Hydration Dynamics Near a Model Protein Surface

Biophysical Journal

Volumn 86, Issue 3, 2004, Pages 1852-1862

  Russo, Daniela ^a   Hura, Greg ^b   Head Gordon, Teresa ^a,b  

^a University of California at Berkeley   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; N ACETYLLEUCINE METHYLAMIDE; UNCLASSIFIED DRUG; WATER;

ARTICLE; HYDRATION; HYDROPHOBICITY; MOLECULAR DYNAMICS; NEUTRON SCATTERING; PROTEIN PROTEIN INTERACTION; X RAY DIFFRACTION;

EID: 1542375172     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(04)74252-6     Document Type: Article

References (47)

1. Anderson, H. C. 1983. Rattle: a "velocity" version of the shake algorithm for molecular dynamics calculations. J. Comp. Phys. 52:24-34.
2. Angell, C. A. 1995. Formation of glasses from liquids and biopolymers. Science. 267:1924-1935. (Review).
3. Barron, L. D., L. Hecht, and G. Wilson. 1997. The lubricant of life-a proposal that solvent water promotes extremely fast conformational fluctuations in mobile heteropolypeptide structure. Biochemistry. 36:13143-13147.
4. Bee, M. 1988. Quasi-Elastic Neutron Scattering. Adam Hilger, Philadelphia, PA.
5. Bee, M. 2003. Localized and long-range diffusion in condensed matter: state of the art of QENS studies and future prospects. Chem. Phys. 292:121-141.
6. Bellissent-Funel, M. C. 2000. Hydration in protein dynamics and function. Journal of Molecular Liquids. 84:39-52.
7. Bellissent-Funel, M. C., J. Teixeira, K. F. Bradley, and S. H. Chen. 1992. Dynamics of hydration water in protein. Journal de Physique I. 2:995-1001.
8. Berendsen, H. J., J. R. Grigera, and T. P. Straatsma. 1987. The missing term in effective pair potentials. J. Phys. Chem. 91:6269-6271.
9. Bizzarri, A. R., and S. Cannistraro. 2002. Molecular dynamics of water at the protein-solvent interface. J. Phys. Chem. B. 106:6617-6633. (Review).
10. Bu, Z. M., D. A. Neumann, S. H. Lee, C. M. Brown, D. M. Engelman, and C. C. Han. 2000. A view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering. J. Mol. Biol. 301:525-536.
11. Careri, G., and M. Peyrard. 2001. Physical aspects of the weakly hydrated protein surface. Cell. Mol. Biol. 47:745-756 (Review).
12. Cheung, M. S., A. E. Garcia, and J. N. Onuchic. 2002. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA. 99:685-690.
13. Cornell, W. D., P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
14. de Gennes, P. G. 1959. Liquid dynamics and inelastic scattering of neutrons. Physica. 25:825-839.
15. Dellerue, S., and M. C. Bellissent-Funel. 2000. Relaxational dynamics of water molecules at protein surface. Chem. Phys. 258:315-325.
16. Denisov, V. P., and B. Halle. 1996. Protein hydration dynamics in aqueous solution. Faraday Discuss. 103:227-244.
17. Denisov, V. P., B. H. Jonsson, and B. Halle. 1999. Hydration of denatured and molten globule proteins. Nat. Struct. Biol. 6:253-260.
18. Diehl, M., W. Doster, W. Petry, and H. Schober. 1997. Water-coupled low-frequency modes of myoglobin and lysozyme observed by inelastic neutron scattering. Biophys. J. 73:2726-2732.
19. Doster, W., and M. Settles. 1998. The dynamical transition: the role of hydrogen bonds. In Hydration Processes in Biology; Les Houches Lectures. M. C. Bellissent-Funel and J. Teixeira, editors. IOS Press, Burke, VA.
20. Ediger, M. D., C. A. Angell, and S. R. Nagel. 1996. Supercooled liquids and glasses. J. Phys. Chem. 100:13200-13212. (Review).
21. Egelstaff, P. A. 1992. An Introduction to the Liquid State. Clarendon, Oxford, UK.
22. Green, J. L., J. Fan, and C. A. Angell. 1994. The protein-class analogy: some insights from homopeptide comparisons. J. Phys. Chem. 98:13780-13790. (Review).
23. Halle, B., and V. P. Denisov. 1995. A new view of water dynamics in immobilized proteins. Biophys. J. 69:242-249.
