Molecular dynamics simulations of valinomycin interactions with potassium and sodium ions in water solvent
- 1
- 2
- 3
Abstract
The aim of this work is to estimate the value of the electric field (potentials) for the system of valinomycin + К+ and Na+ ions based on a molecular dynamics (MD) study. An analysis has been performed of the interaction processes for the system of valinomycin + К+(Na+) ion in water solvent. It is obtained that capturing a К+(Na+) ion in the valinomycin cavity is not possible for all values of the electric field strength. Each of the two kinds of ions (К+ or Na+) has its own critical electric field associated with ion binding to valinomycin, for which to exist, the ion has to remain localized inside the valinomycin cavity. The results obtained for the electrical potential reveal a stronger valinomycin binding—especially with the potassium ion. Valinomycin’s molecular structure efficiently surrounds the K+ ion, as this structure has to exactly correspond to the K+ ion in size. MD simulation results could be a prerequisite for studying a more complex scenario—for estimating ion transport in the cell membrane or physiological electric potential which is formed in the membrane or inside the cell relative to its surrounding medium.
- Steed, I.W. and Atwood, J.L. (2000) Supramolecular chemistry. Wiley.
- Doyle, D.A., Cabral, J.M., Pfuetzner, R.A., Kuo, A., Gulbis, J.M., Cohen, S.L., Chait, B.T. and MacKinnon, R. (1998) The structure of the potassium channel: Molecular basis of K+ conduction and selectivity. Science, 280 (5360), 69-77.
- Forester, T., Smith, W. and Clarke, H.R. (1997) Antibiotic activity of valinomycin. Journal of the Chemical Society Faraday Transactions, 93(4), 613-661.
- Ye, Q., Vincze, A., Horvai, G. and Leermakers, F.A.M. (1998) Partial blocking of ion transport at the interface of an ion-selective liquid membrane electrode by neutral surfactants. Experiment and computer simulations. Electrochimica Acta, 44(1), 125-132.
- Marrone, T.J. and Kenneth, M.M., Jr. (1995) Molecular Recognition of K+ and Na+ by valinomycin in methanol. Journal of American Chemical Society, 117(2), 779-791.
- Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts K. and Watson, Y.D. (1994) Molecular biology of the cell. Garland Publishing, A member of the Taylor & Francis Group, New York.
- Smith, W. and Forester, T. (1996) DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package. Journal of Molecular Graphics, 14(3), 136-141.
- Varma, S., Sabo, D. and Rempe, S.B. (2008) K+/Na+ selectivity in K-channels and valinomycin: Over-coordination vs cavity-size constraints. Journal of Molecular Biology, 376(1), 13-22.
- Forester, T.R., Smith, W. and Clarke, J.H.R. (1995) Capture of potassium ions by valinomycin: A molecular dynamics simulation study. Journal of Physical Chemistry, 99(39), 14418-14423.
- Eisenman, G., Alvarez, O. and Aqvist, J. (1992) Free energy perturbation simulations of cation binding to valinomycin. Journal of Inclusion Phenomena and Macrocyclic Chemistry, 12(1-4), 23-53.
- Smith, W., Forester, T.R. and Todorov, I.T. (2008) The DL poly 2 user manual. STFC Daresbury Laboratory Daresbury, Warrington WA4 4AD Cheshire, UK, Version 2.19.
- van Veggel, C.J.M.F., van Duynhoven, J.P.M., Harkema, S., Wolbers, M.P.O. and Reinhoudt, D.N. (1996) Solid- state structure, dynamical properties in solution and com- putational studies of a new sodium hemispherand comples. Journal of the Chemical Society Perkin Transactions, 2, 449-454.
- Eisenman, G., Aqvist, J. and Alvarez, O. (1991) Free energies underlying ion binding and transport in protein channels: Free energy perturbation simulations of ion binding and selectivity for valinomycin. Journal of the Chemical Society Faraday Transactions, 87, 2099-2109.