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. 2002 Mar;82(3):1460–1468. doi: 10.1016/S0006-3495(02)75500-8

Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane.

Alexander M Smondyrev 1, Gregory A Voth 1
PMCID: PMC1301947  PMID: 11867461

Abstract

The structural and dynamical properties of a hydrated proton near the surface of DMPC membrane were studied using a molecular dynamics simulation. The proton transport between water molecules was modeled using the second generation multistate empirical valence bond model. The proton diffusion was found to be inhibited at the membrane surface. The potential of mean force for the proton adsorption to the membrane surface and its release back into the bulk water was also determined, yielding a small barrier in each direction. An efficient algorithm for Ewald summation calculations for the multistate empirical valence bond model is also introduced.

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Selected References

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  1. Brandsburg-Zabary S., Fried O., Marantz Y., Nachliel E., Gutman M. Biophysical aspects of intra-protein proton transfer. Biochim Biophys Acta. 2000 May 12;1458(1):120–134. doi: 10.1016/s0005-2728(00)00063-3. [DOI] [PubMed] [Google Scholar]
  2. Brewer M. L., Schmitt U. W., Voth G. A. The formation and dynamics of proton wires in channel environments. Biophys J. 2001 Apr;80(4):1691–1702. doi: 10.1016/S0006-3495(01)76140-1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Car R, Parrinello M. Unified approach for molecular dynamics and density-functional theory. Phys Rev Lett. 1985 Nov 25;55(22):2471–2474. doi: 10.1103/PhysRevLett.55.2471. [DOI] [PubMed] [Google Scholar]
  4. Damodaran K. V., Merz K. M., Jr A comparison of DMPC- and DLPE-based lipid bilayers. Biophys J. 1994 Apr;66(4):1076–1087. doi: 10.1016/S0006-3495(94)80889-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Deamer D. W. Water chains in lipid bilayers. Biophys J. 1996 Aug;71(2):543–543. doi: 10.1016/S0006-3495(96)79258-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Futai M., Noumi T., Maeda M. ATP synthase (H+-ATPase): results by combined biochemical and molecular biological approaches. Annu Rev Biochem. 1989;58:111–136. doi: 10.1146/annurev.bi.58.070189.000551. [DOI] [PubMed] [Google Scholar]
  7. Gutman M., Nachliel E., Gershon E. Effect of buffer on kinetics of proton equilibration with a protonable group. Biochemistry. 1985 Jun 4;24(12):2937–2941. doi: 10.1021/bi00333a019. [DOI] [PubMed] [Google Scholar]
  8. Gutman M., Nachliel E., Kiryati S. Dynamic studies of proton diffusion in mesoscopic heterogeneous matrix: II. The interbilayer space between phospholipid membranes. Biophys J. 1992 Jul;63(1):281–290. doi: 10.1016/S0006-3495(92)81585-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Heberle J., Dencher N. A. Surface-bound optical probes monitor protein translocation and surface potential changes during the bacteriorhodopsin photocycle. Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5996–6000. doi: 10.1073/pnas.89.13.5996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Heberle J. Proton transfer reactions across bacteriorhodopsin and along the membrane. Biochim Biophys Acta. 2000 May 12;1458(1):135–147. doi: 10.1016/s0005-2728(00)00064-5. [DOI] [PubMed] [Google Scholar]
  11. Heberle J., Riesle J., Thiedemann G., Oesterhelt D., Dencher N. A. Proton migration along the membrane surface and retarded surface to bulk transfer. Nature. 1994 Aug 4;370(6488):379–382. doi: 10.1038/370379a0. [DOI] [PubMed] [Google Scholar]
