Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: Thermodynamic analysis of effects of coulombic interactions and α-helix induction

Biochemistry

Volumn 36, Issue 17, 1997, Pages 5193-5206

  Padmanabhan, S ^a   Zhang, Wentao ^a   Capp, Michael W ^a   Anderson, Charles F ^a   Record Jr , M Thomas ^a,b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b INSTITUTO DE ESTRUCTURA DE LA MATERIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; DNA BINDING PROTEIN; DOUBLE STRANDED DNA; GLYCINE; OLIGOPEPTIDE;

AMINO ACID SUBSTITUTION; ANIMAL CELL; ARTICLE; BASE PAIRING; BINDING AFFINITY; BINDING KINETICS; BINDING SITE; CATTLE; CONFORMATIONAL TRANSITION; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; THERMODYNAMICS;

ALANINE; AMINO ACID SEQUENCE; CIRCULAR DICHROISM; DNA; GLYCINE; KINETICS; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; OLIGOPEPTIDES; PROTEIN CONFORMATION; THERMODYNAMICS;

ANIMALIA; BOS TAURUS;

EID: 0030917624     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi962927a     Document Type: Article

References (64)

1. Allen, F. S., Gray, D. M., Roberts, G. P., & Tinoco, I. J. (1972) Biopolymers 11, 853-879.
2. Anderson, C. F., & Record, M. T. Jr. (1983) In Structure and Dynamics: Nucleic Acids and Proteins Clementi, E., & Sarma, R., Eds.) pp 301-319, Adenine Press, New York.
3. Anderson, C. F., & Record, M. T., Jr. (1993) J. Phys. Chem. 97, 7116-7126.
4. Anderson, C. F., & Record, M. T., Jr. (1995) Annu. Rev. Phys. Chem. 46, 657-700.
5. Arrowsmith, C. H., Pachter, R., Altman, R. B., Lyer, S. B., & Jardetzky, O. (1990) Biochemistry 29, 6332-6341.
6. Baldwin, R. L. (1995) Biophys. Chem. 55, 127-135.
7. Bleam, M. L., Anderson, C. F., & Record, M. T., Jr. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 3085-3089.
8. Braunlin, W. H., Strick, W. H., & Record, M. T., Jr. (1982) Biopolymers 21, 1301-1314.
9. Braunlin, W. H., Anderson, C. F., & Record, M. T., Jr. (1987) Biochemistry 26, 7724-7731.
10. Chakrabartty, A., Kortemme, T., Padmanabhan, S., & Baldwin, R. L. (1993) Biochemistry 32, 5560-5565.
11. Chakrabartty, A., Kortemme, T., & Baldwin, R. L. (1994) Protein Sci. 3, 843-852.
12. Chan, S. C., Breslauer, K. J., Hogan, M. E., Kessler, D. J., Austin, R. H., Ojemann, J., Passner, J. M., & Wiles, N. C. (1990) Biochemistry 29, 6161-6171.
13. Chen, G. C., & Yang, J. T. (1977) Anal. Lett. 10, 1195-1207.
14. Doig, A. J., & Baldwin, R. L. (1995) Protein Sci. 4, 1325-1336.
15. Doig, A. J., Chakrabartty, A., & Baldwin, R. L. (1994) Biochemistry 33, 3396-3403.
16. Edelhoch, H. (1967) Biochemistry 6, 1948-1954.
17. Holzwarth, G., & Doty, P. (1965) J. Am. Chem. Soc. 87, 218-228.
18. Houghten, R. A. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 5131-5135.
19. Houghten, R. A., Degraw, S. T., Bray, M. K., Hoffman, S. R., & Frizell, N. D. (1986) BioTechniques 4, 522-528.
20. Jen-Jacobson, L., Lesser, D., & Kurpiewski, M. (1986) Cell 45, 619-629.
21. Johnson, M. L., & Frasier, S. G. (1985) Methods Enzymol. 117, 301-342.
22. Johnson, N. P., Lindstrom, J., Baase, W. A., & von Hippel, P. H. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 4840-4845.
23. Latt, S. A., & Sober, H. A. (1967a) Biochemistry 6, 3293-3306.
24. Latt, S. A., & Sober, H. A. (1967b) Biochemistry 6, 3307-3314.
25. Lewis, M., Chang, G., Horton, N. C., Kercher, M. A., Pace, H. C., Schumacher, M. A., Brennan, R. G., & Lu, P. (1996) Science 271, 1247-1254.
26. Lifson, S., & Roig, A. (1961) J. Chem. Phys. 34, 1963-1974.
