The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation

Proteins: Structure, Function and Genetics

Volumn 25, Issue 3, 1996, Pages 366-378

  Abseher, Roger ^a   Schreiber, Hellfried ^a   Steinhauser, Othmar ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

diffusion; hydration solvation; Kohlrausch Williams Watts relaxation; residence time; ubiquitin; Voronoi polyhedra

Indexed keywords

PROTEIN; SOLVENT; UBIQUITIN; WATER;

ARTICLE; HYDRATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; SIMULATION; SOLVATION; TEMPERATURE DEPENDENCE;

PROTEINS; SOLVENTS; TEMPERATURE; WATER;

EID: 0030057862     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199607)25:3<366::AID-PROT8>3.0.CO;2-D     Document Type: Article

References (57)

1. Karplus, P.A., Faerman, C. Ordered water in macromolecular structure. Curr. Opin. Struct. Biol. 4:770-776, 1994.
2. Levitt, M., Park, B.H. Water: Now you see it, now you don't. Structure 1:223-226, 1993.
3. Teeter, M.M. Water-protein interactions: Theory and experiment. Annu. Rev. Biophys. Biophys. Chem. 20:577-600, 1991.
4. Levitt, M., Sharon, R. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. U.S.A. 85:7557-7561, 1988.
5. Daggett, V., Levitt, M. Realistic simulations of native-protein dynamics in solution and beyond. Annu. Rev. Biophys. Biomol. Struct. 22:353-380, 1993.
6. Otting, G., Liepinsh, E., Wuthrich, K. Protein hydration in aqueous solution. Science 254:974-980, 1991.
7. Haselmeier, R., Holz, M., Marbach, W., Weingärtner, H. Water dynamics near a dissolved noble gas. First direct experimental evidence for a retardation effect. J. Phys. Chem. 99:2243-2246, 1995.
8. Miura, N., Hayashi, Y., Shinyashiki, N., Mashimo, S. Observation of unfreezable water in aqueous solution of globule protein by microwave dielectric measurement. Biopolymers 36:9-16, 1995.
9. Gregory, R.B. "Protein-Solvent Interactions." New York: Marcel Dekker, 1995.
10. Muegge, I., Knapp, E.W. Residence times and lateral diffusion of water at protein surfaces: Application to BPTI. J. Phys. Chem. 99:1371-1374, 1995.
11. Lounnas, V., Pettitt, M., Phillips, G.N., Jr. A global model of the protein-solvent interface. Biophys. J. 66:601-614, 1994.
12. Brunne, R.M., Liepinsh, E., Otting, G., Wüthrich, K., van Gunsteren, W.F. Hydration of Proteins. J. Mol. Biol. 231: 1040-1048, 1993.
13. Steinbach, P.J., Brooks, B.R. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl. Acad. Sci. U.S.A. 90:9135-9139, 1993.
14. Lee, S.H., Rossky, P.J. A comparison of the structure and dynamics of liquid water at hydrophobic and hydrophilic surfaces - A molecular dynamics simulation study. J. Chem. Phys. 100:3334-3345, 1994.
15. Gerstein, M., Lynden-Bell, R.M. What is the natural boundary of a protein in solution? J. Mol. Biol. 230:641-650, 1993.
16. Phillips, G.N., Pettitt, M. Structure and dynamics of the water around myoglobin. Protein Sci 4:149-158, 1995.
17. Lounnas, V., Pettitt, M., Findsen, L., Subramaniam, S. A microscopic view of protein solvation. J. Phys. Chem. 96: 7157-7159, 1992.
18. Kuhn, L.A., Siani, M.A., Pique, M.E., Fisher, C.L., Getzoff, E.D., Tainer, J.A. The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures. J. Mol. Biol. 228:13-22, 1992.
19. Vijay-Kumar, S., Bugg, C.E., Cook, W.J. Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol., 194:531-544, 1987.
20. Voronoi, G.F. Nouvelles applications des paramètres continus àla théorie des formes quadratiques. J. Reine Angew. Math. 134:198-287, 1908.
21. Richards, F.M. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6:151-176, 1977.
22. Denisov, V.P., Halle, B. Dynamics of the internal and external hydration of globular proteins. J. Am. Chem. Soc. 116.10324-10325, 1994.
23. Ngai, K.L., Rendell, R.W., Rajagopal, A.K., Teitler, S. Three coupled relations for relaxations in complex systems. Ann. N.Y. Acad. Sci. 484:150-184, 1986.
24. Shlesinger, M.F. Fractal time in condensed matter. Annu. Rev. Phys. Chem. 39:269-290, 1988.
25. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., Hermans, J. "Intermolecular Forces." Dordrecht: Reidel, 1981.
26. Postma, J.P.M. "A Molecular Dynamics Study of Water." Ph.D. thesis, Rijksuniversiteit Groningen, 1985.
27. Van Gunsteren, W.F., Berendsen, H.J.C. "GROningen MOlecular Simulation (GROMOS) Library Manual." Groningen, The Netherlands: Biomos, 1987.
