Noise and functional protein dynamics

Biophysical Journal

Volumn 89, Issue 4, 2005, Pages 2685-2692

  Korb, Jean Pierre ^a   Bryant, Robert G ^b  

^a LABORATOIRE DE PHYSIQUE DE LA MATIÈRE CONDENSÉE   (France)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BOVINE SERUM ALBUMIN; LYSOZYME; POLYPEPTIDE; PROTEIN;

ARTICLE; MACROMOLECULE; MAGNETIC FIELD; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTUM THEORY; VIBRATION;

EID: 25844432997     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.060178     Document Type: Article

References (35)

1. Daniel, R. M., R. V. Dunn, J. L. Finney, and J. C. Smith. 2003. The role of dynamics in enzyme activity. Annu. Rev. Biophys. Biomol. Struct. 32:69-92.
2. Frauenfelder, H., and B. McMahon. 1998. Dynamics and function of proteins: the search for general concepts. Proc. Natl. Acad. Sci. USA. 95:4795-4797.
3. Frauenfelder, H., B. H. McMahon, R. H. Austin, K. Chu, and J. T. Groves. 2001. The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc. Natl. Acad. Sci. USA. 98:2370-2374.
4. 2H labeling and neutron scattering. Proc. Natl. Acad. Sci. USA. 95:4970-4975.
5. Wand, A. J. 2001. Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat. Struct. Biol. 8:926-931.
6. Brooks, B., and M. Karplus. 1983. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA. 80:6571-6575.
7. Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
8. Korzhnev, D. M., X. Salvatella, M. Vendruscolo, A. A. Di Nardo, A. R. Davidson, C. M. Dobson, and L. E. Kay. 2004. Low-populated folding intermediates of Fyn SH3 characterized by relaxation dispersion NMR. Nature. 430:586-590.
9. Halle, B., V. P. Denisov, and K. Venu. 1999. Multinuclear relaxation dispersion studies of protein hydration. In Biological Magnetic Resonance. N.R. Krishna and L.J. Berliner, editors. Kluwer Academic/Plenum, New York. 419-484.
10. Kimmich, R., and E. Anoardo. 2004. Field-cycling NMR relaxometry. Prog. Nucl. Magn. Reson. Spectrosc. 44:257-320.
11. Noack, F. 1986. NMR field-cycling spectroscopy: principles and applications. Prog. Nucl. Magn. Reson. Spectrosc. 18:171-276.
12. Victor, K., A. Van-Quynh, and R. G. Bryant. 2005. High frequency dynamics in hemoglobin measured by magnetic relaxation dispersion. Biophys. J. 88:443-454.
13. Shirley, W. M., and R. G. Bryant. 1982. Proton-nuclear spin relaxation and molecular dynamics in the lysozyme-water system. J. Am. Chem. Soc. 104:2910-2918.
14. Lester, C. C., and R. G. Bryant. 1991. Water-proton nuclear magnetic relaxation in heterogeneous systems: hydrated lysozyme results. Magn. Reson. Med. 22:143-153.
15. Henkelman, R. M., X. Huang, Q. S. Xiang, G. J. Stanisz, S. D. Swanson, and M. J. Bronskill. 1993. Quantitative interpretation of magnetization transfer. Magn. Reson. Med. 29:759-766.
16. Bryant, R. G., D. Mendelson, and C. C. Lester. 1991. The magnetic field dependence of protein-protein spin relaxation in tissues. Magn. Reson. Med. 21:117-126.
17. Korb, J. P., A. Van-Quynh, and R. G. Bryant. 2001. Proton spin relaxation induced by localized spin-dynamical coupling in proteins. Chem. Phys. Lett. 339:77-82.
18. Korb, J. P., and R. G. Bryant. 2001. The physical basis for the magnetic field dependence of proton spin-lattice relaxation rates in proteins. J. Chem. Phys. 115:10964-10974.
19. Korb, J. P., and R. G. Bryant. 2002. Magnetic field dependence of proton spin-lattice relaxation times. Magn. Reson. Med. 48:21-26.
20. Korb, J. P., and R. G. Bryant. 2004. Magnetic field dependence of proton spin-lattice relaxation of confined proteins. C. R. Phys. 5:349-357.
21. Korb, J. P., A. Van-Quynh, and R. G. Bryant. 2001. Low-frequency localized spin-dynamical coupling in proteins. C. R. Acad. Sci. IIC. 4:833-837.
22. Abragam, A. 1961. The Principles of Nuclear Magnetism, Chapt. IX, Sect. 4c. Oxford University Press, Oxford, UK.
23. 1H cross-relaxation in hydrated proteins. Biophys. J. 48:331-335.
24. 3/4 law of proton spin-lattice relaxation in biopolymers. Prog. Colloid Polym. Sci. 71:66-70.
25. Alexander, S., and R. Orbach. 1982. Density of states on fractals: fractons. J. Physique Lett. 43:L625-L631.
26. Courtens, E., R. Vacher, J. Pelous, and T. Woigner. 1988. Observations of fractons in silica aerogels. Europhys. Lett. 6:245.
27. Stapleton, H. J., J. P. Allen, C. P. Flynn, D. G. Stinson, and S. R. Kurtz. 1980. Fractal form of proteins. Phys. Rev. Lett. 45:1456-1459.
28. Allen, J. P., J. T. Colvin, D. G. Stinson, C. P. Flynn, and H. J. Stapleton. 1982. Protein conformation from electron spin relaxation data. Biophys. J. 38:299-310.
29. Miyazawa, T., T. Shimanouchi, and S. Mizushima. 1958. Normal vibrations of N-methyl acetamide. J. Chem. Phys. 29:611-616.
30. Aharony, A., S. Alexander, O. Entin-Wohlman, and R. Orbach. 1987. Scattering of fractons, the Ioffe-Regel criterion, and the 4/3 conjecture. Phys. Rev. Lett. 58:132-135.
31. Orbach, R. 1986. Dynamics of fractal networks. Science. 231:814-819.
32. Bahar, I., B. Erman, R. L. Jernigan, A. R. Atilgan, and D. G. Covell. 1999. Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J. Mol. Biol. 285:1023-1037.
33. Haliloglu, T., I. Bahar, and B. Erman. 1997. Gaussian dynamics of folded proteins. Phys. Rev. Lett. 79:3090-3093.
34. Bahar, I., A. R. Atilgan, and B. Erman. 1997. Direct evaluation of thermal fluctuations in proteins using a single parameter harmonic potential. Fold. Des. 2:173-181.
35. Doruker, P., R. L. Jernigan, and I. Bahar. 2002. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J. Comput. Chem. 23:119-127.