Sampling of protein dynamics in nanosecond time scale by 15N NMR Relaxation and Self-Diffusion Measurements

Journal of Biomolecular Structure and Dynamics

Volumn 17, Issue 1, 1999, Pages 157-174

  Orekhov, Vladislav Yu ^a   Korzhnev, Dmitry M ^a   Pervushin, Konstantine V ^b   Hoffmann, Eberhard ^c   Arseniev, Alexander S ^a  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b ETH ZURICH   (Switzerland)

^c Varian GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN;

ARTICLE; DIFFUSION COEFFICIENT; DNA BINDING; HYDRODYNAMICS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN INTERACTION; PROTON NUCLEAR MAGNETIC RESONANCE; SPECTROMETRY;

COLIPHAGES; COMPUTER SIMULATION; DIFFUSION; DNA-BINDING PROTEINS; MODELS, MOLECULAR; NITROGEN ISOTOPES; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; REPRESSOR PROTEINS; TIME FACTORS; VIRAL PROTEINS;

EID: 0032841498     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1999.10508348     Document Type: Article

References (74)

1. Wagner, G., Hyberts, S., and Peng, J. W., 1993. NMR of Proteins Edited by:Clore, G. M., and Gronenborn, A. M., 220–257. The Macmillan Press LTD.
2. Chou, K. C., 1988. Biophys. Chem., 30:3–48.
3. Tidor, B., and Karplus, M., 1993. Proteins:Structure, Function, and Genetics, 15:71–79.
4. Lipari, G., and Szabo, A., 1982. J. Am. Chem. Soc., 104:4546–4559.
5. Kay, L. E., Torchia, D. A., and Bax, A., 1989. Biochemistry, 28:8972–8979.
6. Clore, G. M., Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., and Gronenborn, A. M., 1990. J. Am. Chem. Soc., 112:4989–4991.
7. Peng, J. W., and Wagner, G., 1992. J. Magn. Reson., 98:308–332.
8. Barbato, G., Ikura, M., Kay, L. E., Pastor, R. W., and Bax, A., 1992. Biochemistry, 31:5269–5278.
9. Szyperski, T., Luginbiihl, P., Otting, G., Güntert, P., and Wütrich, K., 1993. J. Biomol. NMR, 3:151–164.
10. Yu. Orekhov, V., Pervushin, K. V., Korzhnev, D. M., and Arseniev, A. S., 1995. J. Biomol NMR, 6:113–122.
11. Tjandra, N., Kuboniwa, H., Ren, H., and Bax, A., 1995. Eur. J. Biochem., 230:1014–1024.
12. Mandel, A. M., Akke, M., and Palmer, A. G., 1995. J. Mol.Biol., 246:144–163.
13. Woessner, D. E., 1962. J. Chem. Phys., 37:647–654.
14. Schurr, J. M., Babcock, H. P., and Fujimoto, B. S., 1994. J. Magn. Reson., 105:211–224.
15. Korzhnev, D. M., Yu. Orekhov, V., and Arseniev, A. S., 1997. J. Magn. Reson., 127:184–191.
16. Pervushin, K. V., Yu. Orekhov, V., Korzhnev, D. M., and Arseniev, A. S., 1995. J. Biomol NMR, 5:383–396.
17. Hunenberger, P. H., Mark, A. E., and van Gunstern, W. F., 1995. J. Mol. Biol., 252:492–503.
18. Clarage, J. B., Romo, T., Andrews, B. K., Pettitt, B. M., and Phillips, G. N., 1995. Proc. Natl. Acad. Sci., 92:3288–3292.
19. Tolman, J. R., Flanagan, J. M., Kennedy, M. A., and Prestegard, J. H., 1997. Nature Struct. Biol., 4:292–297.
20. Bax, A., and Tjandra, N., 1997. Nature Struct. Biol., 4:254–256.
21. Luginbiihl, P., Pervushin, K. V., Iwai, H., and Wüthrich, K., 1997. Biochemistry, 36:7305–7312.
22. Stejskal, E. O., and Tanner, J. E., 1965. J. Chem. Phys., 42:288–292.
23. Stilbs, P., 1987. Prog. NMR Spectrosc., 19:1–45.
24. Chapman, B. E., and Kuchel, P. W., 1993. J. Magn. Reson. A, 102:105–109.
25. Braun, B. M., and Weingartner, H., 1988. J. Phys. Chem., 92:1342–1346.
26. Holz, M., and Weingartner, H., 1991. J. Magn. Reson., 92:115–125.
27. Goux, W. J., Verkruyse, L. A., and Salter, S. J., 1990. J. Magn. Reson., 88:609–614.
28. Abramovich, D., and Vega, S:. 1993. J. Magn. Reson. A, 105:30–48.
29. Kupce, E., and Freeman, R., 1993. J. Magn. Reson. A, 105:234–238.
30. Shaka, A. J., Barker, P. B., and Freeman, R., 1985. J. Magn. Reson., 64:547–552.
31. Tanner, J. E., 1970. J. Chem. Phys., 52:2523–2526.
