Kinetic mechanism of nucleotide cofactor binding to Escherichia coli replicative helicase DnaB protein. Stopped-flow kinetic studies using fluorescent, ribose-, and base-modified nucleotide analogues

Biochemistry

Volumn 39, Issue 8, 2000, Pages 2106-2122

  Bujalowski, Wlodzimierz ^a   Jezewska, Maria J ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

1,N6 ETHENOADENOSINE TRIPHOSPHATE; ADENOSINE DIPHOSPHATE; ADENOSINE PHOSPHATE; ADENOSINE TRIPHOSPHATE; ADENYLYLIMIDODIPHOSPHATE; FLUORESCENT DYE; HELICASE; NUCLEIC ACID BASE; NUCLEOTIDE DERIVATIVE; RIBOSE;

ARTICLE; CHEMICAL REACTION KINETICS; CONFORMATIONAL TRANSITION; DIFFUSION; DNA REPLICATION; EQUILIBRIUM CONSTANT; ESCHERICHIA COLI; FLUORESCENCE; ISOMERISM; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS;

ADENOSINE DIPHOSPHATE; ADENYLYL IMIDODIPHOSPHATE; ANTHRANILIC ACIDS; BACTERIAL PROTEINS; COMPUTER SIMULATION; DNA HELICASES; DNAB HELICASES; DOSE-RESPONSE RELATIONSHIP, DRUG; ESCHERICHIA COLI; FLUORESCENT DYES; KINETICS; MODELS, CHEMICAL; MODELS, STATISTICAL; NUCLEOTIDES; PROTEIN CONFORMATION; RIBOSE; SPECTROMETRY, FLUORESCENCE; THERMODYNAMICS; TIME FACTORS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0034728364     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi992413m     Document Type: Article

References (45)

1. Kornberg, A., and Baker, T. A. (1992) DNA Replication, Freeman, San Francisco.
2. Matson, S. W., and Kaiser-Rogers, K. A. (1990) Annu. Rev. Biochem. 59, 289-329.
3. LeBowitz, J. H., and McMacken, R. (1986) J. Biol. Chem. 261, 4738-4748.
4. Baker, T. A., Funnell, B. E., and Kornberg, A. (1987) J. Biol. Chem. 262, 6877-6885.
5. Reha-Krantz, L. J., and Hurwitz, J. (1978) J. Biol. Chem. 253, 4051-4057.
6. Bujalowski, W., Klonowska, M. M., and Jezewska, M. J. (1994) J. Biol. Chem. 269, 31350-31358.
7. Jezewska, M. J., and Bujalowski, W. (1996) J. Biol. Chem. 271, 4261-4265.
8. San Martin, M. C., Stamford, N. P. J., Dammerova, N., Dixon, N. E., and Carazo, J. M. (1995) J. Struct. Biol. 114, 167-176.
9. Yu, X., Jezewska, M. J., Bujalowski W., and Egelman, E. H. (1996) J. Mol. Biol. 259, 7-14.
10. Jezewska, M. J., Kim, U.-S., and Bujalowski, W. (1996) Biochemistry 36, 2129-2145.
11. Jezewska, M. J., and Bujalowski, W. (1996a) Biochemistry 35, 2117-2128.
12. Bujalowski, W., and Jezewska, M. J. (1995) Biochemistry 34, 8513-8519.
13. Jezewska, M. J., Rajendran, S., and Bujalowski, W. (1997) Biochemistry 36, 10320-10326.
14. Jezewska, M. J., Rajendran, S., and Bujalowski, W. (1998) Biochemistry 37, 3116-3136.
15. Jezewska, M. J., Rajendran S., and Bujalowski, W. (1998) J. Biol. Chem. 273, 9058-9069.
16. Jezewska, M. J., Rajendran S., Bujalowska, D., and Bujalowski, W. (1998) J. Biol. Chem. 273, 10515-10529.
17. Lohman, T. M., and Bjorson, K. P. (1996) Annu. Rev. Biochem. 65, 169-214.
18. Arai, K., and Kornberg, A. (1981) J. Biol. Chem. 256, 5260-5266.
19. Bujalowski, W., and Klonowska, M. M. (1993) Biochemistry 32, 5888-5900.
20. Bujalowski, W., and Klonowska, M. M. (1994) Biochemistry 33, 4682-4694.
21. Bujalowski, W., and Klonowska, M. M. (1994) J. Biol. Chem. 269, 31359-31371.
22. Jezewska, M. J., Kim U.-S., and Bujalowski W. (1996) Biophys. J. 71, 2075-2086.
23. Secrist, J. A., Bario, J. R., Leonard, N. J., and Weber, G. (1972) Biochemistry 11, 3499-3506.
24. Hiratsuka, T. (1983) Biochim. Biophys. Acta 742, 496-508.
25. Pilar, F. L. (1968) Elementary Quantum Cemistry, Chapter 9, McGraw-Hill, New York.
26. Bernasconi, C. F. (1976) Relaxation Kinetics, Academic Press, New York.
27. Fraser, R. A., Duncan, W. J., and Collar, A. R. (1965) Elementary Matrixes and Some Applications to Dynamics and Differential Equations, Cambridge University Press.
28. Jezewska, M. J., and Bujalowski, W. (1997) Biophys. Chem. 64, 253-269.
29. Moore, J. K., and Lohman, T. M. (1994) Biochemistry 33, 14550-14564.
30. Moore, J. K., and Lohman, T. M. (1994) Biochemistry 33, 14565-14578.
31. Berry, R. S., Rice, S. A., and Ross, J. (1980) Physical Chemistry, J. Wiley & Sons, New York.
32. Moore, J. W., and Pearson, R. G. (1981) Kinetics and Mechanism, J. Wiley & Sons, New York.
33. Lakowicz, J. R. (1999) Principle of Fluorescence Spectroscopy, Kluwer Academic/Plenum Publishers.
34. Hammes, G. G., and Schimmel, P. R. (1970) The Enzymes. Kinetics and Mechanism, Vol. II, Chapter 2, Academinc Press, New York.
35. Baker, B. M., Vanderkooi, J., and Kallenbach, N. R. (1978) Base Stacking in a Fluorescent Dinucleotiside Monophosphate: ∈Ap∈A. Biopolymers 17, 1361-1372.
36. Jencks, W. P. (1980) Adv. Enzymol. 51, 75-106.
37. Dong, F., Gogol, E. P., and von Hippel, P. H. (1995) J. Biol. Chem. 270, 7462-7473.
38. Egelman, E. H., Yu, X., Wild, R., Hingorani, M. M., and Patel, S. S. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 3869-3873.
39. Hacker, K. J., and Johnson, K. A. (1997) Biochemistry 36, 14080-14087.
40. Bjorson, K. P., Moore, K. J., and Lohman, T. M. (1996) Biochemistry 35, 2268-2282.
41. Bjorson, K. P., Hsieh, J., Amaratunga, M., and Lohman, T. M. (1998) Biochemistry 37, 891-899.
42. Wong, I., Moore, K. J., Bjorson, K. J., Hsieh, J., and Lohman, T. M. (1996) Biochemistry 35, 5726-5734.
43. Bujalowski, W., Greaser, E., McLaughlin, L. W., and Porschke, D. (1986) Biochemistry 25, 6365-6378.
44. Bujalowski, W., Jung, M., McLaughlin, L. W., and Porschke, D. (1986) Biochemistry 25, 6372-6371.
45. San Martin, C., Radermacher, M., Wolpensinger, B., Engel, A., Miles, C. S., Dixon, N. E., and Carazo, J. M. (1998) Structure 6, 501-509.