Control of oxidation-reduction potentials in flavodoxin from Clostridium beijerinckii: The role of conformation changes

Biochemistry

Volumn 36, Issue 6, 1997, Pages 1259-1280

  Ludwig, Martha L ^a   Pattridge, Katherine A ^a   Metzger, Anita L ^a   Dixon, Melinda M ^a   Eren, Mesut ^b   Feng, Yucheng ^b   Swenson, Richard P ^b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; FLAVODOXIN; MUTANT PROTEIN;

ARTICLE; BINDING SITE; CLOSTRIDIUM; CRYSTAL STRUCTURE; ELECTRON TRANSPORT; ENERGY TRANSFER; HYDROGEN BOND; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; CLOSTRIDIUM; CRYSTALLOGRAPHY, X-RAY; FLAVIN MONONUCLEOTIDE; FLAVINS; FLAVODOXIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; OXIDATION-REDUCTION; PROTEIN CONFORMATION; SPECTROPHOTOMETRY, ATOMIC; SPECTROPHOTOMETRY, ULTRAVIOLET; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0031024423     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi962180o     Document Type: Article

References (86)

1. Alexandrescu, A. T., Ulrich, E. L., & Markley, J. L. (1989) Biochemistry 28, 204-211.
2. Amman, E., Brosious, J., & Ptashne, M. (1983) Gene 25, 167-178.
3. Anderson, A. G., & Hermans, J. (1988) Proteins: Struct., Funct., and Genet. 3, 262-265.
4. Anderson, R. F. (1983) Biochim. Biophys. Acta 722, 158-162.
5. Brünger, A. T. (1992) X-PLOR, Version 3.1, Yale University, New Haven, CT.
6. Brünger, A. T., Krukowski, A., & Erickson, J. (1990) Acta Crystallogr. A 46, 585-593.
7. Bull, C., & Ballou, D. P. (1988) J. Biol. Chem. 256, 12673-12680.
8. Burkhart, B. M., Ramakrishnan, B., Yan, H., Reedstom, R. J., Markley, J. L., Straus, N. A., & Sundaralingam, M. (1995) Acta Crystallogr. D 51, 318-330.
9. Burnett, R. M., Darling, G. D., Kendall, D. S., LeQuesne, M. E., Mayhew, S. G., Smith, W. W., & Ludwig, M. L. (1974) J. Biol. Chem. 249, 4383-4392.
10. Caldeira, J., Palma, P. N., Regalla, M., Lampreia, J., Calvete, J., Schafer, W., LeGall, J., Moura, I., & Moura, J. J. (1994) Eur. J. Biochem. 220, 987-995.
11. Cambillau, C., & Horjales, E. (1987) J. Mol. Graphics 5, 174-177.
12. Cheng, H. N., & Bovey, F. A. (1977) Biopolymers 16, 1465-1472.
13. Clark, W. M. (1972) Oxidation-Reduction Potentials of Organic Systems, Robert E. Krieger Publishing Co., Huntington, NY.
14. Correll, C. C. (1992) Ph.D. Thesis, University of Michigan, Ann Arbor, MI.
15. Draper, R. D., & Ingraham, L. L. (1968) Arch. Biochem. Biophys. 125, 802-808.
16. Dutton, P. L., & Wilson, D. F. (1974) Biochim. Biophys. Acta 346, 165-212.
17. Eaton, W. A., Hofrichter, J., Makinen, M. W., Andersen, R. D., & Ludwig, M. L. (1975) Biochemistry 14, 2146-2151.
18. Eberhardt, E. S., Loh, S. N., Hinck, A. P., & Raines, R. T. (1992) J. Am. Chem. Soc. 114, 5437-5439.
19. Engh, R. A., & Huber, R. (1991) Acta Crystallogr. A 47, 392-400.
20. Eren, M., & Swenson, R. P. (1989) J. Biol. Chem. 264, 14874-14879.
21. Fox, R. O., Evans, P. A., & Dobson, C. M. (1986) Nature 320, 192-194.
22. Franken, H.-D., Ruterjans, H., & Müller, F. (1984) Eur. J. Biochem. 138, 481-489.
23. Fukuyama, K., Wakabayashi, S., Matsubara, H., & Rogers, L. J. (1992) J. Mol. Biol. 225, 775-789.
