Diffusion of solvent around biomolecular solutes: A molecular dynamics simulation study

Biophysical Journal

Volumn 75, Issue 1, 1998, Pages 150-158

  Makarov, Vladimir A ^a,b   Feig, Michael ^b   Andrews, B Kim ^b   Pettitt, B Montgomery ^b  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b University of Houston   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORIDE ION; DNA; MYOGLOBIN; SODIUM ION; SOLVENT; WATER;

ARTICLE; BULK DENSITY; DIFFUSION; MACROMOLECULE; MOLECULAR DYNAMICS; SIMULATION; SOLUBILITY; SOLVATION; SURFACE PROPERTY;

EID: 0031807764     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77502-2     Document Type: Article

References (47)

1. Abseher, R., H. Schreiber, and O. Steinhauser. 1996. The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation. Proteins Struct. Funct. Genet. 25:366-378.
2. Ahlström, P., O. Teleman, and B. Jönsson. 1988. Molecular dynamics simulation of interfacial water structure, and dynamics in a parvalbumin solution. J. Am. Chem. Soc. 110:4198-4203.
3. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Clarendon Press, Oxford. 191-196.
4. Alper, H. E., D. Bassolino, and T. R. Stouch. 1993a. Computer simulation of a phospholipid monolayer-water system: the influence of long range forces on water structure and dynamics. J. Chem. Phys. 98:9798-9807.
5. Alper, H. E., D. Bassolino-Klimas, and T. R. Stouch. 1993b. The limiting behavior of water hydrating a phospholipid monolayer: a computer simulation study. J. Chem. Phys. 99:5547-5559.
6. Andrews, B. K., T. Romo, J. B. Clarage, B. M. Pettitt, and G. N. Phillips. 1998. Characterizing global substates of myoglobin. Structure. (in press).
7. Berendsen, H. J. C., J. P. M. Potsma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. Reidel, Dordrecht, The Netherlands. 331-342.
8. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. J. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
9. Beveridge, D. L., S. Swaminathan, G. Ravishanker, J. M. Withka, J. Srinivasan, C. Prevost, S. Louise-May, D. R. Langley, F. M. DiCapua, and P. H. Bolton. 1993. Molecular dynamics simulations on the hydration, structure, and motions of DNA oligomers. In Water and Biological Macromolecules. E. Westhof, editor. CRC Press, Boca Raton, FL.
10. Bizzarri, A. R., and S. Cannistraro. 1996. Molecular dynamics simulation evidence of anomalous diffusion of protein hydration water. Phys. Rev. E. 53:3040-3043.
11. Bizzarri, A. R., and S. Cannistraro. 1997. Anomalous, and anisotropic diffusion of plastocyanin hydration water. Europhys. Lett. 37:201-206.
12. Bizzarri, A. R., C. Rocchi, and S. Cannistraro. 1996. Origin of the anomalous diffusion observed by MD simulation at the protein-water interface. Chem. Phys. Lett. 263:559-566.
13. Brooks, C. L., and M. Karplus. 1989. Solvent effects on protein motion, and protein effects on solvent motion. Dynamics of the active site region of lysozyme. J. Mol. Biol. 208:159-181.
14. Brunne, R. M., E. Liepinsh, G. Otting, K. Wüthrich, and W. F. van Gunsteren. 1993. Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 231: 1040-1048.
15. Burling, F. T., W. I. Weis, K. M. Flaherty, and A. T. Brünger. 1996. Direct observation of protein solvation, and discrete disorder with experimental crystallographic phases. Science. 271:72-77.
16. Chiu, S.-W., M. Clark, V. Balaji, S. Subramaniam, H. L. Scott, and E. Jakobsson. 1995. Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. Biophys. J. 69:1230-1245.
17. 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.
18. Feig, M., and B. M. Pettitt. 1997. Experiment vs. force fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B. 101:7361-7363.
19. Garcia, A. E., and L. Stiller. 1993. Computation of the mean residence time of water in the hydration shells of biomolecules. J. Comp. Chem. 14:1396-1406.
20. Hartsough, D. S., and K. M. Merz. 1993. Protein dynamics, and solvation in aqueous, and nonaqueous environments. J. Am. Chem. Soc. 115: 6529-6537.
21. Hertz, H. G. 1973. Nuclear magnetic relaxation spectroscopy. In Water: A Comprehensive Treatise, Vol. 3. F. Franks, editor. Plenum Press, New York. 301-395.