32. Piotto, M., Saudek, V., and Sklenar, V., 1992. J. Biomol. NMR, 2:661–665.
33. Merril, M. R., 1993. J. Magn. Reson. A, 103:223–225.
34. Dötsch, V., Wider, G., Siegal, G., and Wüthrich, K., 1995. FEBS Lett., 366:6–10.
35. Garsia de la Torre, J., and Bloomfield, V. A., 1977. Biopolymers, 16:1747–1763.
36. Garcia de la Torre, J., and Bloomfield, V. A., 1977. Biopolymers, 16:1765–1778.
37. Garcia de la Torre, J., and Bloomfield, V. A., 1981. Quart. Rev. Biophys., 14:81–139.
38. Lamm, G., and Szabo, A., 1986. J. Chem. Phys., 85:7334–7348.
39. Pastor, R. W., and Karplus, M., 1988. J. Phys. Chem., 92:2636–2641.
40. Venable, R. M., and Pastor, R. W., 1988. Biopolymers., 27:1001–1014.
41. Happel, J., and Brenner, H., 1973. Low Reynolds Number Hydrodynamics. Leyden:Nordoff.
42. Lee, B., and Richards, F. M., 1971. J. Mol. Biol., 55:379–400.
43. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M., 1983. J. Comput. Chem., 4:187–217.
44. Müller, J. J., 1991. Biopolymers, 31:149–160.
45. Blanco, M., 1991. J. Comp. Chem., 12:237–247.
46. Yu. Orekhov, V., Nolde, D. E., Golovanov, A. P., Korzhnev, D. M., and Arseniev, A. S., 1995. Appl. Magn. Reson., 9:581–588.
47. Abragam, A., 1961. The Principles of Nuclear Magnetism London:Oxford University Press.
48. Palmer, A. G., Rance, M., and Wright, P. E., 1991. J. Am. Chem. Soc., 113:4371–4380.
49. Brune, D., and Kim, S., 1993. Proc. Nat. Acad. Sci., 90:3835–3839.
50. Cantor, C. R., and Schimmel, P. R., 1980. Biophysical Chemistry San Francisco:W.H. Freeman and Co.
51. Kuntz, I. D., and Kauzmann, W., 1974. Adv. Protein Chem., 28:236–345.
52. Jiang, J., and Brünger, A., 1994. J. Mol. Biol., 243:100–115.
53. Ilyina, E., Roongta, V., Pan, H., Woodward, C., and Mayo, K., 1997. Biochemistry, 36:3383–3388.
54. Lloyd, E., 1984. “ Statistics in ”. In Handbook of Applicable Mathematics Edited by:Ledermann, W., Vol. 6, 615–615. Chichester:John Wiley & Sons.
55. Tjandra, N., Wingfield, P., Stahl, S., and Bax, A., 1996. J. Biomol. NMR, 8:273–284.
56. Neri, D., Billeter, M., and Wüthrich, K., 1992. J. Mol. Biol., 223:743–767.
57. Mondragon, A., Wolberger, C., and Harrison, S. C., 1989. J. Mol. Biol., 205:179–188.
58. Pervushin, K. V., Billeter, M., Siegal, G., and Wüthrich, K., 1996. J. Mol. Biol., 264:1002–1012.
59. Brüschweiler, R., Liao, X., and Wright, P. E., 1995. Science, 268:886–889.
60. Cordier, F., Bernhard, B., and Marion, D., 1996. J. Biomol. NMR, 7:163–168.
61. Zeng, L., Fischer, M. W., and Zuiderweg, E. R., 1996. J. Biomol. NMR, 7:157–162.
62. Wand, A. J., Urbauer, J. L., McEvoy, R. P., and Bieber, R. J., 1996. Biochemistry, 35:6116–6125.
63. Smith, L. J., Mark, A. E., Dobson, C. M., and van Gunsteren, W. F., 1995. Biochemistry, 34:10918–10931.
64. Lefevre, J. F., Dayie, K. T., Peng, J. W., and Wagner, G., 1996. Biochemistry, 35:2674–2686.
65. Dubin, S. B., Clark, N. A., and Benedek, G. B., 1971. J. Chem. Phys., 54:5158–5164.
66. Buck, M., Boyd, J., Redfield, C., MacKenzie, D. A., Jeenes, D. J., Archer, D. B., and Dobson, C. M., 1995. Biochemistry, 34:4041–4055.
67. Gallagher, W. H., and Woodward, C. K., 1989. Biopolymers, 28:2001–2024.
68. Mackay, J. P., Shaw, G. L., and King, G. F., 1996. Boichemistry, 35:4867–4877.
69. Schneider, D. M., Dellwo, M. J., and Wand, A. J., 1992. Biochemistry, 31:3645–3652.
70. Barchi, J. J., Grasberger, B., Gronenborn, A. M., and Clore, G. M., 1994. Protein Sci., 3:15–21.
71. Peng, J. W., and Wagner, G., 1995. Biochemistry, 34:16733–16752.
72. Phan, I. Q., Boyd, J., and Campbell, D. I., 1996. J. Biomol. NMR, 8:369–378.
73. Clubb, R. T., Omichinski, J. G., Sakaguchi, K., Apella, E., Gronenborn, A. M., and Clore, G. M., 1995. Protein Sci., 4:855–862.
74. Stivers, J. T., Abeygunawardana, C., and Mildvan, A. S., 1996. Biochemistry, 35:16036–16047.