Hydration of an α-helical peptide: Comparison of theory and molecular dynamics simulation

Proteins: Structure, Function and Genetics

Volumn 27, Issue 4, 1997, Pages 471-480

  García, Angel E ^a   Hummer, Gerhard ^a   Soumpasis, Dikeos Mario ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

hydrophilic hydration; hydrophobic hydration; potentials of mean force; protein hydration

Indexed keywords

PEPTIDE;

ALPHA HELIX; ARTICLE; HYDRATION; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; STATISTICS;

COMPUTER SIMULATION; MODELS, MOLECULAR; MODELS, THEORETICAL; PEPTIDES; PROTEIN STRUCTURE, SECONDARY; WATER;

EID: 0030906757     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199704)27:4<471::AID-PROT1>3.0.CO;2-E     Document Type: Article

References (57)

1. Nemethy, G., Scheraga, H.A. The structure of water and hydrophobic bonding in proteins. III. The thermodynamic properties of hydrophobic bonds in proteins. J. Phys. Chem. 66:1773-1789, 1962.
2. Singer, P.T., Smalas, A., Carty, R.P., Mangel, W.F., Sweet, R.M. The hydrolytic water molecule in trypsin, revealed by time-resolved Laue crystallography. Science 259:669-673, 1993.
3. Kuntz Jr., I.D., Kauzmann, W. Hydration of proteins and polypeptides. Adv. Protein Chem. 28:239-345, 1974.
4. Finney, J.L., Gellatly, B.J., Golton, I.C., Goodfellow, J. Solvent effects and polar interactions in the structural stability and dynamics of globular proteins. Biophys. J. 32:17-33, 1990.
5. Savage, H.F.J. Water-structure in crystalline solids: Ices to proteins. Water Sci. Rev. 2:67-148, 1986.
6. Saenger, W. Structure and dynamics of water surrounding biomolecules. Annu. Rev. Biophys. Biophys. Chem 16:93-114, 1987.
7. Rupley, J.A., Careri, G. Protein hydration and function. Adv. Protein Chem. 41:37-172, 1991.
8. Teeter, M.M. Water-protein interactions - theory and experiment. Annu. Rev. Biophys. Biophys. Chem. 20:577-600, 1991.
9. Meyer, E. Internal water molecules and H-bonding in biological macromolecules: A review of structural features with functional implications. Protein Sci. 1:1543-1562, 1992.
10. Schoenborn, B.P., García, A.E., Knott, R. Hydration in protein crystallography. Prog. Rep. Biophys. 64:105-119, 1996.
11. Cheng, X., Schoenborn, B.P. Hydration in protein crystals: A neutron diffraction analysis of carbonmonoxymyoglobin. Acta Crystallogr. B 46:195-208, 1990.
12. Otting, G., Liepinsh, E., Wüthrich, K. Protein hydration in aqueous solution. Science 254:974-980, 1991.
13. Kubinec, M.G., Wemmer, D.E. NMR evidence for DNA bound water in solution. J. Am. Chem. Soc. 114:8739-8740, 1992.
14. Thanki, N., Thornton, J.M., Goodfellow, J.M. Distributions of water around amino acid residues in proteins. J. Mol. Biol. 202:637-657, 1988.
15. Thanki, N., Thornton, J.M., Goodfellow, J.M. Influence of secondary structure on the hydration of serine, threonine and tyrosine residues in proteins. Protein Eng. 3:495-508, 1990.
16. Thanki, N., Umrania, Y., Thornton, J.M., Goodfellow, J.M. Analysis of protein main-chain solvation as a function of secondary structure. J. Mol. Biol. 221:669-691, 1991.
17. Roe, S.M., Teeter, M.M. Patterns for prediction of hydration around polar residues in proteins. J. Mol Biol. 229:419-427, 1993.
18. Savage, H.F.J., Finney, J.L. Repulsive regularities of water structure in ices and crystalline hydrates. Nature 322:717-720, 1986.
