Skip to main content
SpringerLink
Log in

Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

  • Conference paper
Nonlinear Excitations in Biomolecules

Part of the book series: Centre de Physique des Houches ((LHWINTER,volume 2))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Rupley J. A. and Careri G., Adv. Protein Chem. 41 (1991) 37–172.

    Article  Google Scholar 

  2. Hansen J.-P. and McDonald I. R., Theory of Simple Liquids (Academic Press, London, UK, 1986).

    Google Scholar 

  3. Münster A., Statistical Thermodynamics (Springer, Berlin, 1969), Vol. 1, p. 338.

    MATH  Google Scholar 

  4. Kirkwood J. G., J. Chem. Phys. 3 (1935) 300–313.

    Article  ADS  Google Scholar 

  5. Fisher I. Z. and Kopeliovich B. L., Dokl. Akad. Nauk. SSSR 133 (1960) 81–83 [Sov. Phys.-Dokl. 5 (1960) 761–763].

    Google Scholar 

  6. Saenger W., Principles of Nucleic Acid Structure (Springer, Berlin, 1984).

    Book  Google Scholar 

  7. Jovin T. M., Soumpasis D. M., and Mcintosh L. P., Ann. Rev. Phys. Chem. 38 (1987) 521–560.

    Article  ADS  Google Scholar 

  8. Soumpasis D. M., Proc. Natl. Acad. Sci. USA 81 (1984) 5116–5120.

    Article  ADS  Google Scholar 

  9. Soumpasis D. M., Wiechen J., and Jovin T. M., J. Biomol. Struct. Dyn. 4 (1987) 535–552.

    Article  Google Scholar 

  10. Soumpasis D. M., Robert-Nicoud M., and Jovin T. M., FEBS Lett. 213 (1987) 341–344.

    Article  Google Scholar 

  11. 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.

    Google Scholar 

  12. 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.

    Chapter  Google Scholar 

  13. Klement R., Soumpasis D. M., von Kitzing E., and Jovin T. M., Biopol. 29 (1990) 1089–1103.

    Article  Google Scholar 

  14. Garcia A. E. and Soumpasis D. M., Proc. Natl. Acad. Sci. USA 86 (1989) 3160–3164.

    Article  ADS  Google Scholar 

  15. Hummer G. and Soumpasis D. M., J. Chem. Phys. 98 (1993) 581–591.

    Article  ADS  Google Scholar 

  16. Hummer G., Ph.D. thesis (University of Vienna, Austria, 1992).

    Google Scholar 

  17. Soumpasis D. M., J. Biomol. Struct. Dyn. 6 (1988) 563–574.

    Article  Google Scholar 

  18. Garcia A. E., Gupta G., Soumpasis D. M., and Tung C. S., J. Biomol. Struct. Dyn. 8 (1990) 173–186.

    Article  Google Scholar 

  19. Texter J., Prog. Biophys. Mol. Biol. 33 (1978) 83–97.

    Article  Google Scholar 

  20. Westhof E. and Beveridge D. L., Water Science Reviews, Franks F., Ed. (Cambridge Univ. Press, Cambridge, UK, 1990), Vol. 5, pp. 24–136.

    Google Scholar 

  21. Berman H. M., Current Opinion Struct. Biol. 4 (1994) 345–350.

    Article  Google Scholar 

  22. Drew H. R. and Dickerson R. E., J. Mol. Biol. 151 (1981) 535–556.

    Article  Google Scholar 

  23. Kopka M. L., Fratini A. V., Drew H. R., and Dickerson R. E., J. Mol. Biol. 163 (1983) 129–146.

    Article  Google Scholar 

  24. Marky L. A. and Kupke D. W., Biochem. 28 (1989) 9982–9988.

    Article  Google Scholar 

  25. Klement R., Soumpasis D. M., and Jovin T. M., Proc. Natl. Acad. Sci. USA 88 (1991) 4631–4635.

    Article  ADS  Google Scholar 

  26. 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.

    Chapter  Google Scholar 

  27. Hummer G. and Soumpasis D. M., Phys. Rev. E 49 (1994) 591–596.

    Article  ADS  Google Scholar 

  28. 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.

    Google Scholar 

  29. Ewald P., Ann. Phys. 64 (1921) 253–287.

    Article  MATH  Google Scholar 

  30. Hummer G., Soumpasis D. M., and Neumann M., J. Phys.: Condens. Matt. 23 A (1994) A141–A144.

    Article  Google Scholar 

  31. 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.

    Google Scholar 

  32. Garcia A. E., Hummer G., and Soumpasis D. M., Biophys. J. 66 (1994) A130.

    Article  Google Scholar 

  33. Forester T. R. and McDonald I. R., Mol. Phys. 72 (1991) 643–660.

    Article  ADS  Google Scholar 

  34. Soumpasis D. M., Procacci P., and Corongiu G., IBM DSD report, October 1991, IBM.

    Google Scholar 

  35. Niesar U., Corongiu G., Clementi E., Kneller G. R., and Bhattacharya D. K., J. Phys. Chem. 94 (1990) 7949–7956.

    Article  Google Scholar 

  36. Soumpasis D. M., Tung C.-S., and Garcia A. E., J. Biomol. Struct. Dyn. 8 (1991) 867–888.

    Article  Google Scholar 

  37. Westhof E., J. Biomol. Struct. Dyn. 5 (1987) 581–600.

    Article  Google Scholar 

  38. Yoon C., Privé G. G., Goodsell D. S., and Dickerson R. E., Proc. Natl. Acad. USA 85 (1988) 6332–6336.

    Article  ADS  Google Scholar 

  39. DiGabriele A. D., Sanderson M. R., and Steitz T. A., Proc. Natl. Acad. Sci. USA 86 (1989) 1816–1820.

    Article  ADS  Google Scholar 

  40. Quintana J. R., Grzeskowiak K., Yanagi K., and Dickerson R. E., J. Mol. Biol. 225 (1992) 379–395.

    Article  Google Scholar 

  41. Chuprina V. P., Nucleic Acids Res. 15 (1987) 293–311.

    Article  Google Scholar 

  42. Arnott S. and Hukins D. W. L., Biochem. Biophys. Res. Commun. 47 (1972) 1504–1509.

    Article  Google Scholar 

  43. Leroy J.-L., Charretier E., Kochoyan M., and Guéron M., Biochem. 27 (1988) 8894–8898.

    Article  Google Scholar 

  44. Burkhoff A. M. and Tullius T. D., Nature 331 (1988) 455–457.

    Article  ADS  Google Scholar 

  45. Hosur R. V., Govjl G., Hosur M. V., and Viswamitra M. A., J. Mol. Struct. 72 (1981) 261–267.

    Article  ADS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Theoretical Biology and Biophysics Group T-10, MS K710, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA

    G. Hummer & A. E. García

  2. Biocomputation Group, Max-Planck-Institute for Biophysical Chemistry, P.O. Box 2841, 37018, Göttingen, Germany

    D. M. Soumpasis

Authors
  1. G. Hummer
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. D. M. Soumpasis
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. E. García
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

M. Peyrard

Rights and permissions

Reprints and permissions

Copyright information

© 1995 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

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

Download citation

  • DOI: https://doi.org/10.1007/978-3-662-08994-1_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-59250-1

  • Online ISBN: 978-3-662-08994-1

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation