Simple models for hydrophobic hydration

Chemical Society Reviews

Volumn 34, Issue 12, 2005, Pages 1012-1020

  Höfinger, Siegfried ^a   Zerbetto, Francesco ^b  

^a Novartis Inst for Biomed Research   (Austria)

^b UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 29144470089     PISSN: 03060012     EISSN: 14604744     Source Type: Journal    
DOI: 10.1039/b504088b     Document Type: Article

References (55)

1. K. Lum, D. Chandler, J. D. Weeks, Hydrophobicity at Small and Large Length Scales. J. Phys. Chem. B, 1999, 103, 4570-4577
2. A. Wallqvist, B. J. Berne, Computer Simulation of Hydrophobic Hydration Forces on Stacked Plates at Short Range. J. Phys. Chem. 1995, 99, 2893-2899
3. N. N. Alder, A. E. Johnson, Cotranslational membrane protein biogenesis at the endoplasmic reticulum. J. Biol. Chem. 2004, 279, 22787-22790
4. S. H. White, G. von Heijne, The machinery of membrane protein assembly. Curr. Opin. Struct. Biol. 2004, 14, 397-404
5. S. J. Kim, D. Mitra, J. R. Salerno, R. S. Hegde, Signal sequences control gating of the protein translocation channel in a substrate-specific manner. Dev. Cell, 2002, 2, 207-217
6. V. Goder, M. Spiess, Topogenesis of membrane proteins: determinants and dynamics. FEBS Lett. 2001, 504, 87-93
7. V. Goder, M. Spiess, Molecular mechanism of signal sequence orientation in the endoplasmic reticulum. EMBO J. 2003, 22, 3645-3653
8. K. Melen, A. Krogh, G. von Heijne, Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol. 2003, 327, 735-744
9. S. H. White, The progress of membrane protein structure determination. Protein Sci. 2004, 7, 1948-1949
10. J. Wagoner, N. A. Baker, Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. J. Comput. Chem. 2004, 13, 1623-1629
11. J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, D. A. Case, Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices. J. Am. Chem. Soc. 1998, 37, 120, 9401-9409
12. H. A. Carlson, W. L. Jorgensen, An Extended Linear Response Method for Determining Free Energies of Hydration. J. Phys. Chem. 1995, 99, 10667-10673
13. J. W. Pitera, W. F. van Gunsteren, The Importance of Solute-Solvent van der Waals Interactions with Interior Atoms of Biopolymers. J. Am. Chem. Soc. 2001, 123, 3163-3164
14. B. Roux, Implicit Solvent Models, Computational Biophysics, O. Becker, A. D. MacKerrel, B. Roux, M. Watanabe, Eds. Marcel Dekker Inc, New York, 2001
15. H. Reiss, H. L. Frisch, J. L. Lebowitz, Statistical mechanics of rigid spheres. J. Chem. Phys. 1959, 31, 369-380
16. E. Wilhelm, R. Battino, Estimation of Lennard-Jones (6,12) Pair Potential Parameters from Gas Solubility Data. J. Chem. Phys. 1971, 55, 4012-4017
17. F. H. Stillinger, Structure in Aqueous Solutions of Nonpolar Solutes from the Standpoint of Scaled-Particle Theory. Solution Chem. 1973, 2, 141-158
18. R. A. Pierotti, A Scaled Particle Theory of Aqueous and Nonaqueous Solutions. Chem. Rev. 1976, 76, 717-726
19. L. R. Pratt, D. Chandler, Theory of the Hydrophobic Effect. J. Chem. Phys. 1977, 67, 3683-3704
20. P. M. Postma, H. J. C. Berendsen, J. R. Haak, Thermodynamics of Cavity Formation in Water: A Molecular Dynamics Study. Faraday Symp. Chem. Soc. 1982, 17, 55-67
21. R. W. Zwanzig, High temperature equation of state by a perturbation method in nonpolar gases. J. Chem. Phys. 1954, 22, 1420-1426
22. T. Simonson, G. Archontis, M. Karplus, Protein-Ligand Recognition: Free Energy Simulations Come of Age. Acc. Chem. Res. 2002, 35, 430-437
23. A. Pohorille, L. R. Pratt, Cavities in Molecular Liquids and the Theory of Hydrophobic Solubilities. J. Am. Chem. Soc. 1990, 112, 5066-5074
24. L. R. Pratt, A. Pohorille, Theory of hydrophobicity: Transient cavities in molecular liquids. Proc. Natl. Acad. Sci. U. S. A. 1992, 89, 2995-2999
25. L. R. Pratt, Molecular Theory of Hydrophobic Effects: She is too mean to have her name repeated. Annu. Rev. Phys. Chem. 2002, 53, 409-436
26. G. Hummer, S. Garde, A. E. Garcia, A. Pohorille, L. R. Pratt, An information theory model of hydrophobic interactions. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 8951-8955
27. F. M. Floris, M. Selmi, A. Tani, J. Tomasi, Free energy and entropy for inserting cavities in water: Comparison of Monte Carlo simulation and scaled particle theory results. J. Chem. Phys. 1997, 107, 6353-6365
