Solvent-induced free energy landscape and solute-solvent dynamic coupling in a multielement solute

Biophysical Journal

Volumn 77, Issue 5, 1999, Pages 2470-2478

  San Biagio, P L ^a   Martorana, V ^a   Bulone, D ^a   Palma Vittorelli, M B ^b   Palma, M U ^b,c  

^a CNR   (Italy)

^b UNIVERSITY OF PALERMO   (Italy)

^c Fisica   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

SOLVENT; WATER;

ARTICLE; HYDRATION; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; PROTEIN ANALYSIS; PROTEIN FOLDING; SIMULATION;

EID: 0032757309     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77083-9     Document Type: Article

References (46)

1. Brugé, F., G. Cottone, R. Noto, and S. L. Fornili. 1996a. Microscopic aspects of solute-solute interactions induced by the solvent. J. Chim. Phys. 93:1858-1878.
2. Brugé, F., S. L. Fornili, G. G. Malenkov, M. B. Palma-Vittorelli, and M. U. Palma. 1996b. Solvent-induced forces on a molecular scale: nonadditivity, modulation and causal relation to hydration. Chem. Phys. Lett. 254:283-291.
3. Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and energy landscape of protein folding: a synthesis. Proteins Struct. Funct. Genet. 21:167-195.
4. Bulone, D., V. Martorana, P. L. San Biagio, and M. B. Palma-Vittorelli. 1997. Effects of the electric charges on hydrophobic forces. Phys. Rev. E. 56:R4939-R4942.
5. Bulone, D., M. B. Palma-Vittorelli, and M. U. Palma. 1992. Enthalpic and entropic contributions of water molecules to functional T→R transition of human hemoglobin in solution. Int. J. Quantum Chem. 42:1427-1437.
6. Bulone, D., P. L. San Biagio, M. B. Palma-Vittorelli, and M. U. Palma. 1993. On the role of water in hemoglobin function and stability. Science. 259:1335-1336.
7. Case, D. A., D. A. Pearlman, J. W. Caldwell, T. E. Cheatham III, W. S. Ross, C. L. Simmerling, T. A. Darden, K. M. Mertz, R. V. Stanton, A. L. Cheng, J. J. Vincent, M. Crowley, D. M. Ferguson, R. J. Radmer, G. L. Seibel, U. C. Singh, P. K. Weiner, and P. A. Kollmann. 1997. AMBER 5. University of California, San Francisco.
8. Dill, K. A., S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan. 1995. A perspective from simple exact models. Protein Sci. 39:561-602.
9. Duan, Y., and P. A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:740-744.
10. Franks, F. 1973. The hydrophobic interaction, In Water: A Comprehensive Treatise, Vol. 4. F. Franks, editor. Plenum, New York. 1-94.
11. Frauenfelder, H., S. G. Sligar, and P. G. Wolynes. 1991. The energy landscapes and motions of proteins. Science. 254:1598-1603.
12. Friedman, H. L., and C. V. Krishnan. 1973. Thermodynamics of ion hydration. In Water: A Comprehensive Treatise, Vol. 3. F. Franks, editor. Plenum, New York. 1-93.
13. Garcia, A. E., G. Hummer, and D. M. Soumpasis. 1997. Hydration of an α-helical peptide: comparison of theory and molecular dynamics simulation. Proteins Struct. Dyn. Funct. 27:471-480.
14. Garde, S., G. Hummer, A. F. Garcia, L. R. Pratt, and M. B. Paulaitis. 1996. Hydrophobic hydration: inhomogeneous water structure near nonpolar molecular solutes. Phys. Rev. E. 53:R4310-R4313.
15. Hill, T. L. 1956. Statistical Mechanics. Dover, New York.
16. Hirata, F., B. M. Pettitt, and P. J. Rossky. 1982. Application of an extended RISM equation to dipolar and quadrupolar fluids. J. Chem. Phys. 77: 509-520.
17. Hummer, G., A. E. Garcia, and D. M. Soumpasis. 1996. A statistical mechanical description of biomolecular hydration. Faraday Discuss. 103:175-190.
18. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential function for simulating liquid water. J. Chem. Phys. 79:926-935.
19. Kitao, A., F. Hirata, and N. Go. 1991. The effects of solvent on the conformational and collective motions of proteins: normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum. Chem. Phys. 158:447-472.
20. Klement, R., D. M. Soumpasis, and T. M. Jovin. 1991. Computation of ionic distribution around charged biomolecular structures: results for right-handed and left-handed DNA. Proc. Natl. Acad. Sci. USA. 88: 4631-4635.
21. Lazaridis, T., G. Archontis, and M. Karplus. 1995. Enthalpic contribution to protein stability: insights from atom based calculations and statistical mechanics. Adv. Protein Chem. 47:231-306.
22. Lynden-Bell, R. M., and J. C. Rosaiah. 1997. From hydrophobic to hydrophilic behaviour: a simulation study of solvation entropy and free energy of simple solutes. J. Chem. Phys. 107:1981-1991.