24. Hagler, A. T., Osguthorpe, P., Dauber-Osguthorpe, P., & Hempel, J. C. (1985) Science 227, 1309-1315.
25. Hall, L. H., Bowers, M. L., & Durfor, C. N. (1987a) Biochemistry 26, 7401-7409.
26. Hall, L. H., Orchard, B. J., & Tripathy, S. K. (1987b) Int. J. Quantum Chem. 31, 217-242.
27. Hendrickson, W. A. (1985) Methods Enzymol. 115, 252-270.
28. Herzberg, O., & Moult, J. (1991) Proteins: Struct., Funct., Genet. 11, 223-229.
29. Hinck, A. P., Eberhardt, E. S., & Markley, J. L. (1993) Biochemistry 32, 11810-11818.
30. Hoard, L. H., & Nordman, C. E. (1979) Acta Crystallogr. A 35, 1010-1015.
31. Hodel, A., Rice, L. M., Simonson, T., Fox, R. O., & Brünger, A. (1995) Protein Sci. 4, 636-654.
32. Hoover, D. M., Matthews, R. G., & Ludwig, M. L. (1994) in Flavins and Flavoproteins 1993 (Yagi, K., Ed.) pp 359-362, Walter de Gruyter & Co., Berlin.
33. Janin, J., Wodak, S., Levitt, M., & Maigret, B. (1978) J. Mol. Biol. 125, 357-386.
34. Jorgensen, W. L., & Gao, J. (1988) J. Am. Chem. Soc. 110, 4212-4216.
35. Kabsch, W., & Sander, C. (1983) Biopolymers 22, 2577-2637.
36. Kazarinova, N. F., Solomko, K. A., & Kotelenets, M. N. (1967) Chem. Abstr. 67, 2975d.
37. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.
38. Kunkel, A. T., Roberts, J. D., & Zakour, R. A. (1987) Methods Enzymol. 154, 367-382.
39. Laudenbach, D. E., Straus, N. A., Pattridge, K. A., & Ludwig, M. L. (1988) in Flavins and Flavoproteins 1987 (Edmondson, D. E., & McCormick, D. B., Eds.) pp 249-260, Walter de Gruyter & Co., Berlin, New York.
40. Leenders, R., Kooijman, M., van Hoek, A., Veeger, C., & Visser, A. J. W. G. (1993) Eur. J. Biochem. 211, 27-45.
41. Leenders, R., van Gunsteren, W. F., Berendsen, H. J. C., & Visser, A. J. W. G. (1994) Biophys. J. 66, 634-645.
42. Lewis, P. N., Momany, F. A., & Scheraga, H. A. (1973) Biochim. Biophys. Acta 303, 211-229.
43. Ludwig, M. L., & Luschinsky, C. L. (1992) in Chemistry and Biochemistry of Flavoenzymes III (Müller, F., Ed.) pp 427-466, CRC Press, Boca Raton, FL.
44. Ludwig, M. L., Andersen, R. D., Mayhew, S. G., & Massey, V. (1969) J. Biol. Chem. 244, 6047-6048.
45. Ludwig, M. L., Burnett, R. M., Darling, G. D., Jordan, S. R., Kendall, D. S., & Smith, W. W. (1976) in Flavins and Flavoproteins (Singer, T. P., Ed.) pp 393-404, Elsevier Scientific Publishing Co., Amsterdam.
46. Ludwig, M. L., Schopfer, L. M., Metzger, A. L., Pattridge, K. A., & Massey, V. (1990) Biochemistry 29, 10364-10375.
47. Ludwig, M. L., Pattridge, K. A., Eren, M., & Swenson, R. P. (1991) in Flavins and Flavoproteins 1990 (Curti, B., Ronchi, S., & Zanetti, G., Eds.) pp 423-428, Walter de Gruyter & Co., Berlin.
48. Ludwig, M. L., Dixon, M. M., Pattridge, K. A., & Swenson, R. P. (1994) in Flavins and Flavoproteins 1993 (Yagi, K., Ed.) pp 363-366, Walter de Gruyter & Co., Berlin.
49. Luschinsky, C. L., Dunham, W. R., Osborne, C., Pattridge, K. A., & Ludwig, M. L. (1991) in Flavins and Flavoproteins 1990 (Curti, B., Ronchi, S., & Zanetti, G., Eds.) pp 409-413, Walter de Gruyter & Co., Berlin.
50. Maigret, B., Perahia, D., & Pullman, B. (1970) J. Theor. Biol. 29, 275-291.
