Rat polymerase β binds double-stranded DNA using exclusively the 8-kDa domain. Stoichiometries, intrinsic affinities, and cooperativities

Biochemistry

Volumn 42, Issue 19, 2003, Pages 5955-5970

  Jezewska, Maria J ^a   Galletto, Roberto ^a   Bujalowski, Wlodzimierz ^a  

^a University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENCE ENERGY TRANSFER;

BINDING ENERGY; CONFORMATIONS; DNA; ENERGY TRANSFER; FLUORESCENCE; TITRATION;

ENZYMES;

DOUBLE STRANDED DNA;

ARTICLE; BINDING AFFINITY; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DNA ADDUCT; DNA BINDING; DNA REPAIR; DNA SYNTHESIS; MISMATCH REPAIR; MOLECULAR INTERACTION; NONHUMAN; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN DOMAIN; RECEPTOR AFFINITY; RESIDUE ANALYSIS; STOICHIOMETRY; THERMODYNAMICS;

ANIMALS; BASE SEQUENCE; BINDING SITES; DNA; DNA POLYMERASE BETA; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; MACROMOLECULAR SUBSTANCES; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR WEIGHT; PROTEIN STRUCTURE, TERTIARY; RATS; THERMODYNAMICS; TRYPTOPHAN;

EID: 0038290256     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi030046f     Document Type: Article

References (50)

