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. 2000 Dec;79(6):2840–2857. doi: 10.1016/S0006-3495(00)76522-2

A combined molecular dynamics and diffusion model of single proton conduction through gramicidin.

M F Schumaker 1, R Pomès 1, B Roux 1
PMCID: PMC1301164  PMID: 11106593

Abstract

We develop a model for proton conduction through gramicidin based on the molecular dynamics simulations of Pomès and Roux (Biophys. J. 72:A246, 1997). The transport of a single proton through the gramicidin pore is described by a potential of mean force and diffusion coefficient obtained from the molecular dynamics. In addition, the model incorporates the dynamics of a defect in the hydrogen bonding structure of pore waters without an excess proton. Proton entrance and exit were not simulated by the molecular dynamics. The single proton conduction model includes a simple representation of these processes that involves three free parameters. A reasonable value can be chosen for one of these, and the other two can be optimized to yield a good fit to the proton conductance data of, Ann. N.Y. Acad. Sci. 339:8-20) for pH > or = 1.7. A sensitivity analysis shows the significance of this fit.

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Selected References

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  1. Akeson M., Deamer D. W. Proton conductance by the gramicidin water wire. Model for proton conductance in the F1F0 ATPases? Biophys J. 1991 Jul;60(1):101–109. doi: 10.1016/S0006-3495(91)82034-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Andersen O. S. Ion movement through gramicidin A channels. Interfacial polarization effects on single-channel current measurements. Biophys J. 1983 Feb;41(2):135–146. doi: 10.1016/S0006-3495(83)84415-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arseniev A. S., Barsukov I. L., Bystrov V. F., Lomize A. L., Ovchinnikov YuA 1H-NMR study of gramicidin A transmembrane ion channel. Head-to-head right-handed, single-stranded helices. FEBS Lett. 1985 Jul 8;186(2):168–174. doi: 10.1016/0014-5793(85)80702-x. [DOI] [PubMed] [Google Scholar]
  4. Boyer P. D. The ATP synthase--a splendid molecular machine. Annu Rev Biochem. 1997;66:717–749. doi: 10.1146/annurev.biochem.66.1.717. [DOI] [PubMed] [Google Scholar]
  5. Busath D. D., Thulin C. D., Hendershot R. W., Phillips L. R., Maughan P., Cole C. D., Bingham N. C., Morrison S., Baird L. C., Hendershot R. J. Noncontact dipole effects on channel permeation. I. Experiments with (5F-indole)Trp13 gramicidin A channels. Biophys J. 1998 Dec;75(6):2830–2844. doi: 10.1016/S0006-3495(98)77726-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chang G., Spencer R. H., Lee A. T., Barclay M. T., Rees D. C. Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. Science. 1998 Dec 18;282(5397):2220–2226. doi: 10.1126/science.282.5397.2220. [DOI] [PubMed] [Google Scholar]
  7. Cooper K. E., Gates P. Y., Eisenberg R. S. Diffusion theory and discrete rate constants in ion permeation. J Membr Biol. 1988 Dec;106(2):95–105. doi: 10.1007/BF01871391. [DOI] [PubMed] [Google Scholar]
  8. Cooper K., Jakobsson E., Wolynes P. The theory of ion transport through membrane channels. Prog Biophys Mol Biol. 1985;46(1):51–96. doi: 10.1016/0079-6107(85)90012-4. [DOI] [PubMed] [Google Scholar]
  9. Cowan S. W., Schirmer T., Rummel G., Steiert M., Ghosh R., Pauptit R. A., Jansonius J. N., Rosenbusch J. P. Crystal structures explain functional properties of two E. coli porins. Nature. 1992 Aug 27;358(6389):727–733. doi: 10.1038/358727a0. [DOI] [PubMed] [Google Scholar]