28. S. Höfinger, F. Zerbetto, On the Cavitation Energy of Water. Chem. Eur. J. 2003, 9, 566-569
29. S. Höfinger, F. Zerbetto, The Free Energy of Nanobubbles in Organic Liquids. J. Phys. Chem. A, 2003, 107, 11253-11257
30. S. Höfinger, F. Zerbetto, The costly process of creating a cavity in n-octanol. Theor. Chem. Acc. 2004, 112, 240-246
31. T. Simonson, Free energy of particle insertion. An exact analysis of the origin singularity for simple liquids. Mol. Phys. 1993, 80, 441-447
32. T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, W. F. van Gunsteren, Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Lett. 1994, 222, 529-539
33. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr. R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, N. Rega, P. Salvador, J. J. Dannenberg, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle and J. A. Pople, Gaussian 98, Revision A.11.3, Gaussian, Inc. Pittsburgh PA, 2002
34. J. J. Jasper, The surface tension of pure liquid compounds. J. Phys. Chem. Ref. Data, 1972, 1, 841-980
35. N. Morel-Desrosiers, J.-P. Morel, Evaluation of thermodynamic functions relative to cavity formation in liquids: uses and misuses of Scaled Particle Theory. Can. J. Chem. 1981, 59, 1-7
36. H. De Voe, Structural Entropy Changes in Infinitely Dilute Solutions and Pure Liquids. J. Am. Chem. Soc. 1976, 98, 1724-1729
37. K. E. S. Tang, V. A. Bloomfield, Excluded Volume in Solvation: Sensitivity of Scaled-Particle Theory to Solvent Size and Density. Biophys. J. 2000, 79, 2222-2234
38. V. Gogonea, C. Bãleanu-Gogonea, E. Osawa, Solvent hard sphere diameter from van der Waals volume. A statistical analysis of computed and solubility determined solvent diameters. J. Mol. Struct. 1998, 432, 177-189
39. H. M. Neumann, Some Observations on the Scaled-Particle Theory of Solutions and the Surface Tension of Solvents. J. Solution Chem. 1977, 6, 33-38
40. G. D. Hawkins, C. J. Cramer, D. G. Truhlar, Parameterized Model for Aqueous Free Energies of Solvation Using Geometry-Dependent Atomic Surface Tensions with Implicit Electrostatics. J. Phys. Chem. B, 1997, 101, 7147-7157
41. D. A. Pearlman, D. A. Case, J. W. Caldwell, W. R. Ross, T. E. Cheatham, S. De Bolt, III, D. C. Ferguson, G. Seibel, P. A. Kollman, AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules. Comp. Phys. Commun. 1995, 91, 1-41
42. T. Darden, D. York, L. Pedersen, Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092
43. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, M. L. Klein, Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79, 926-935
44. W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. C. Ferguson, D. C. Spellmayer, T. Fox, J. W. Caldwell, P. A. Kollman, A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197
45. J.-H. Lii, N. L. Allinger, Directional Hydrogen Bonding in the MM3 Force Field. J. Comput. Chem. 1998, 19, 1001-1016
46. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Di Nola, J. R. Haak, Molecular Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984, 81, 3684-3690
47. Y. N. Vorobjev, J. Hermans, SIMS: Computation of a Smooth Invariant Molecular Surface. Biophys. J. 1997, 73, 722-732
48. A. Wallqvist, B. J. Berne, Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute Curvature and Surface Area. J. Phys. Chem. 1995, 99, 2885-2892
49. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren and J. Hermans, Intermolecular Forces, B. Pullman, Ed. D. Reidel Publishing Company, Dordrecht, The Netherlands, 1981, p. 331
50. Y. Kong, J. W. Ponder, Calculation of the Reaction Field Due to Off-Center Point Multipoles. J. Chem. Phys. 1997, 107, 481-492
51. J. W. Pitera, W. Swope, Understanding folding and design: Replica-exchange simulations of “Trp-cage” miniproteins. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 7587-7592
52. D. M. Huang, D. Chandler, Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding. Proc. Natl. Acad. Sci. U. S. A. 2000, 97, 8324-8327
53. K. P. Murphy, Hydration and convergence temperatures: on the use and interpretation of correlation plots. Biophys. Chem. 1994, 51, 311-326
54. R. C. Weast, CRC Handbook of Chemistry and Physics, 67th Edition, CRC Press Inc. Boca Raton, Florida, USA, 1986
55. D. Chandler, Interfaces and the driving force of hydrophobic assembly. Nature, 2005, 437, 640-647