24. Hura, G., J. M. Sorenson, R. M. Glaeser, and T. Head-Gordon. 1999. Solution x-ray scattering as a probe of hydration-dependent structuring of aqueous solutions. Perspectives in Drug Discovery & Design. 17:97-118. (Review).
25. Janin, J. 1999. Wet and dry interfaces: the role of solvent in protein-protein and protein-DNA recognition. Struct. Fold. Des. 7:R277-R279. (Review).
26. Marchi, M., F. Sterpone, and M. Ceccarelli. 2002. Water rotational relaxation and diffusion in hydrated lysozyme. J. Am. Chem. Soc. 124:6787-6791.
27. Mattos, C. 2002. Protein-water interactions in a dynamic world. Trends Biochem. Sci. 27:203-208. (Review).
28. Mentre, P. 2001. An introduction to water in the cell: tamed hydra? Cellular & Molecular Biology. 47:709-715.
29. Merzel, F., and J. C. Smith. 2002. Is the first hydration shell of lysozyme of higher density than bulk water? Proc. Natl. Acad. Sci. USA. 99:5378-5383.
30. Nishikawa, K., and N. Kitagawa. 1980. X-ray-diffraction study of liquid water. Bulletin of the Chemical Society of Japan. 53:2804-2808.
31. Otting, G. 1997. NMR studies of water bound to biological molecules. Progress in Nuclear Magnetic Resonance Spectroscopy. 31:259-285. (Review).
32. Pal, S. K., J. Peon, and A. H. Zewail. 2002. Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution. Proc. Natl. Acad. Sci. USA. 99:1763-1768.
33. Pande, V. S., and D. S. Rokhsar. 1999. Molecular dynamics simulations of unfolding and refolding of a beta-hairpin fragment of protein G. Proc. Natl. Acad. Sci. USA. 96:9062-9067.
34. Rupley, J. A., and G. Careri. 1991. Protein hydration and function. Adv. Protein Chem. 41:37-172.
35. Russo, D., P. Baglioni, E. Peroni, and J. Teixeira. 2003. Picosecond hydration water dynamics of a completely hydrophobic small peptide. Chem. Phys. 292:235-245.
36. Russo, D., J. Perez, J. M. Zanotti, M. Desmadril, and D. Durand. 2002. Dynamic transition associated with the thermal denaturation of a small beta protein. Biophys. J. 83:2792-2800.
37. Sears, V. F. 1966. Theory of cold neutron scattering by homonuclear diatomic liquids. I. Free rotation. Canadian Journal of Physics. 44:1299.
38. Shea, J. E., J. N. Onuchic, and C. L. Brooks. 2002. Probing the folding free energy landscape of the src-SH3 protein domain. Proc. Natl. Acad. Sci. USA. 99:16064-16068.
39. Sheinerman, F. B., and C. L. Brooks. 1998. Molecular picture of folding of a small alpha/beta protein. Proc. Natl. Acad. Sci. USA. 95:1562-1567.
40. Sorenson, J. M., G. Hura, A. K. Soper, A. Pertsemlidis, and T. Head-Gordon. 1999. Determining the role of hydration forces in protein folding. J. Phys. Chem. B. 103:5413-5426.
41. Svergun, D. I., S. Richard, M. H. J. Koch, Z. Sayers, S. Kuprin, and G. Zaccai. 1998. Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc. Natl. Acad. Sci. USA. 95:2267-2272.
42. Tarek, M., and D. J. Tobias. 1999. Environmental dependence of the dynamics of protein hydration water. J. Am. Chem. Soc. 121:9740-9741.
43. Tarek, M., and D. J. Tobias. 2000. The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments. Biophys. J. 79:3244-3257.
44. Tarek, M., and D. J. Tobias. 2002. Role of protein-water hydrogen bond dynamics in the protein dynamical transition. Phys. Rev. Lett. 88:138101.
45. Tournier, A. L., J. C. Xu, and J. C. Smith. 2003. Translational hydration water dynamics drives the protein glass transition. Biophys. J. 85:1871-1875.
46. Zanotti, J. M., M. C. Bellissentfunel, and J. Parello. 1997. Dynamics of a globular protein as studied by neutron scattering and solid-state NMR. Physica B. 234:228-230.
47. Zanotti, J. M., M. C. Bellissent-Funel, and J. Parello. 1999. Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin. Biophys. J. 76:2390-2411.