Two conformational states of Turkey ovomucoid third domain at low pH: Three-dimensional structures, internal dynamics, and interconversion kinetics and thermodynamics

Biochemistry

Volumn 42, Issue 21, 2003, Pages 6380-6391

  Song, Jikui ^a   Laskowski Jr , Michael ^b   Qasim, M A ^b   Markley, John L ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b PURDUE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL BONDS; ISOMERIZATION; PH; POLYPEPTIDES; X RAY CRYSTALLOGRAPHY;

PEPTIDE BONDS;

CONFORMATIONS;

ALANINE; AROMATIC COMPOUND; ASPARTIC ACID; GLUTAMIC ACID; GLYCINE; HISTIDINE; LEUCINE; LYSINE; MUTANT PROTEIN; NITROGEN 15; OVOMUCOID; PEPTIDE DERIVATIVE; PROLINE; PROLINE DERIVATIVE; TYROSINE;

ALPHA HELIX; ARTICLE; BETA SHEET; CALCULATION; CHEMICAL BOND; CONFORMATIONAL TRANSITION; DISULFIDE BOND; ISOMERISM; KINETICS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MUTATION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PARAMETER; PH; PKA; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; TECHNIQUE; TEMPERATURE DEPENDENCE; THERMODYNAMICS; TURKEY (BIRD); X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; CRYSTALLOGRAPHY, X-RAY; DISULFIDES; HYDROGEN BONDING; HYDROGEN-ION CONCENTRATION; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OVOMUCIN; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; TEMPERATURE; THERMODYNAMICS; TURKEY;

AVES; MELEAGRIS GALLOPAVO;

EID: 0038687242     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi034053f     Document Type: Article

References (69)