  12. Hoover WG. Canonical dynamics: Equilibrium phase-space distributions. Phys Rev A Gen Phys. 1985 Mar;31(3):1695–1697. doi: 10.1103/physreva.31.1695. [DOI] [PubMed] [Google Scholar]
  13. Junge W., McLaughlin S. The role of fixed and mobile buffers in the kinetics of proton movement. Biochim Biophys Acta. 1987 Jan 16;890(1):1–5. doi: 10.1016/0005-2728(87)90061-2. [DOI] [PubMed] [Google Scholar]
  14. Malmström B. G. The mechanism of proton translocation in respiration and photosynthesis. FEBS Lett. 1989 Jun 19;250(1):9–21. doi: 10.1016/0014-5793(89)80675-1. [DOI] [PubMed] [Google Scholar]
  15. Marrink S. J., Jähnig F., Berendsen H. J. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophys J. 1996 Aug;71(2):632–647. doi: 10.1016/S0006-3495(96)79264-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Mathies R. A., Lin S. W., Ames J. B., Pollard W. T. From femtoseconds to biology: mechanism of bacteriorhodopsin's light-driven proton pump. Annu Rev Biophys Biophys Chem. 1991;20:491–518. doi: 10.1146/annurev.bb.20.060191.002423. [DOI] [PubMed] [Google Scholar]
  17. Nachliel E., Gutman M. Quantitative evaluation of the dynamics of proton transfer from photoactivated bacteriorhodopsin to the bulk. FEBS Lett. 1996 Sep 16;393(2-3):221–225. doi: 10.1016/0014-5793(96)00870-8. [DOI] [PubMed] [Google Scholar]
  18. Nagle J. F., Dilley R. A. Models of localized energy coupling. J Bioenerg Biomembr. 1986 Feb;18(1):55–64. doi: 10.1007/BF00743612. [DOI] [PubMed] [Google Scholar]
  19. Nagle J. F., Tristram-Nagle S. Hydrogen bonded chain mechanisms for proton conduction and proton pumping. J Membr Biol. 1983;74(1):1–14. doi: 10.1007/BF01870590. [DOI] [PubMed] [Google Scholar]
  20. Nagle J. F., Tristram-Nagle S. Structure of lipid bilayers. Biochim Biophys Acta. 2000 Nov 10;1469(3):159–195. doi: 10.1016/s0304-4157(00)00016-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nagle J. F., Wiener M. C. Structure of fully hydrated bilayer dispersions. Biochim Biophys Acta. 1988 Jul 7;942(1):1–10. doi: 10.1016/0005-2736(88)90268-4. [DOI] [PubMed] [Google Scholar]
  22. Prats M., Tocanne J. F., Teissié J. Lateral proton conduction at a lipid/water interface. Its modulation by physical parameters. Experimental and mathematical approaches. Eur J Biochem. 1985 Jun 18;149(3):663–668. doi: 10.1111/j.1432-1033.1985.tb08975.x. [DOI] [PubMed] [Google Scholar]
  23. Scherrer P., Alexiev U., Marti T., Khorana H. G., Heyn M. P. Covalently bound pH-indicator dyes at selected extracellular or cytoplasmic sites in bacteriorhodopsin. 1. Proton migration along the surface of bacteriorhodopsin micelles and its delayed transfer from surface to bulk. Biochemistry. 1994 Nov 22;33(46):13684–13692. doi: 10.1021/bi00250a019. [DOI] [PubMed] [Google Scholar]
  24. Schumaker M. F., Pomès R., Roux B. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophys J. 2000 Dec;79(6):2840–2857. doi: 10.1016/S0006-3495(00)76522-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Schumaker M. F., Pomès R., Roux B. Framework model for single proton conduction through gramicidin. Biophys J. 2001 Jan;80(1):12–30. doi: 10.1016/S0006-3495(01)75992-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sugrue R. J., Hay A. J. Structural characteristics of the M2 protein of influenza A viruses: evidence that it forms a tetrameric channel. Virology. 1991 Feb;180(2):617–624. doi: 10.1016/0042-6822(91)90075-M. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Tu K., Tobias D. J., Blasie J. K., Klein M. L. Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer. Biophys J. 1996 Feb;70(2):595–608. doi: 10.1016/S0006-3495(96)79623-6. [DOI] [PMC free article] [PubMed] [Google Scholar]

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