27. Lohman, T. M., & Mascotti, D. P. (1992) Methods Enzymol. 212, 424-458.
28. Lohman, T. M., deHaseth, P. L., & Record, M. T., Jr. (1980) Biochemistry 19, 3522-3530.
29. Manning, G. S. (1978) Q. Rev. Biophys. 11, 179-246.
30. Marqusee, S., & Baldwin, R. L. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8898-8902.
31. Mascotti, D. P., & Lohman, T. M. (1990) Proc. Nat. Acad. Sci. U.S.A. 87, 3142-3146.
32. Mascotti, D. P., & Lohman, T. M. (1992) Biochemistry 31, 8932-8946.
33. Mascotti, D. P., & Lohman, T. M. (1993) Biochemistry 32, 10568-10579.
34. Mascotti, D. P., & Lohman, T. M. (1995) Biochemistry 34, 2908-2915.
35. McClarin, J. A., Frederick, C. A., Wang, B.-C., Greene, P., Boyer, H. W., Grable, J., & Rosenberg, J. M. (1986) Science 234, 1526-1541.
36. McGhee, J. D., & von Hippel, P. H. (1974) J. Mol. Biol. 86, 469-489.
37. Misra, V. K. , Sharp, K. A., Friedman, R. A., & Honig, B. (1994) J. Mol. Biol. 238, 245-263.
38. Nelson, J. W., & Kallenbach, N. R. (1986) Proteins 1, 211-217.
39. Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I., & Aggarwal, A. (1995) Science 269, 656-663.
40. Olmsted, M. C., Anderson, C. F., & Record, M. T., Jr. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 7766-7770.
41. Olmsted, M. C., Bond, J. P., Anderson, C. F., & Record, M. T., Jr. (1995) Biophys. J. 68, 634-647.
42. O'Neil, K. T., Hoess, R. H., & DeGrado, W. F. (1990) Science 249, 774-778.
43. O'Neil, K. T., Shuman, J. D., Ampe, C., & DeGrado, W. F. (1991) Biochemistry 30, 9030-9034.
44. Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., & Baldwin, R. L. (1990) Nature 344, 268-270.
45. Padmanabhan, S., Brushaber, V. M., Anderson, C. F., & Record, M. T., Jr. (1991) Biochemistry 30, 7550-7559.
46. Percipalle, P., Simonscits, A., Zakhariev, S., Guarnaccia, C., Sanchez, R., & Pongor, S. (1995) EMBO J. 14, 3200-3205.
47. Plum, G. E., & Bloomfield, V. A. (1988) Biopolymers 27, 1045-1051.
48. Qian, H., & Schellman, J. A. (1992) J. Phys. Chem. 96, 3987-3994.
49. Record, M. T., Jr., & Anderson, C. F. (1995) Biophys. J. 68, 786-794.
50. Record, M. T., Jr., Lohman, T. M., & de Haseth, P. (1976) J. Mol. Biol. 107, 145-158.
51. Record, M. T., Jr., Anderson, C. F., & Lohman, T. M. (1978) Q. Rev. Biophys. 11, 103-178.
52. Record, M. T., Jr., Ha, J.-H., & Fisher, M. A. (1991) Methods Enzymol. 208, 291-343.
53. Rouzina, I., & Bloomfield, V. A. (1996) J. Phys. Chem. 100, 4292-4304.
54. Schellman, J. A. (1975) Biopolymers 14, 999-1018.
55. Scholtz, J. M., Qian, H., York, E. J., Stewart, J. M., & Baldwin, R. L. (1991a) Biopolymers 31, 1463-1470.
56. Scholtz, J. M., Marqusee, S., Baldwin, R. L., York, E. J., Stewart, J. M., Santoro, M., & Bolen, W. (1991b) Proc. Natl. Acad. Sci. U.S.A. 88, 2854-2858.
57. Scholtz, J., M., York, E. J., Stewart, J. M., & Baldwin, R. L. (1991c) J. Am. Chem. Soc. 113, 5103-5104.
58. Sharp, K. A. (1995) Biopolymers 36, 227-243.
59. Spolar, R. S., & Record, M. T., Jr. (1994) Science 263, 777-784.
60. Stein, V. M., Bond, J. P., Capp, M. W., Anderson, C. F., & Record, M. T., Jr. (1995) Biophys. J. 68, 1063-1072.
61. Talanian, R. V., McKnight, C. J., & Kim, P. S. (1990) Science 249, 769-771.
62. Wang, L., Ferrari, M., & Bloomfield, V. A. (1990) BioTechniques 9, 24-27.
63. Zhang, H., Zhao, D., Revington, M., Lee, W., Jia, X., Arrowsmith, C., & Jardetzky, O. (1994) J. Mol. Biol. 238, 592-614.
64. Zhang, W., Bond, J. P., Anderson, C. F., Lohman, T. M., & Record, M. T., Jr. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 2511-2516.