1. Schechter, I., and Berger, A, (1967) Biochem. Biophys. Res. Commun. 27, 157-162.
2. Laskowski, M., Jr., and Kato, I. (1980) Annu. Rev. Biochem. 49, 593-626.
3. Bode, W., and Huber, R. (1992) Eur. J. Biochem. 204, 433-451.
4. Lineweaver, H., and Murray, C. W. (1947) J. Biol. Chem. 171, 565-581.
5. Schaller, W., and Robertson, A. D. (1995) Biochemistry 34, 4714-4723.
6. Donovan, J. W, (1967) Biochemistry 6, 3918-3927.
7. Choe, S. (1997) Ph.D. Thesis, University of Wisconsin - Madison, Madison, WI.
8. Lu, S. M., Lu, W., Qasim, M. A., Anderson, S., Apostol, I., Ardelt, W., Bigler, T., Chiang, Y. W., Cook, J., James, M. N., Kato, I., Kelly, C., Kohr, W., Komiyama, T., Lin, T. Y., Ogawa, M., Otlewski, J., Park, S. J., Qasim, S., Ranjbar, M., Tashiro, M., Wame, N., Whatley, H., Wieczorek, A., Wieczorek, M., Wilusz, T., Wynn, R., Zhang, W., and Laskowski, M., Jr. (2001) Proc, Natl. Acad. Sci. U.S.A, 98, 1410-1415.
9. Qasim, M. A., Lu, S. M., Ding, J. H., Bateman, K, S., James, M. N. G., Anderson, S., Song, J. K., Markley, J. L., Ganz, P. J., Saunders, C. W., and Laskowski, M., Jr. (1999) Biochemistry 38, 7142-7150.
10. Hinck, A. P., Walkenhorst, W, F., Westler, W. M., Choe, S., and Markley, J, L. (1993) Protein Eng. 6, 221-227.
11. Song, J., Laskowski, M., Jr., Qasim, M. A., and Markley, J, L. (2003) Biochemistry 42(10), 2847-2856.
12. Fejzo, J., Westler, W, M., Macura, S., and Markley, J. L. (1991) J. Magn. Reson. 92, 195-202.
13. Wang, Y. X., Jacob, J., Cordier, F., Wingfield, P. T., Stahl, S. J., Lee-Huang, S., Torchia, D. A., Grzesiek, S., and Bax, A, (1999) J. Biomol. NMR 14, 181-184.
14. Farrow, N. A., Muhandiram, R., Singer, A. U., Pascal, S. M., Kay, C. M., Gish, G., Shoelson, S. E., Pawson, T., Forman-Kay, J. D., and Kay, L. E. (1994) Biochemistry 33, 5984-6003.
15. Wishart, D. S., Bigam, C. G., Yao, J., Abildgaard, F., Dyson, H. J., Oldfield, E., Markley, J. L., and Sykes, B. D. (1995) J. Biomol, NMR 6, 135-140.
16. Güntert, P., Mumenthaler, C., and Wuthrich, K. (1997) J. Mol. Biol, 273, 283-298.
17. Bundi, A., and Wüthrich, K. (1979) Biopolymers 18, 299-311.
18. Comilescu, G., Delaglio, F., and Bax, A. (1999) J. Biomol. NMR 13, 289-302.
19. Koradi, R., Billeter, M., and Wüthrich, K. (1996) J. Mol. Graphics 14, 51-55.
20. Otting, G., Liepinsh, E., and Wüthrich, K. (1993) Biochemistry 32, 3571-3582.
21. Choe, S., Džakula, Z., Kuloglu, E. S., and Markley, J. L. (1998) J. Biomol. NMR 12, 193-195.
22. Robertson, A. D., Westler, W. M., and Markley, J. L. (1988) Biochemistry 27, 2519-2529.
23. Robertson, A. D., Rhyu, G.-I., Westler, W. M., and Markley, J. L. (1990) Biopolymers 29, 461-467.
24. Brandts, J. F., Halvorson, H. R., and Brennan, M. (1975) Biochemistry 14, 4953-4963.
25. Kamen, D. E., and Woody, R. W. (2002) Biochemistry 41, 4724-4732.
26. Hinck, A. P., Eberhardt, E. S., and Markley, J. L. (1993) Biochemistry 32, 11810-11818.
27. Dorman, D. E., Torchia, D. A., and Bovey, F. A. (1973) Macromolecules 6, 80-82.
28. Grathwohl, C., and Wüthrich, K. (1976) Biopolymers 15, 2025-2041.
29. Schubert, M., Labudde, D., Oschkinat, H., and Schmieder, P., (2002) J. Biol. NMR 24, 149-154.
30. Fujinaga, M., Read, R. J., Sielecki, A., Ardelt, W., Laskowski, M., Jr., and James, M. N. (1982) Proc. Natl. Acad. Sci. US.A. 79, 4868-4872.
31. Fujinaga, M., Sielecki, A. R., Read, R. J., Ardelt, W., Laskowski, M., Jr., and James, M. N. G. (1987) J. Mol. Biol. 195, 397-418.
32. Hoogstraten, C. G., Choe, S., Westler, W. M., and Markley, J. L. (1995) Protein Sci. 4, 2289-2299.
33. Krezel, A. M., Darba, P., Robertson, A. D., Fejzo, J., Macura, S., and Markley, J. L. (1994) J. Mol. Biol. 242, 203-214.
34. Schneider, D. M., Dellwo, M. J., and Wand, A. J. (1992) Biochemistry 31, 3645-3652.
35. Grathwohl, C., and Wüthrich, K. (1981) Biopolymers 20, 2623-2633.
