Evidence for domain motion in proteins affecting global diffusion properties: A nuclear magnetic resonance study

Journal of Physical Chemistry B

Volumn 113, Issue 19, 2009, Pages 7003-7011

  Shapiro, Yury E ^a   Meirovitch, Eva ^a  

^a BAR ILAN UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AMINES; BIOMATERIALS; CALCIUM; CAMS; DIFFUSION IN SOLIDS; FLUID DYNAMICS; HYDRATION; LIGANDS; MAGNETIC DOMAINS; MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE; POWDERS; PROTEINS; VISCOSITY;

ACTIVATION ENTHALPIES; ACTIVATION ENTROPIES; ADENYLATE KINASE; APPARENT ACTIVATION ENERGY; BULK WATER; DOMAIN MOTIONS; ELECTROSTATIC INTERACTIONS; GLOBAL DIFFUSION; HYDRATION LAYERS; HYDRODYNAMIC PROPERTIES; MOBILE LIGANDS; MULTIDOMAIN PROTEINS; NUCLEAR MAGNETIC RESONANCE STUDIES; OUTER SURFACE; PROTEIN STRUCTURES; ROTATIONAL DIFFUSION; SPIN RELAXATION; STAPHYLOCOCCAL NUCLEASE; SURFACE SITES; WATER VISCOSITY;

ACTIVATION ENERGY;

EID: 67650069432     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp9009806     Document Type: Article

References (99)

