Abstract
To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. However, large biological macromolecules are not the only players in the field. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems [1]. It mediates biochemical reactions and has a strong influence on the structural equilibrium of certain molecules. Therefore, the development and application of theoretical descriptions of solute-solvent interactions provides relevant insight into biological processes.
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References
Rupley J. A. and Careri G., Adv. Protein Chem. 41 (1991) 37–172.
Hansen J.-P. and McDonald I. R., Theory of Simple Liquids (Academic Press, London, UK, 1986).
Münster A., Statistical Thermodynamics (Springer, Berlin, 1969), Vol. 1, p. 338.
Kirkwood J. G., J. Chem. Phys. 3 (1935) 300–313.
Fisher I. Z. and Kopeliovich B. L., Dokl. Akad. Nauk. SSSR 133 (1960) 81–83 [Sov. Phys.-Dokl. 5 (1960) 761–763].
Saenger W., Principles of Nucleic Acid Structure (Springer, Berlin, 1984).
Jovin T. M., Soumpasis D. M., and Mcintosh L. P., Ann. Rev. Phys. Chem. 38 (1987) 521–560.
Soumpasis D. M., Proc. Natl. Acad. Sci. USA 81 (1984) 5116–5120.
Soumpasis D. M., Wiechen J., and Jovin T. M., J. Biomol. Struct. Dyn. 4 (1987) 535–552.
Soumpasis D. M., Robert-Nicoud M., and Jovin T. M., FEBS Lett. 213 (1987) 341–344.
Soumpasis D. M., Garcia A., Klement R., and Jovin T., “The potentials of mean force (PMF) approach for treating ionic effects on biomolecular structures in solution”, Theoretical Biochemistry and Molecular Biophysics, Beveridge D. L. and Lavery R., Eds. (Adenine Press, Schenectady, NY, 1990), pp. 343–360.
Soumpasis D. M., “Formal aspects of the potentials of mean force approach”, Computation of Biomolecular Structures, Soumpasis D. M. and Jovin T. M., Eds. (Springer, Berlin, 1993), pp. 223–239.
Klement R., Soumpasis D. M., von Kitzing E., and Jovin T. M., Biopol. 29 (1990) 1089–1103.
Garcia A. E. and Soumpasis D. M., Proc. Natl. Acad. Sci. USA 86 (1989) 3160–3164.
Hummer G. and Soumpasis D. M., J. Chem. Phys. 98 (1993) 581–591.
Hummer G., Ph.D. thesis (University of Vienna, Austria, 1992).
Soumpasis D. M., J. Biomol. Struct. Dyn. 6 (1988) 563–574.
Garcia A. E., Gupta G., Soumpasis D. M., and Tung C. S., J. Biomol. Struct. Dyn. 8 (1990) 173–186.
Texter J., Prog. Biophys. Mol. Biol. 33 (1978) 83–97.
Westhof E. and Beveridge D. L., Water Science Reviews, Franks F., Ed. (Cambridge Univ. Press, Cambridge, UK, 1990), Vol. 5, pp. 24–136.
Berman H. M., Current Opinion Struct. Biol. 4 (1994) 345–350.
Drew H. R. and Dickerson R. E., J. Mol. Biol. 151 (1981) 535–556.
Kopka M. L., Fratini A. V., Drew H. R., and Dickerson R. E., J. Mol. Biol. 163 (1983) 129–146.
Marky L. A. and Kupke D. W., Biochem. 28 (1989) 9982–9988.
Klement R., Soumpasis D. M., and Jovin T. M., Proc. Natl. Acad. Sci. USA 88 (1991) 4631–4635.
Klement R., “Computation of ionic distributions around charged biomolecular structures using the PMF approach”, Computation of Biomolecular Structures, Soumpasis D. M. and Jovin T. M., Eds. (Springer, Berlin, 1993), pp. 207–222.
Hummer G. and Soumpasis D. M., Phys. Rev. E 49 (1994) 591–596.
Berendsen H. J. C., Postma J. P. M., van Gunsteren W. F., and Hermans J., “Interaction models for water in relation to protein hydration”, Intermolecular Forces: Proceedings of the 14th Jerusalem Symposium on Quantum Chemistry and Biochemistry, Pullman B., Ed. (Reidel, Dordrecht, Holland, 1981), pp. 331–342.
Ewald P., Ann. Phys. 64 (1921) 253–287.
Hummer G., Soumpasis D. M., and Neumann M., J. Phys.: Condens. Matt. 23 A (1994) A141–A144.
Hummer G. and Soumpasis D. M., “A new approach to calculate the hydration of DNA molecules”, Structural Biology: The State of the Art; Proceedings of the Eighth Conversations in the Discipline Biomolecular Stereodynamics, Sarma R. H. and Sarma M. H., Eds. (Adenine Press, Schenectady, NY, 1994), Vol. 2, pp. 273–278.
Garcia A. E., Hummer G., and Soumpasis D. M., Biophys. J. 66 (1994) A130.
Forester T. R. and McDonald I. R., Mol. Phys. 72 (1991) 643–660.
Soumpasis D. M., Procacci P., and Corongiu G., IBM DSD report, October 1991, IBM.
Niesar U., Corongiu G., Clementi E., Kneller G. R., and Bhattacharya D. K., J. Phys. Chem. 94 (1990) 7949–7956.
Soumpasis D. M., Tung C.-S., and Garcia A. E., J. Biomol. Struct. Dyn. 8 (1991) 867–888.
Westhof E., J. Biomol. Struct. Dyn. 5 (1987) 581–600.
Yoon C., Privé G. G., Goodsell D. S., and Dickerson R. E., Proc. Natl. Acad. USA 85 (1988) 6332–6336.
DiGabriele A. D., Sanderson M. R., and Steitz T. A., Proc. Natl. Acad. Sci. USA 86 (1989) 1816–1820.
Quintana J. R., Grzeskowiak K., Yanagi K., and Dickerson R. E., J. Mol. Biol. 225 (1992) 379–395.
Chuprina V. P., Nucleic Acids Res. 15 (1987) 293–311.
Arnott S. and Hukins D. W. L., Biochem. Biophys. Res. Commun. 47 (1972) 1504–1509.
Leroy J.-L., Charretier E., Kochoyan M., and Guéron M., Biochem. 27 (1988) 8894–8898.
Burkhoff A. M. and Tullius T. D., Nature 331 (1988) 455–457.
Hosur R. V., Govjl G., Hosur M. V., and Viswamitra M. A., J. Mol. Struct. 72 (1981) 261–267.
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Hummer, G., Soumpasis, D.M., García, A.E. (1995). Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems. In: Peyrard, M. (eds) Nonlinear Excitations in Biomolecules. Centre de Physique des Houches, vol 2. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-08994-1_5
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