36. Kim, P. S., and Baldwin, R. L. (1982) Annu. Rev. Biochem. 51, 459-489.
37. Richardson, J. S. (1981) Adv. Protein Chem. 34, 167-339.
38. Schmid, F. X., and Baldwin, R. L. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4764-4768.
39. Schmid, F. X., and Baldwin, R. L. (1979) J. Mol. Biol. 133, 285-287.
40. Dalessio, P. M., and Ropson, I. J. (2000) Biochemistry 39, 860-871.
41. Dyson, H. J., Rance, M., Houghten, R. A., Lerner, R. A., and Wright, P. E. (1988) J. Mol. Biol. 201, 161-200.
42. Dyson, H. J., and Wright, P. E. (1998) Nat. Struct. Biol. 5, Suppl., 499-503.
43. Galardy, R. E., Bleich, H. E., Ziegler, P., and Craig, L. C. (1976) Biochemistry 15, 2303-2309.
44. Kiefhaber, T., Quaas, R., Hahn, U., and Schmid, F. X. (1990) Biochemistry 29, 3053-3061.
45. Lin, X., Kaul, S., Rounsley, S., Shea, T. P., Benito, M. I., Town, C. D., Fujii, C. Y., Mason, T., Bowman, C. L., Bamstead, M., Feldblyum, T. V., Buell, C. R., Ketchum, K. A., Lee, J., Ronning, C. M., Koo, H. L., Moffat, K. S., Cronin, L. A., Shen, M., Pai, G., Van Aken, S., Umayam, L., Tallon, L. J., Gill, J. E., and Venter, J. C. (1999) Nature 402, 761-768.
46. Skjeldahl, L., Westler, W. M., Oh, B.-H., Krezel, A. M., Holden, H. M., Jacobson, B. L., Rayment, I., and Markley, J. L. (1991) Biochemistry 30, 7363-7368.
47. Tollinger, M., Skrynnikov, N. R., Mulder, F. A., Forman-Kay, J. D., and Kay, L. E. (2001) J. Am. Chem. Soc. 123, 11341-11352.
48. Read, R. J., Fujinaga, M., Sielecki, A. R., and James, M. N. G. (1983) Biochemistry 22, 4420-4433.
49. Clore, G. M., Gronenborn, A. M., James, M. N., Kjaer, M., McPhalen, C. A., and Poulsen, F. M. (1987) Protein Eng. 1, 313-318.
50. Eijkelenboom, A. P., Lutzke, R. A., Boelens, R., Plasterk, R. H., Kaptein, R., and Hård, K. (1995) Nat. Struct. Biol. 2, 807-810.
51. Holak, T. A., Bode, W., Huber, R., Otlewski, J., and Wilusz, T. (1989) J. Mol. Biol. 210, 649-654.
52. Wagner, G., Braun, W., Havel, T. F., Schaumann, T., Go, N., and Wüthrich, K. (1987) J. Mol. Biol. 196, 611-639.
53. Wlodawer, A., Nachman, J., Gilliland, G. L., Gallagher, W., and Woodward, C. (1987) J. Mol. Biol. 198, 469-480.
54. Yao, J., Dyson, H. J., and Wright, P. E. (1994) J. Mol. Biol. 243, 754-766.
55. Yao, J., Feher, V. A., Espejo, B. F., Reymond, M. T., Wright, P. E., and Dyson, H. J. (1994) J. Mol. Biol. 243, 736-753.
56. MacArthur, M. W., and Thornton, J. M. (1991) J. Mol. Biol. 218, 397-412.
57. Wu, W. J., and Raleigh, D. P. (1998) Biopolymers 45, 381-394.
58. Hodel, A., Kautz, R. A., and Fox, R. O. (1995) Protein Sci. 4, 484-495.
59. Forsyth, W. R., Gilson, M. K., Antosiewicz, J., Jaren, O. R., and Robertson, A. D. (1998) Biochemistry, 37, 8643-8652.
60. Forsyth, W. R., and Robertson, A. D. (2000) Biochemistry 39, 8067-8072.
61. Garcia-Moreno, B., Dwyer, J. J., Gittis, A. G., Lattman, E. E., Spencer, D. S., and Stites, W. E. (1997) Biophys. Chem. 64, 211-224.
62. Honig, B., and Nicholls, A. (1995) Science 268, 1144-1149.
63. Ibarra, C., Nieslanik, B. S., and Atkins, W. M. (2001) Biochemistry 40, 10614-10624.
64. Matthew, J. B., Gurd, F. R., Garcia-Moreno, B., Flanagan, M. A., March, K. L., and Shire, S. J. (1985) CRC Crit. Rev. Biochem. 18, 91-197.
65. Warshel, A., and Russell, S. T. (1984) Q. Rev. Biophys. 17, 283-422.
66. March, C. J. (1980) Ph.D. Thesis, Purdue University, West Lafayette, IN.
67. Croll, D. H. (1982) Ph.D. Thesis, Purdue University, West Lafayette, IN.
68. Hemmi, H., Kumazaki, T., Yamazaki, T., Kojima, S., Yoshida, T., Kyogoku, Y., Katsu, M., Shinohara, F., Yokosawa, H., Miura, K., and Kobayashi, Y. (2003) Biochemistry 42, 2524-2534.
69. Hemmi, H., Yoshida, T., Kumazaki, T., Nemoto, N., Hasegawa, J., Nishioka, F., Kyogoku, Y., Yokosawa, H., and Kobayashi, Y. (2002) Biochemistry 41, 10657-10664.