  10. Crouzy S., Woolf T. B., Roux B. A molecular dynamics study of gating in dioxolane-linked gramicidin A channels. Biophys J. 1994 Oct;67(4):1370–1386. doi: 10.1016/S0006-3495(94)80618-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cukierman S. Proton mobilities in water and in different stereoisomers of covalently linked gramicidin A channels. Biophys J. 2000 Apr;78(4):1825–1834. doi: 10.1016/S0006-3495(00)76732-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Decker E. R., Levitt D. G. Use of weak acids to determine the bulk diffusion limitation of H+ ion conductance through the gramicidin channel. Biophys J. 1988 Jan;53(1):25–32. doi: 10.1016/S0006-3495(88)83062-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Duca K. A., Jordan P. C. Ion-water and water-water interactions in a gramicidinlike channel: effects due to group polarizability and backbone flexibility. Biophys Chem. 1997 Apr 22;65(2-3):123–141. doi: 10.1016/s0301-4622(96)02233-8. [DOI] [PubMed] [Google Scholar]
  14. Eisenman G., Enos B., Hägglund J., Sandblom J. Gramicidin as an example of a single-filing ionic channel. Ann N Y Acad Sci. 1980;339:8–20. doi: 10.1111/j.1749-6632.1980.tb15964.x. [DOI] [PubMed] [Google Scholar]
  15. Elston T. C., Oster G. Protein turbines. I: The bacterial flagellar motor. Biophys J. 1997 Aug;73(2):703–721. doi: 10.1016/S0006-3495(97)78104-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Everitt C. T., Haydon D. A. Electrical capacitance of a lipid membrane separating two aqueous phases. J Theor Biol. 1968 Mar;18(3):371–379. doi: 10.1016/0022-5193(68)90084-2. [DOI] [PubMed] [Google Scholar]
  17. Heinemann S. H., Sigworth F. J. Estimation of Na+ dwell time in the gramicidin A channel. Na+ ions as blockers of H+ currents. Biochim Biophys Acta. 1989 Dec 11;987(1):8–14. doi: 10.1016/0005-2736(89)90448-3. [DOI] [PubMed] [Google Scholar]
  18. Jordan P. C., Bacquet R. J., McCammon J. A., Tran P. How electrolyte shielding influences the electrical potential in transmembrane ion channels. Biophys J. 1989 Jun;55(6):1041–1052. doi: 10.1016/S0006-3495(89)82903-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jordan P. C. Electrostatic modeling of ion pores. Energy barriers and electric field profiles. Biophys J. 1982 Aug;39(2):157–164. doi: 10.1016/S0006-3495(82)84503-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ketchem R. R., Hu W., Cross T. A. High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. Science. 1993 Sep 10;261(5127):1457–1460. doi: 10.1126/science.7690158. [DOI] [PubMed] [Google Scholar]
  21. Phillips L. R., Cole C. D., Hendershot R. J., Cotten M., Cross T. A., Busath D. D. Noncontact dipole effects on channel permeation. III. Anomalous proton conductance effects in gramicidin. Biophys J. 2008 Nov 21;77(5):2492–2501. doi: 10.1016/S0006-3495(99)77085-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pomès R., Roux B. Structure and dynamics of a proton wire: a theoretical study of H+ translocation along the single-file water chain in the gramicidin A channel. Biophys J. 1996 Jul;71(1):19–39. doi: 10.1016/S0006-3495(96)79211-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Roux B. Statistical mechanical equilibrium theory of selective ion channels. Biophys J. 1999 Jul;77(1):139–153. doi: 10.1016/S0006-3495(99)76878-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Schumaker M. F., Kentler C. J. Far-field analysis of coupled bulk and boundary layer diffusion toward an ion channel entrance. Biophys J. 1998 May;74(5):2235–2248. doi: 10.1016/S0006-3495(98)77933-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schumaker M. F., MacKinnon R. A simple model for multi-ion permeation. Single-vacancy conduction in a simple pore model. Biophys J. 1990 Oct;58(4):975–984. doi: 10.1016/S0006-3495(90)82442-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Walz D., Bamberg E., Läuger P. Nonlinear electrical effects in lipid bilayer membranes. I. Ion injection. Biophys J. 1969 Sep;9(9):1150–1159. doi: 10.1016/S0006-3495(69)86442-8. [DOI] [PMC free article] [PubMed] [Google Scholar]

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