19. Clementi, E., Corongiu, G. Interactions of water with DNA single-helix in the A conformation. Biopolymers 18:2431-2450, 1979.
20. Parak, F., Hartmann, H., Schmidt, M., Corongiu, G., Clementi, E. The hydration shell of myoglobin. Eur. Biophys. J. 21:313-320, 1992.
21. Steinbach, P.J., Brooks, B.R. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl. Acad. Sci. USA 90:9135-9139, 1993.
22. Loncharich, R.J., Brooks, B.R. Temperature dependence of dynamics of hydrated myoglobin. J. Mol. Biol. 215:435-455, 1990.
23. Levitt, M., Sharon, R. Accurate simulations of protein dynamics in solution. Proc. Natl. Acad. Sci. USA 85:7557-7561, 1988.
24. Levitt, M. Molecular dynamics of macromolecules in water. Chem. Scripta, 29a:197-203, 1989.
25. García, A.E., Stiller, L. Computation of the mean residence time of water in the hydration shells of biomolecules. J. Comp. Chem. 14:1396-1406, 1993.
26. Brunne, R.M., Liepinsh, E., Otting, G., Wüthrich, K., van Gunsteren, W.F. 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, 1993.
27. Gerstein, M., Lynden-Bell, R.M. Simulation of water around a model protein helix. 1. Two-dimensional projections of solvent structure. J. Phys. Chem. 97:2982-2990, 1993.
28. Gerstein, M., Lynden-Bell, R.M. Simulation of water around a model protein helix. 2. The relative contributions of packing, hydrophobicity, and hydrogen bonding. J. Phys. Chem. 97:2991-2999, 1993.
29. Vedani, A., Huhta, D.W. An algorithm for the systematic solvation of proteins based on the directionality of hydrogen bonds. J. Am. Chem. Soc. 113:5860-5862, 1991.
30. Pitt, W.R., Murray-Rust, J., Goodfellow, J. Aquarius 2: Knowledge-based modeling of solvent sites around proteins. J. Comp. Chem. 14:1007-1018, 1993.
31. Hummer, G., Soumpasis, D.M. Computation of the water density distribution at the ice-water interface using the potentials-of-mean-force expansion. Phys. Rev. E 49:591-596, 1994.
32. Hummer, G., Soumpasis, D.M. A new approach to calculate the hydration of DNA molecules. In: "Structural Biology: The State of the Art; Proceedings of the Eighth Conversations in the Discipline of Biomolecular Stereodynamics. Vol. 2. Sarma, R.H., Sarma, M.H. (eds.). Schenectady, NY: Adenine Press, 1994:273-278.
33. Hummer, G., Soumpasis, D.M. Statistical mechanical treatment of the structural hydration of biological macromolecules: Results for B-DNA. Phys. Rev. E 50:5085-5095, 1994.
34. Hummer, G., Soumpasis, D.M., Garcia, A.E. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems. In: Nonlinear Excitations in Biomolecules. Peyrard, M. (ed.). Les Editions de Physique. Berlin: Springer, 1995:83-99.
35. García, A.E., Hummer, G., Soumpasis, D.M. Theoretical description of biomolecular hydration - application to A-DNA. In: Neutrons in Biology. Schoenborn, B.P., and Knott, R. (eds) Plenum Press, New York, 1997.
36. Hummer, G., Garcia, A.E., Soumpasis, D.M. Hydration of nucleic-acid fragments: Comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. Biophys. J 68:1639-1652, 1995.
37. Forester, T.R., McDonald, I.R. Molecular dynamics studies of the behaviour of water molecules and small ions in concentrated solutions of polymeric B-DNA. Mol. Phys. 72:643-660, 1991.