28. Ewald, P.P. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 64:253-287, 1921.
29. De Leeuw, S.W., Perram, J.W., Smith, E.R. Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants. Proc. R. Soc. Lond. [A] 373:27-56, 1980.
30. Adams, D.J., Dubey, G.S. Taming the Ewald sum in the computer simulation of charged systems. J. Comput. Phys., 72:156-176, 1987.
31. Van Gunsteren, W.F., Berendsen, H.J.C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1311-1327, 1977
32. Berendsen, H.J.C., Postma, J.P.M., DiNola, A., Haak, J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690, 1984.
33. Kell, G.S. Thermodynamic and Transport Properties of Liquid Water. Franks, F. (ed.). "Water. A Comprehensive Treatise," vol. 1. New York: Plenum Press, 1972.
34. Bernal, J.D., King, S.V. "Physics of Simple Liquids." Amsterdam: North Holland, 1968.
35. Gerstein, M., Tsai, J., Levitt, M. The volume of atoms on the protein surface: Calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249:955-966, 1995.
36. Neumann, M., Vesely, F.J., Steinhauser, O., Schuster, P. Solvation of large dipoles. A molecular dynamics study II. Mol. Phys. 37:1725-1743, 1979.
37. Gerstein, M., Lynden-Bell, RM. Simulation of water around a model protein helix. 1. Two-dimensional projections of solvent structure. J. Phys. Chem. 97:2982-2990, 1993.
38. Hubbard, S.J., Thornton, J.M. NACCESS. Computer Program. Technical report, Department of Biochemistry and Molecular Biology, University College London, 1993.
39. Kohlrausch, R. Ann. Phys. "Über das Dellmann'sche Elektrometer." (Leipzig) 12:353, 1847.
40. Williams, G. Watts, D.C. Trans. "Non-symmetrical dielectric relaxation behavior arising from a simple empirical decay function." Faraday Soc. 66:80, 1970.
41. Press, W.H., Flannery, B.P., Teukolsky, S.A., Vetterling, W.T. "Numerical Recipes. The Art of Scientific Computing." Cambridge and New York: Cambridge University Press, 1986.
42. Palmer, R.G., Stein, D.L., Abrahams, E., Anderson, P.W. Models of hierarchically constrained dynamics for glassy relaxation. Phys. Rev. Lett. 53:958-961, 1984.
43. Neumann, M. Struktur und Dynamik von Solvathüllen um hochpolare Moleküle: Eine Molekulardynamik-Prinzipstudie. Ph.D. thesis, Universität Wien, 1978.
44. Frattini, R., Ricci, M.A., Ruocco, G., Sampoli, M. Temperature evolution of single particle correlation functions of liquid water. J. Chem. Phys. 92:2540-2547, 1990.
45. Stillinger, F.H., Rahman, A. Molecular dynamics study of temperature effects on water structure and kinetics. J. Chem. Phys. 57:1281-1292, 1972.
46. Rahman, A., Stillinger, F.H. Molecular dynamics study of liquid water. J. Chem. Phys. 55:3336-3359, 1971.
47. \47. Rottmann, K. "Mathematische Formelsammlung." Bibliographisches Institut, Mannheim, 1984.
48. Lounnas, V., Pettitt, B.M. Distribution function implied dynamics versus residence times and correlations: Solvation shells of myoglobin. Proteins 18:148-160, 1994.
49. Finney, J.L., Poole, P.L. "Protein hydration and enzyme activity: The role of hydration-induced conformation and dynamic changes in the activity of lysozyme." Comments Mol. Cell. Biophys. 2:129-151, 1984.
50. Garcia, A.E., Stiller, L. Computation of the mean residence time of water in the hydration shells of biomolecules. J. Comput. Chem. 14:1396-1406, 1993.
51. Komeiji, Y., Uebayasi, M., Someya, J., Yamato, I. A molecular dynamics study of solvent behavior around a protein. Proteins 16:268-277, 1993.
52. Schreiber, H., Steinhauser, O. Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. Biochemistry 31:5856-5860, 1992.
53. Schreiber, H., Steinhauser, O. Taming cut-off induced artifacts in molecular dynamics studies of solvated polypeptides. J. Mol. Biol. 228:909-923, 1992.
54. Brüschweiler, R., Roux, B., Blackledge, M., Griesinger, C., Karplus, M., Ernst, R.R. Influence of rapid intramolecular motion on NMR cross-relaxation rates. A molecular dynamics study of antamanide in solution. J. Am. Chem. Soc. 114:2289-2302, 1992.
55. Smith, P.E., van Gunsteren, W.F. Translational and rotational diffusion of proteins. J. Mol. Biol. 236:629-636, 1994.
56. Van Belle, D., Wodak, S.J. Molecular dynamics study of methane hydration and methane association in a polarizable water phase. J. Am. Chem. Soc. 115:647-652, 1993.
57. Ahlström, P., Wallqvist, A., Engström, S., Jönsson, B. A molecular dynamics study of polarizable water. Mol. Phys. 68:563-581, 1989.