Free energy profiles for H+ conduction along hydrogen-bonded chains of water molecules

Biophysical Journal

Volumn 75, Issue 1, 1998, Pages 33-40

  Pomès, Régis ^a,b   Roux, Benoît ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

WATER;

ARTICLE; DIPOLE; DISSOCIATION; HYDROGEN BOND; MEMBRANE TRANSPORT; MOLECULAR DYNAMICS; MOLECULAR MODEL; POLARIZATION; PROTON TRANSPORT; SIMULATION; THERMODYNAMICS;

EID: 0031862465     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77492-2     Document Type: Article

References (31)

1. Agmon, N. 1995. The Grotthuss mechanism. Chem. Phys. Lett. 244: 456-462.
2. Akeson, M., and D. W. Deamer. 1991. Proton conductance by the gramicidin water wire. Biophys. J. 60:101-109.
3. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulations of Liquids. Clarendon Press, Oxford.
4. Ando, K., and J. T. Hynes. 1994. Ionization of acids in water. In Structure and Reactivity in Aqueous Solution. C. J. Cramer and D. G. Truhlar, editors. ACS Books, Washington, DC. 143-153.
5. B. Biochemistry. 34: 7967-7972.
6. Breed, J., R. Sankararamakrishnan, I. D. Kerr, and M. S. P. Sansom. 1996. Molecular dynamics simulations of water within models of ion channels. Biophys. J. 70:1643-1661.
7. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comput. Chem. 4:187-217.
8. Chiu, S.-W., S. Subramaniam, E. Jacobsson, and J. A. McCammon. 1991. Water and polypeptide conformations in the gramicidin channel. Biophys. J. 56:253-261.
9. Deamer, D. W., and J. W. Nichols. 1989. Proton flux mechanisms in model and biological membranes. J. Membr. Biol. 107:91-103.
10. DeCoursey, T. E., and V. V. Cherny. 1997. Deuterium isotope effects on permeation and gating of proton channels in rat alveolar epithelium. J. Gen. Physiol. 109:415-434.
11. Duca, K. A., and P. C. Jordan. 1997. Ion-water and water-water interactions in a gramicidinlike channel: effects due to group polarizability and backbone flexibility. Biophys. Chem. 65:123-141.
12. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
13. Kumar, S., D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations in biomolecules. 1. The method. J. Comp. Chem. 13:1011-1021.
14. Mackerell, A. D., Jr., D. Bashford, M. Bellot, R. L. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reither, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies ot proteins. J. Phys. Chem. B. 102:3586-3616.
15. Marrink, S. J., F. Jähnig, and H. J. C. Berendsen. 1996. Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. Biophys. J. 71:632-647.
16. Martinez, S. E., D. Huang, M. Ponomarev, W. A. Cramer, and J. L. Smith. 1996. The heme redox center of chloroplast cytochrome-f is linked to a buried 5-water chain. Protein Sci. 5:1081-1092.
17. Nagle, J. F. 1987. Theory of passive proton conductance in lipid bilayers. J. Bioenerg. Biomembr. 19:413-426.
18. Nagle, J. F., and H. J. Morowitz. 1978. Molecular mechanisms tor proton transport in membranes. Proc. Natl. Acad. Sci. USA. 75:298-302.
19. Nagle, J. F., and S. Tristam-Nagle. 1983. Hydrogen bonded chain mechanisms for proton conduction and proton pumping. J. Membr. Biol. 74:1-14.
20. Paula, S., G. Volkov, N. van Hoek, T. H. Haines, and D. W. Deamer. 1996. Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness. Biophys. J. 70:339-348.
21. Pomès, R., and B. Roux. 1995. Quantum effects on the structure and energy of a protonated linear chain of hydrogen-bonded water molecules. Chem. Phys. Lett. 234:416-424.
22. + translocation along a model proton wire. J. Phys. Chem. 100:2519-2527.
23. + translocation along the single-file water chain in the gramicidin A channel. Biophys. J. 71:19-39.
24. Roux, B. 1995. The calculation of the potential of mean force using computer simulations. Comp. Phys. Comm. 91:275-282.
25. Roux, B., and M. Karplus. 1994. Molecular dynamics simulations of the gramicidin channel. Annu. Rev. Biophys. Biomol. Struct. 23:731-761.
26. Sagnella, D. E., K. Laasonen, and M. L. Klein. 1996. Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A. Biophys. J. 71:1172-1178.
27. Stillinger, F. H. 1979. Dynamics and ensemble averages for the polarization models of molecular interactions. J. Chem. Phys. 71:1647-1651.
28. Stillinger, F. H., and C. W. David. 1978. Polarization model for water and its ionic dissociation products. J. Chem. Phys. 69:1473-1484.
29. - ions in water. J. Phys. Chem. 99:5749-5752.
30. - studied with the polarization model. J. Phys. Chem. 86: 1314-1318.
31. Woolf, T. B., and B. Roux. 1997. The binding site of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data. Biophys. J. 72:1930-1945.