38. Forsyth, V.T., Mahendrasingam, A., Pigram, W.J., Greenall, R.J., Bellamy, K., Fuller, W., Mason, S.A. Neutron fibre diffraction study of DNA hydration. Int. J. Biol. Macromol. 11:236-240, 1989.
39. Jorgensen, W.L., Tirado-Rives, J. The OPLS potential energy functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666, 1988.
40. Kirkwood, J.G., Statistical mechanics of fluid mixtures. J. Chem. Phys. 3:300-313, 1935.
41. Soumpasis, D.M. Statistical mechanics of the B-Z transition of DNA: Contribution of diffuse ionic interactions. Proc. Natl. Acad. Sci. USA 81:5116-5120, 1984.
42. García, A.E., Soumpasis, D.M. Harmonic vibrations and thermodynamic stability of a DNA oligomer in monovalent salt solution. Proc. Natl. Acad. Sci. USA 86:3160-3164, 1989.
43. García, A.E., Gupta, G., Soumpasis, D.M., Tung, C.S. Energetics of the hairpin to mismatched duplex transition of d(GCCGCAGC) on NaCl solution. J. Biomol. Struct. Dyn. 8:173-186, 1990.
44. Klement, R., Soumpasis, D.M., Jovin, T.M. Computation of ionic distributions around charged biomolecular structures: Results for right-handed and left-handed DNA. Proc. Natl. Acad. Sci. USA 88:4631-4635, 1991.
45. Chen, Y.Z., Prohofsky, E.W. Salt dependent premelting base pair opening probabilities of B and Z DNA poly[d(G-C)] and significance for the B-Z transition. Biophys. J. 64:1394-1397, 1993.
46. Soumpasis, D.M., Procacci, P., Corongiu, G. Part A: On the computation of N-particle correlations in classical fluids via computer simulations. Part B: Triplet correlations in NCC water. IBM DSD Report. IBM, October 1991.
47. Fisher, I.Z., Kopeliovich, B.L. On a refinement of the superposition approximation in the theory of fluids. Dokl. Akad. Nauk. SSSR, 133:81-83, 1960, [1960. Sov. Phys.-Dokl. 5:761-763].
48. Fisher, I.Z., Kopeliovich, B.L. On a refinement of the superposition approximation in the theory of fluids. Dokl. Akad. Nauk. SSSR, 133:81-83, 1960, [1960. Sov. Phys.-Dokl. 5:761-763].
49. Garde, S., Hummer, G., García, A.E., Pratt, L.R., Paulaitis, M.E. Hydrophobic hydration: Inhomogeneous water structure near nonpolar molecular solutes. Phys. Rev. E. 53: R4310-R4313, 1996.
50. Ashbaugh, H.S., Paulaitis, M.E. Entropy of hydrophobic hydration - extension to hydrophobic chains. J. Phys. Chem. 100:1900-1913, 1996.
51. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R. W., Klein, M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935, 1983.
52. Jorgensen, W.L., Madura, J.D., Swenson, C.J. Optimized intermolecular potential functions for liquid hydrocarbons. J. Am. Chem. Soc. 106:6638-6646, 1984.
53. Pratt, L.R., Hummer, G., García, A.E. Ion pair potentials-of-mean-force in water. Biophys. Chem. 51:147-165, 1994.
54. Hummer, G., Soumpasis, D.M. Correlations and free energies in restricted primitive model descriptions of electrolytes. J. Chem. Phys. 98:581-591, 1993.
55. Ryckaert, J.P., Cicotti, G., Berendsen, H.J.C. Numerical integration of the cartesian equations of motions of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341, 1977.
56. Hummer, G., Garcia, A.E., Soumpasis, D.M. A statistical mechanical description of biomolecular hydration. Faraday Discuss. Chem. Soc. 113, 1997 in press.
57. Oprea, T.I., Hummer, G., García, A.E. Identification of a functional water channel in cytochrome P450 enzymes. Proc. Natl. Acad. Sci. USA, 1997 in press.