C., Gustafsson, J.-A., Carlstedt-Duke, J., and Härd, T. (1993). Biochemistry, 32, 5074.
35. Morton, C.J. and Ladbury, J.E. (1996). Protein Science. 5, 2115.
36. Connelly, P.R. (1997). In: Thermodynamics and structure based drug design. R.G. Landes: Austin, TX.
37. Horvath, M., Choi, J., Kim, Y., Wilkosz, P.A., Chandresekhar, K., Grable, J.C., Greene, P., Hager, P., and Rosenberg, J.M. Proteins. Struct. Funct. Genet. submitted.
38. Karplus, P.A. and Faerman, C. (1994). Curr. Opin. Struct. Biol. 4, 770.
39. Dunitz, J.D. (1995). Chemistry & Biology. 2, 709.
40. Kurpiewski, M.R., Chi, D.J., and Jen-Jacobson, L., unpublished results.
41. Engler, L.E., Welch, K.K., and Jen-Jacobson, L. (1997). J. Mol. Biol. 269, 82.
42. Grable, J.C. (1990). Ph.D. Thesis, University of Pittsburgh, Pittsburgh, PA.
43. Becker, M.M., Lesser, D., Kurpiewski, M., Baranger, A., and Jen-Jacobson, L. (1988). Proc. Natl. Acad. Sci. 85.
44. Leroy, J.L., Charretier, E., Kochoyan, M., and Guéron, M. (1988). Biochemistry. 29, 4227.
45. Zhurkin, V.B., Ulyanov, N.B., Gorin, A.A., and Jernigan, R.L. (1991). Proc. Natl. Acad. Sci. USA. 88, 7046.
46. Kurpiewski, M.R., Koziolkiewicz, M., Wilk, A., Stec, W.J., and Jen-Jacobson, L. (1996). Biochemistry. 35, 8846.
47. Baldwin, R.L. (1986). Proc. Natl. Acad. Sci. 83, 8069.
48. Leffler, J.E. and Grunwald, E., Rates and Equilibria of Organic Reactions, Wiley, New York, 1963, reprinted by Dover, 1989.
49. Lumry, R. and Rajender, S. (1970). Biopolymers. 9, 1125.
50. Exner, O. (1973). Progr. Phys. Org. Chem. 10, 414.
51. Krug, R.R., Hunter, W.G., and Grieger, R.A. (1976). J. Phys. Chem. 80, 2335.
52. Tomlinson, E. (1983). Int. J. Pharmaceutics. 13, 115.
53. Eftink, M.R., Anusiem, A.C., and Biltonen, R.L. (1983). Biochemistry. 22, 3884.
54. Searle, M.S., Westwell, M.S., and Williams, D.H. (1995). J. Chem. Soc. Perkin Trans. 2, 141.
55. Grunwald, E. and Comeford, L.L In: Protein-Solvent Interactions, R.B. Gregory, (Ed.), Marcel Dekker, Inc, New York, 1995, p. 421.
56. Lundback, T. and Hard, T. (1996). Proc. Natl. Acad. Sci. USA. 93, 4754.
57. Krug, R.R., Hunter, W.G., and Grieger, R.A. (1976). J. Phys. Chem. 80, 2341.
58. Linert, W. (1994). Chem. Soc. Rev. 23, 429.
59. Jen-Jacobson, L., Kurpiewski, M., Lesser, D., Grable, J.C., Boyer, H.W., Rosenberg, J.M., and Greene, P.J. (1983). J. Biol. Chem. 258, 14638.
60. Jack, W.E., Greenough, L., Dorner, L.F., Xu, S.-Y., Strzelecka, T., Aggarwal, A.K., and Schildkraut, I. (1991). Nucl. Acids Res. 19, 1825.
61. Lesser, D.R., Grajkowski, A., Kurpiewski, M.R., Koziolkiewicz, M., Stec, W.J., and Jen-Jacobson, L. (1992). J. Biol. Chem. 267, 24810.
62. Wiseman, T., Williston, S., Brandts, J.F., and Lin, L.N. (1989). Anal. Biochem. 179, 131.