1. Friedberg, E. C., Walker, G. C., and Siede, W. (1995) DNA Repair and Mutagenesis, pp 317-365, ASM Press, Washington, DC.
2. Kornberg, A., and Baker, T. A. (1992) DNA Replication, pp 197-225, W. H. Freeman, New York.
3. Budd, M. E., and Campbell, J. L. (1997) Mutat. Res. 384, 157-167.
4. Fry, M., and Loeb, L. A. (1986) Animal Cell DNA Polymerases, pp 75-183, CRC Press, Inc., Boca Raton, FL.
5. Hubscher, U., Nasheuer, H.-P., and Syvaoja, J. E. (2000) Trends Biochem. Sci. 25, 143-147.
6. Masumoto, Y., and Kim, K. (1995) Science 269, 699-702.
7. Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., and Kraut, J., (1996) Biochemistry 35, 12762-12777.
8. Nagasawa, K.-I., Kitamura, K., Yasui, A., Nimura, Y., Ikeda, K., Hirai, M., Matsukage, A., and Nakanishi, M. (2000) J. Biol. Chem. 275, 31233-31238.
9. Dominguez, O., Ruiz, J. F., Lain de Lera, T., Garcia-Diaz, M., Gonzalez, M. A., Kirchhoff, T., Martinez, A. C., Bernad, A., and Blanco, L. (2000) EMBO J. 19, 1731-1742.
10. Garcia-Diaz, M., Dominguez, O., Lopez-Fernandez, L. A., Lain de Lera, T., Saniger, M. L., Ruiz, J. F., Parraga, M., Gacia-Ortiz, M. J., Kirchhoff, T., del Mazo, J., Bernad, A., and Blanco, L. (2000) J. Mol. Biol. 301, 851-867.
11. Oliveros, M., Yanez, R. J., Salas, M. L., Vinuela, E., and Blanco, L. (1997) J. Biol. Chem. 272, 30899-30910.
12. Rajendran, S., Jezewska, M. J., and Bujalowski, W. (1998) J. Biol. Chem. 273, 31021-31031.
13. Jezewska, M. J., Rajendran, S., and Bujalowski, W. (1998) J. Mol. Biol. 284, 1113-1131.
14. Rajendran, S., Jezewska, M. J., and Bujalowski, W. (2001) J. Mol. Biol. 308, 477-500.
15. Jezewska, M. J., Rajendran, S., and Bujalowski, W. (2001) J. Biol. Chem. 276, 16123-16136.
16. Jezewska, M. J., Rajendran, S., and Bujalowski, W. (2001) Biochemistry 40, 3295-3307
17. Matsumoto, Y., Kim, K., Katz, D. S., and Feng, J.-A. (1998) Biochemistry 37, 6456-6464.
18. Jezewska, M. J., Rajendran, S., Galletto, R., and Bujalowski, W. (2001) J. Mol. Biol. 313, 977-1002.
19. Rajendran, S., Jezewska, M. J., and Bujalowski, W. (2001) Biochemistry 40, 11794-11810.
20. Jezewska, M. J., Galletto, R., and Bujalowski, W. (2002) J. Biol. Chem. 277, 20316-20327.
21. Edeldoch, H. (1967) Biochemistry 6, 1948-1954.
22. Gill, S. C., and von Hippel, P. H. (1989) Anal. Biochem. 182, 319-326.
23. Jezewska, M. J., Rajendran, S., and Bujalowski, W. (1998) Biochemistry 37, 3116-3136.
24. Jezewska, M. J., Rajendran S., and Bujalowski, W. (1998) J. Biol. Chem. 273, 9058-9069.
25. Jezewska, M. J., Rajendran, S., Bujalowska, D., and Bujalowski, W. (1998) J. Biol. Chem. 273, 10515-10529.
26. Azumi, T., and McGlynn, S. P. (1962) J. Chem. Phys. 37, 2413-2420.
27. Lakowicz, J. R. (1999) Principle of Fluorescence Spectroscopy, pp 367-443, Plenum Press, New York.
28. Parker, C. A., and Reese, W. T. (1960) Analyst 85, 587-592.
29. Parker, C. A. (1962) Anal. Chem. 34, 502-505.
30. Scott, T. G., Spencer, R. D., Leonard, N. J., and Weber, G. (1970) J. Am. Chem. Soc. 92, 687-695.
31. Berman, H. A., Yguerabide, J., and Taylor, P. (1980) Biochemistry 19, 2226-2235.
32. Dale, R. E., Esinger, J., and Blumberg, W. E. (1979) Biophys. J. 26, 161-194.
33. Lohman, T. M., and Bujalowski, W. (1991) Methods Enzymol. 208, 258-290.
34. Bujalowski, W., and Klonowska, M. M. (1993) Biochemistry 32, 5888-5900.
35. Jezewska, M. J., and Bujalowski, W. (1996) Biochemistry 35, 2117-2128.
36. Bujalowski, W., and Jezewska, M. J. (1995) Biochemistry 34, 8513-8519.
37. Bujalowski, W., and Jezewska, M. J. (2000) in Spectrophotometry & Spectrofluorimetry. A Practical Approach (Gore, M. G., Ed.). pp 141-165, Oxford University Press, Oxford, U.K.
38. Hill, T. L. (1985) Cooperativity Theory in Biochemistry, pp 167-234, Springer-Verlag, New York.
39. Epstein, I. R. (1978) Biophys. Chem. 8, 327-339.
40. McGhee, J. D., and von Hippel, P. H. (1974) J. Mol. Biol. 86, 469-489.
41. Bujalowski, W., Lohman, T. M., and Anderson, C. F. (1989) Biopolymers 28, 1637-1643.
42. Record, M. T., Jr., Anderson, C. F., and Lohman, T. M. (1978) Q. Rev. Biophys. 11, 103-178.
43. Record, M. T., Lohman, T. M., and deHaseth, P. L. (1976) J. Mol. Biol. 107, 145-158.
44. Olmsted, M. C., Bond, J. P., Anderson, C. F., and Record, M. T. (1995) Biophys. J. 68, 634-647.
45. Cantor, C. R., and Schimmel, P. R. (1980) Biophysical Chemistry, Part II, pp 433-466, W. H Freeman and Company, New York.
46. Eftink, M. R., Selvidge, L. A., Callis, P. R., and Rehms, A. A. (2000) J. Phys. Chem. 94, 3469-3479.
47. Doherty, A. J., Serpell, L. C., and Ponting, C. P. (1996) Nucleic Acids Res. 24, 2488-2497.
48. von Hippel, P. H., and Schleich T. (1969) in Structure of Biological Macromolecules (Timasheff, S., Fasman G. D., Eds.), pp 417-575, M. Dekker, New York.
49. Manning, G. (1978) Q. Rev. Biophys. 11, 103-178.
50. Zhong, X., Patel, S. S., Werneburg, B. G., and Tsai, M.-D. (1997) Biochemistry 36, 11891-11900.