51. Maniatis, T., Fritsch, E. F., & Sambrook, J. (1982) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, NY.
52. Massey, V., & Hemmerich, P. (1978) Biochemistry 17, 9-16.
53. Mayhew, S. G. (1971) Biochim. Biophys. Acta 235, 276-288.
54. Mayhew, S. G. (1977) Eur. J. Biochem. 85, 535-547.
55. Mayhew, S. G., & Massey, V. (1969) J. Biol. Chem. 244, 794-802.
56. Mayhew, S. G., & Ludwig, M. L. (1975) in The Enzymes (Boyer, P., Ed.) 3rd ed., Vol. 12, pp 57-117, Academic Press, New York.
57. Mayhew, S. G., & Tollin, G. (1992) in Chemistry and Biochemistry of Flavoenzymes III (Müller, F., Ed.) pp 389-426, CRC Press, Boca Raton, FL.
58. Mayr, L. M., Willbold, D., Rosch, P., & Schmid, F. X. (1994) J. Mol. Biol. 240, 288-293.
59. Milner-White, E. J., & Poet, R. (1986) Biochem. J. 240, 289-292.
60. Peters, D., & Peters, J. (1981) J. Mol. Biol. 85, 107-123.
61. Pettitt, B. M., & Karplus, M. (1985) Chem. Phys. Lett. 121, 194-201.
62. Rao, S. T., Shaffie, F., Yu, C., Satyshur, K. A., Stockman, B. J., Markley, J. L., & Sundaralingam, M. (1992) Protein Sci. 1, 1413-1427.
63. Reid, L. S., & Thornton, J. M. (1989) Proteins 5, 170-182.
64. Richardson, J. S. (1981) Adv. Protein Chem. 34, 167-339.
65. Sanger, F., Nicklen, S., & Coulson, A. R. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 5463-5467.
66. Schulz, G. E., & Schirmer, R. H. (1979) Principles of Protein Structure, Springer-Verlag, New York.
67. Scully, J., & Hermans, J. (1994) J. Mol. Biol. 235, 682-694.
68. Sibanda, B. L., & Thornton, J. (1985) Nature 316, 170-174.
69. Smith, J. A., & Pease, L. G. (1980) CRC Crit. Rev. Biochem. 8, 315-399.
70. Smith, W. W. (1977) Ph.D. Thesis, University of Michigan, Ann Arbor, MI.
71. Smith, W. W., Burnett, R. M., Darling, G. D., & Ludwig, M. L. (1977) J. Mol. Biol. 117, 195-225.
72. Smith, W. W., Pattridge, K. A., Ludwig, M. L., Petsko, G. A., Tsernoglou, D., Tanka, M., & Yasanobu, K. T. (1983) J. Mol. Biol. 165, 737-753.
73. Stockman, B. J., Krezel, A. M., & Markley, J. L. (1990) Biochemistry 29, 9600-9609.
74. Stockman, B. J., Richardson, T. E., & Swenson, R. P. (1994) Biochemistry 33, 15298-15308.
75. Swenson, R. P., & Krey, G. D. (1994) Biochemistry 33, 8505-8514.
76. Taylor, R., & Kennard, O. (1984) Acc. Chem. Res. 17, 320-326.
77. van Mierlo, C. P. M., Lijnzaad, P., Veervoort, J., Müller, F., Berendsen, H. J. C., & de Vlieg, J. (1990) Eur. J. Biochem. 194, 185-198.
78. Venkatachalam, C. M. (1968) Biopolymers 6, 1425-1436.
79. Watenpaugh, K. D., Sicker, L. C., & Jensen, L. H. (1976) in Flavins and Flavoproteins, 1976 (Singer, T. P., Ed.) pp 405-410, Elsevier Scientific Publishing Co., Amsterdam.
80. Watt, W., Tulinsky, A., Swenson, R. P., & Watenpaugh, K. D. (1991) J. Mol. Biol. 218, 195-208.
81. Weiner, S. J.. Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S., Jr., & Weiner, P. (1984) J. Am. Chem. Soc. 106, 765-784.
82. Whitby, L. G. (1953) Biochem. J. 54, 437-442.
83. Wilmot, C. M., & Thornton, J. M. (1988) J. Mol. Biol. 203, 221-232.
84. Yang, A.-S., Hitz, B., & Honig, B. (1996) J. Mol. Biol. 259, 873-882.
85. Zhou, Z., & Swenson, R. P. (1995) Biochemistry 34, 3183-3192.
86. Zhou, Z., & Swenson, R. P. (1996) Biochemistry 35, 15980-15988.