1. Hammes, G. Biochemistry 2002, 41, 8221.
2. Benkovic, S. J.; Hammes-Schiffer, S. Science 2003, 301, 1196.
3. Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. Science 2004, 303, 186.
4. Woessner, D. E. J. Chem. Phys. 1962, 36, 1;
5. ibid 1962, 36, 647.
6. Lee, A. L.; Sharp, K. A.; Kranz, J. K.; Song, X.-J.; Wand, A. J. Biochemistry 2002, 41, 13814.
7. Edwards, D. Quart, J. Pure Appl. Math 1892, 26, 70.
8. Jeffrey, G. B. Proc. Lond. Math. Soc. 1915, 14, 327.
9. Halle, B.; Davidovic, M. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12135.
10. Halle, B. Philos. Trans. R. Soc. London, Ser. B 2004, 359, 1207.
11. de la Torre, J. G.; Huertas, M. L.; Carasco, B. J. Magn. Reson. 2000, 147, 138.
12. Bernado, P.; de la Torre, J. G.; Pons, M. J. Biomol. NMR 2002, 23, 139.
13. Ortega, A.; de la Torre, J. G. J. Am. Chem. Soc. 2005, 127, 12764.
14. Ryabov, Y. E.; Geraghty, C.; Varshney, A.; Fushman, D. J. Am. Chem. Soc. 2006, 128, 15432.
15. Barone, V.; Zerbetto, M.; Polimeno, A. J. Comput. Chem. 2009, 30, 2.
16. de la Torre, J. G.; del Rio Echenique, G.; Ortega, A. J. Phys. Chem. B 2007, 111, 955.
17. Kirkwood, J.; Riseman, J. J. Chem. Phys. 1948, 16, 565.
18. Bessire, D. R.; Quitevis, E. L. J. Phys. Chem. 1994, 98, 13083.
19. Pizzitutti, F.; Marchi, M.; Sterpone, F.; Rossky, P. J. J. Phys. Chem. B 2007, 111, 7584.
20. Bandyopadhyay, S.; Chakraborty, S.; Badchi, B. J. Am. Chem. Soc. 2005, 127, 16660.
21. Chakraborty, S.; Bandyopadhyay, S. J. Phys. Chem. B 2007, 111, 7626.
22. Rouse, P. J. Chem. Phys. 1953, 21, 1272.
23. Zimm, B. J. Chem. Phys. 1956, 24, 269.
24. Ottinger, H. C. Phys. Rev. 1994, E50, 2696.
25. Nyland, G. H.; Skjetne, P.; Mikkelsen, A.; Elgsaeter, A. J. Chem. Phys. 1996, 105, 1198.
26. de Gennes, P.-G. J. Chem. Phys. 1971, 55, 572.
27. Semenov, A. N. J. Chem. Soc, Faraday Trans. 1985, 2, 82.
28. Doi, M. J. Polym. Sci., Polym. Symp. 1985, 73, 93.
29. Wierenga, A. M.; Philipse, A. P. Colloids Surf., A 1998, 137, 355.
30. Griffiths, P. C.; Stilbs, P.; Yu, G. E.; Booth, C. J. Phys. Chem. 1995, 99, 16752.
31. Shapiro, Yu. E.; Pykhteeva, E. G.; Levashov, A. V. J. Colloid Interface Sci. 1998, 206, 168.
32. Shapiro, Yu. E. J. Colloid Interface Sci. 1999, 212, 453.
33. Shapiro, Yu. E.; Shapiro, T. I. J. Colloid Interface Sci. 1999, 217, 322.
34. Shapiro, Yu. E. Colloids Surf., A 2000, 164, 71.
35. Tyrrel, H. J. V.; Harris, K. R. Diffusion in Liquids; Butterworths: London, 1984.
36. Peng, J. W.; Wagner, G. In Methods in Enzymology (James, T. L. and Oppenheimer, N. J., eds.) 1994,Vol. 239, 563-595, Academic Press, New York.
37. Abragam, A. Principles of Nuclear Magnetism, Oxford University Press (Clarendon): London, 1961.
38. Shapiro, Yu. E.; Sinev, M. A.; Sineva, E. V.; Tugarinov, V.; Meirovitch, E. Biochemistry 2000, 39, 6634.
39. Shapiro, Yu. E.; Kahana, E.; Tugarinov, V.; Liang, Z.; Freed, J. H.; Meirovitch, E. Biochemistry 2002, 41, 6271.
40. Tugarinov, V.; Shapiro, Yu. E.; Liang, Z.; Freed, J. H.; Meirovitch, E. J. Mol. Biol. 2002, 315, 155.
41. Shapiro, Yu. E.; Meirovitch, E. J. Phys. Chem, B 2006, 110, 11519.
42. Baber, J. L.; Szabo, A.; Tjandra, N. J. Am. Chem. Soc. 2001, 123, 3953.
43. Chang, S.-L.; Szabo, A.; Tjandra, N. J. Am. Chem. Soc. 2003, 125, 11379.
44. Pawley, N. H.; Koide, S.; Nicholson, L. K. J. Mol. Biol. 2002, 324, 991.
45. Yang, D.; Mok, Y.-K.; Forman-Kay, J. D.; Farrow, N. A.; Kay, L. E. J. Mol. Biol. 1997, 272, 790.
46. Vugmeyster, L.; Trott, O.; McKnight, C. J.; Raleigh, D. P.; Palmer, A. G. J. Mol. Biol. 2002, 320, 841.
47. Seewald, M. J.; Pichumani, K.; Stowell, C.; Tibbals, B. V.; Regan, L.; Stone, M. J. Protein Sci. 2000, 9, 1177.
48. Evenäs, J.; Forsen, S.; Malmendal, A.; Akke, M. J. Mol. Biol. 1999, 289, 603-617.
49. Chang, S.-L.; Tjandra, N. J. Magn. Reson. 2005, 174, 43.
50. Mispelter, J.; Izadi-Pruneyre, N.; Quiniou, E.; Adjadj, E. J. Magn. Reson. 2000, 143, 229.
51. Kovrigin, E. L.; Cole, R.; Loria, J. P. Biochemistry 2003, 42, 5279.
52. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. J. Biomol. NMR 1995, 6, 277.
53. Burlacu-Miron, S.; Perrier, V.; Gilles, A.-M.; Mispelter, J.; Barzu, O.; Craescu, C. T. J. Biomol. NMR 1999, 13, 93.
54. Meirovitch, E.; Sinev, M. A.; Sineva, E. V. J. Biomol. NMR 1999, 13, 195.
55. Palmer, A. G.; Skelton, N. J.; Chazin, W. J.; Wright, P. E.; Rance, M. Mol. Phys. 1992, 75, 699.
56. Grzesiek, S.; Bax, A. J. Am. Chem. Soc. 1993, 115, 12593.
57. 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.; Kay, L. E. Biochemistry 1994, 33, 5984.
58. Polimeno, A.; Freed, J. H. Adv.. Chem. Phys. 1993, 83, 89.
59. Polimeno, A.; Freed, J. H. J. Phys. Chem. 1995, 99, 10995.
60. Tugarinov, V.; Liang, Z.; Shapiro, Yu. E.; Freed, J. H.; Meirovitch, E. J. Am. Chem. Soc. 2001, 123, 3055.
61. Meirovitch, E.; Shapiro, Yu. E.; Polimeno, A.; Freed, J. H. J. Phys. Chem. A 2006, 110, 8366.
62. Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546. ibid., 4559.
63. Kay, L. E.; Torchia, D. A.; Bax, A. Biochemistry 1989, 28, 8972.
64. Pawley, N. H.; Wang, C.; Koide, S.; Nicholson, L. K. J. Biomol. NMR 2001, 20, 149.
65. Noda, L. In The Enzymes, 3rd ed.; Boyer, P. D., Ed.; Academic Press: London, 1973; Vol. 8, pp 279.
66. Vornhein, C.; Schlauderer, G J.; Schulz, G. Structure 1995, 3, 483.
67. Müller-Dickermann, H.-J.; Schulz, G. J. Mol. Biol. 1995, 246, 522.
68. Richard, J. P.; Frey, P. A. J. Am. Chem. Soc. 1978, 110, 7757.
69. Aden, M. J.; Wolf-Watz, M. J. Am. Chem. Soc. 2007, 129, 14003.
70. Müller, C. W.; Schlauderer, G. J.; Reinstein, J.; Schulz, G. Structure 1996, 4, 147.
71. Müller, C. W.; Schulz, G. J. Mol. Biol. 1992, 224, 159.
72. Kraulis, P. J. J. Appl. Crystallogr. 1991, 24, 946.
73. Clore, G. M.; Szabo, A.; Bax, A.; Kay, L. E.; Driscoll, P. C.; Gronenborn, A. M. J. Am. Chem. Soc. 1990, 112, 4989.
74. Henzler-Wildman, K. A.; Lei, M.; Thai, V.; Kerns, S. J.; Karplus, M.; Kern, D. Nature (London) 2007, 450, 913.
75. Chen, K.; Tjandra, N. J. Am. Chem. Soc. 2008, 130, 12745.
76. Ryabov, Y. E.; Fushman, D. Proteins 2006, 63, 787.
77. Ryabov, Y. E.; Fushman, D. J. Am. Chem. Soc. 2007, 129, 3315.
78. Babu, Y. S.; Bugg, C. E.; Cook, W. J. J. Mol. Biol. 1988, 204, 191.
79. Copié, V.; Tomita, Y.; Akiyama, S. K.; Aota, A.; Yamada, K. M.; Venable, R. M.; Pastor, R. W.; Krueger, S.; Torchia, D. A. J. Mol. Biol. 1998, 277, 663.
80. Osborne, M. J.; Wright, P. E. J. Biomol. NMR 2001, 19, 209.
81. Wolf-Watz, M.; Thai, V.; Henzler-Wildman, K. A.; Hadjipavlou, G; Eisenmesser, E. Z.; Kern, D. Nat. Struct. Mol. Biol. 2004, 11, 945.
82. Henzler-Wildman, K. A.; Thai, V.; Lei, M.; Ott, M.; Wolf-Watz, M.; Fenn, T.; Pozharski, E.; Wilson, M. A.; Petsko, G. A.; Karplus, M.; Hubner, C. G.; Kern, D. Nature (London) 2007, 450, 838.
83. Henzler-Wildman, K. A.; Kern, D. Nature (London) 2007, 450, 964.
84. Arora, K.; Brooks III, C. L. Proc. Natl. Acad. Sci. U.SA. 2007, 104, 18496.
85. Sampedro, J. G.; Munoz-Clares, R. A.; Uribe, S. J. Bacteriology 2002, 184, 4384.
86. Peinelt, C.; Apell, H.-J. Biophys. J. 2004, 86, 815.
87. Dellwo, M. J.; Wand, A. J. J. Am. Chem. Soc. 1989, 111, 4571.
88. Lee, L. K.; Rance, M.; Chazin, W. J.; Palmer III, A. G. J. Biomol. NMR 1997, 9, 287.
89. Fushman, D.; Cahill, S.; Cowburn, D. J. Mol. Biol. 1997, 266, 173.
90. Handbook of Chemistry and Physics; Lide, D. R., Ed.; 84th Edition, CRC Press, 2004, pp 6-3.
91. Shapiro, Yu. E.; Gorbatyuk, V. Ya.; Levashov, A. V.; Klyachko, N. L. Biol. Membr. 1994, 7, 277.
92. Rejou-Michel, A.; Henry, F.; de Villardi, M.; Delmotte, M. Phys. Med. Biol. 1985, 30, 831.
93. Moelwyn-Hughes, E. A. Physical Chemistry; Pergamon Press: Oxford, 1964, p 715.
94. Evans, M. G.; Polanyi, M. Trans. Faraday Soc. 1935, 31, 875.
95. Eyring, H. J. Chem. Phys. 1935, 3, 107.
96. Eyring, H.; Polanyi, M. Z. Phys. Chem. Abt. 1931, 12, 279.
97. Eirich, F. Rep. Prog. Phys. 1940, 7, 329.
98. Crivici, A.; Ikura, M. Annu. Rev. Biophys. Biomol. Struct. 1995, 24, 85-116.
99. Alexandrescu, A. T.; Jahnke, W.; Wiltscheck, R.; Blommers, M. J. J. J. Mol. Biol. 1996, 260, 570.