22. Jiang, J.-S., and A. T. Brünger. 1994. Protein hydration observed by x-ray diffraction. Solvation properties of penicillopepsin, and neuraminidase crystal structures. J. Mol. Biol. 243:100-115.
23. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
24. Knapp, E. W., and I. Muegge. 1993. Heterogeneous diffusion of water at protein surfaces: application to BPTI. J. Phys. Chem. 97:11339-11343.
25. Komeiji, Y., M. Uebayasi, J. Someya, and I. Yamato. 1993. A molecular dynamics study of solvent behavior around a protein. Proteins Struct. Funct. Genet. 16:268-277.
26. Lau, K. F., H. E. Alper, T. S. Thacher, and T. R. Stouch. 1994. Effects of switching functions on the behavior of liquid water in molecular dynamics simulations. J. Phys. Chem. 98:8785-8792.
27. Levitt, M., and R. Sharon. 1988. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. USA. 85:7557-7561.
28. Lounnas, V., B. M. Pettitt, and G. N. Phillips. 1994. A global model of the protein-solvent interface. Biophys. J. 66:601-614.
29. MacKerell, A. D., D. Bashford, M. Bellott, R. L. Dunbrack, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, B. Roux, M. Schlenkrich, J. C. Smith., R. Stote, J. Straub, J. Wiorkiewicz-Kuczera, and M. Karplus. 1992. Self-consistent parameterization of biomolecules for molecular modeling, and condensed phase simulations. FASEB J. 6A:143.
30. Makarov, V. A., B. K. Andrews, and B. M. Pettitt. 1997. Reconstructing the protein-water interface. Biopolymers. (in press).
31. Mezei, M., and D. L. Beveridge. 1986. Structural chemistry of biomolecular hydration via computer simulation: the proximity criterion. Methods Enzymol. 127:21-47.
32. Muegge, I., and E. W. Knapp. 1995. Residence times, and lateral diffusion of water at protein surfaces: application to BPTI. J. Phys. Chem. 99: 1371-1374.
33. Norin, M., F. Haeffner, K. Hult, and O. Edholm. 1994. Molecular dynamics simulations of an enzyme surrounded by vacuum, water, or a hydrophobic solvent. Biophys. J. 67:548-559.
34. Phillips, G. N., and B. M. Pettitt. 1995. Structure and dynamics of the water around myoglobin. Protein Sci. 4:149-158.
35. Quillin, M. L., R. M. Arduini, J. S. Olson, and G. N. Phillips. 1993. High-resolution crystal structures of distal histidine mutants of sperm whale myoglobin. J. Mol. Biol. 234:140-155.
36. Raghavan, K., M. R. Reddy, and M. L. Berkowitz. 1992. A molecular dynamics study of the structure and dynamics of water between dilauroylphosphatidylethanolamine bilayers. Langmuir. 8:233-240.
37. Rocchi, C., A. R. Bizzarri, and S. Cannistraro. 1997. Water residence times around copper plastocyanin: a molecular dynamics simulation approach. Chem. Phys. 214:261-276.
38. Roux, B., B. Prodhom, and M. Karplus. 1995. Ion transport in the gramicidin channel: molecular dynamics study of single and double occupancy. Biophys. J. 68:876-892.
39. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1997. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys. 23: 327-341.
40. Smith, P. E., M. E. Holder, L. X. Dang, M. Feig, and B. M. Pettitt. 1996. ESP. University of Houston, Houston, TX.
41. Smith, P. E., and B. M. Pettitt. 1991. Peptides in ionic solutions: a comparison of the Ewald and switching function techniques. J. Chem. Phys. 95:8430-8441.
42. Smith, P. E., and B. M. Pettitt. 1995. Efficient Ewald electrostatic calculations for large systems. Comp. Phys. Comm. 91:339-344.
43. Teeter, M. M. 1991. Water-protein interactions: theory, and experiment. Annu. Rev. Biophys. Biophys. Chem. 20:577-600.
44. Tirado-Rives, J., and W. L. Jorgensen. 1990. Molecular dynamics of proteins with the OPLS potential functions. Simulation of the third domain of silver pheasant ovomucoid in water. J. Am. Chem. Soc. 112:2773-2781.
45. Tyrrell, H. J. V., and K. R. Harris. 1984. Diffusion in electrolytes. In Diffusion in Liquids. Butterworths, London. 387-437.
46. Wang, C. X., W. Z. Chen, V. Tran, and R. Douillard. 1996. Analysis of interfacial water structure, and dynamics in α-maltose solution by molecular dynamics simulation. Chem. Phys. Lett. 251:268-274.
47. Wong, C. F., and J. A. McCammon. 1987. Computer simulation and the design of new biological molecules. Isr. J. Chem. 27:211-215.