23. Marcus, Y. 1994. A simple empirical model describing the thermodynamics of hydration of ions of widely varying charges, sizes and shapes. Biophys. Chem. 51:111-127.
24. Martorana, V., D. Bulone, P. L. San Biagio, M. B. Palma-Vittorelli, and M. U. Palma. 1997. Collective properties of hydration: long range and specificity of hydrophobic interactions. Biophys. J. 73:31-37.
25. Martorana, V., G. Corongiu, and M. U. Palma. 1996. Correlated solvent-induced forces on a protein at single residue resolution: relation to conformation, stability, dynamics and function. Chem. Phys. Lett. 254: 292-301.
26. Martorana, V., G. Corongiu, and M. U. Palma. 1998. Interaction of explicit solvent with hydrophobic/philic/charged residues of a protein: residue character vs. conformational context. Proteins Struct. Funct. Genet. 32:129-135.
27. Migliore, M., G. Corongiu, E. Clementi, and G. C. Lie. 1988. Monte Carlo study of free energy of hydration for Li, Na, K, F and Cl with ab-initio potentials. J. Chem. Phys. 88:7766-7771.
28. Palma, M. U., P. L. San Biagio, D. Bulone, and M. B. Palma-Vittorelli. 1994. Physical origin and biological significance of solvent induced forces. In Hydrogen Bond Networks. M. C. Bellissent-Funel and J. C. Dore, editors. NATO ASI Series C, Vol. 435. Kluwer, Dordrecht, the Netherlands. 457-479.
29. Pellegrini, M., and S. Doniach. 1995. Modeling solvation contributions to conformational free energy changes of biomolecules, using a potential of mean force expansion. J. Chem. Phys. 103:2696-2702.
30. Pepke, E., and J. Lyons. 1993. SciAn Users Manual. Supercomputer Computation Research Institute, Florida State University, Tallahassee, FL.
31. Perkyns, J. S., and B. H. Pettitt. 1995. Peptide conformations are restricted by solution stability. J. Phys. Chem. 99:1-2.
32. Pettitt, B. M., and M. Karplus. 1988. Conformational free energy of hydration for alanine dipeptide: thermodynamic analysis. J. Phys. Chem. 92:3994-3997.
33. Pettitt, B. M., M. Karplus, and P. J. Rossky. 1986. Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion of biomolecules. J. Phys. Chem. 90:6335-63345.
34. Plotikin, S. S., J. Wong, and P. G. Wolynes. 1996. Correlated energy landscape model for finite, random heteropolymers. Phys. Rev. E. 53: 6271-6296.
35. Plotikin, S. S., J. Wong, and P. G. Wolynes. 1997. Statistical mechanics of a correlated energy landscape model for protein folding funnels. J. Chem. Phys. 106:2932-2948.
36. San Biagio, P. L., D. Bulone, V. Martorana, M. B. Palma-Vittorelli, and M. U. Palma. 1998. Physics and biophysics of solvent induced forces: hydrophobic interactions and context-dependent hydration. Eur. Biophys. J. 27:183-196.
37. Shoemaker, B. A., J. Wang, and P. G. Wolynes. 1999. Exploring structures in protein folding funnels with free energy functional: the transition state ensemble. J. Mol. Biol. 287:675-694.
38. Shoemaker, B. A., and P. G. Wolynes. 1999. Exploring structures in protein folding funnels with free energy functionals: the denatured ensemble. J. Mol. Biol. 287:657-674.
39. Smith, P. E., and B. M. Pettitt. 1994. Modeling solvent in biomolecular systems. J. Phys. Chem. 98:9700-9711.
40. Stillinger, F. H. 1988. Supercooled liquids, glass transitions and Kauzmann paradox. J. Chem. Phys. 88:7818-7825.
41. Straatsma, T. P., and H. J. C. Berendsen. 1988. Free energy of ionic hydration. Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamic simulations. J. Chem. Phys. 89:5876-1603.
42. Tobias, D. J., and C. L. Brooks, III. 1992. Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solutions: a comparison of theoretical results. J. Phys. Chem. 96:3864-3870.
43. Wallqvist, A., and B. J. Berne. 1995a. Molecular dynamics study of the dependence of water solvation free energy on solute curvature and surface area. J. Phys. Chem. 99:2885-2892.
44. Wallqvist, A., and B. J. Berne. 1995b. Computer simulation of hydrophobic hydration forces on stacked plates at short range. J. Phys. Chem. 99:2893-2899.
45. Wallqvist, A., and D. G. Covell. 1995. Free energy cost of bending n-dodecane in aqueous solution. Influence of the hydrophobic effect and solvent exposed area. J. Phys. Chem. 99:13118-13125.
46. Weber, T. A., and F. H. Stillinger. 1984. The effect of density on the inherent structure in liquids. J. Chem. Phys. 80:2742-2764.