Molecular dynamics simulation of proton transport tnrougn tne influenza A virus M2 channel

Biophysical Journal

Volumn 83, Issue 4, 2002, Pages 1987-1996

  Smondyrev, Alexander M ^a   Voth, Gregory A ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ION CHANNEL;

AQUEOUS SOLUTION; ARTICLE; BIOENERGY; DIFFUSION; ELECTROPHYSIOLOGY; INFLUENZA VIRUS A; LIPID BILAYER; MOLECULAR DYNAMICS; NONHUMAN; PHENOMENOLOGY; PROTEIN DOMAIN; PROTON TRANSPORT; SOLVATION;

INFLUENZA A VIRUS; INFLUENZA VIRUS;

EID: 0036789499     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)73960-X     Document Type: Article

References (28)

1. Brewer, M. L., U. W. Schmitt, and G. A. Voth. 2001. The formation and dynamics of proton wires in channel environments. Biophys. J. 80: 1691-1702.
2. Cornell, W. D., P. Cieplak, C. B. Bayly, I. R. Gould, K. M. Mertz, Jr., D. M. Ferguson, D. S. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179.
3. Cuma, M., U. W. Schmitt, and G. A. Voth. 2001. A multi-state empirical valence bond model for weak acid dissociation in aqueous solution. J. Phys. Chem. A. 105:2814-2823.
4. Duff, K. C., and R. H. Ashley. 1992. The transmembrane domain of influenza A M2 protein forms amantadine-sensitive proton channels in planar lipid bilayer. Virology. 190:485-489.
5. Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103:8577-8593.
6. Forrest, L. R., A. Kukol, I. T. Arkin, D. P. Tieleman, and M. S. P. Sansom. 2000. Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. Biophys. J. 78:55-69.
7. Hille, B. 1992. Ionic Channels in Excitable Membranes, 2nd Ed. Sinauer Associates Inc., Sunderland, MA.
8. Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
9. 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.
10. Kovacs, F. A., and T. A. Cross. 1997. Transmembrane four-helix bundle of influenza A M2 protein channel: structural implications from helix tilt and orientation. Biophys. J. 73:2511-2517.
11. + channel. J. Mol. Biol. 286:951-962.
12. Pinto, L. H., G. R. Dieckmann, C. S. Gandhi, C. G. Papworth, J. Braman, M. A. Shaughnessy, J. D. Lear, R. A. Lamb, and W. F. DeGrado. 1997. A functionally defined model for the M2 proton channel of influenza A virus suggests a mechanism for its ion selectivity. Proc. Natl. Acad. Sci. U.S.A. 94:11301-11306.
13. Ryckaert, W. E., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23: 327-341.
14. Sansom, M. S. P., 1. D. Kerr, G. R. Smith, and H. S. Son. 1997. The influenza A virus M2 channel: a molecular modelling and simulation study. Virology. 233:163-173.
15. Schmitt, U. W., and G. A. Voth. 1998. Multistate empirical valence bond model for proton transport in water. J. Phys. Chem. B. 102:5547.
16. Schmitt, U. W., and G. A. Voth. 1999a. The computer simulation of proton transport in water. J. Chem. Phys. 111:9361.
17. Schmitt, U. W., and G. A. Voth. 1999b. Quantum properties of the excess proton in liquid wate. Isr. J. Chem. 39:483.
18. Schumaker, M. F., R. Pomes, and B. Roux. 2000. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. Biophys. J. 79:2840-2857.
19. Schumaker, M. F., R. Pomes, and B. Roux. 2001. Framework model for single proton conduction through gramicidin. Biophys. J. 80:12-30.
20. Schweighofer, K. J., and A. Pohorille. 2000. Computer simulation of ion channel gating: the M2 channel of influenza A virus in a lipid bilayer. Biophys. J. 78:150-163.
21. Smart, O. S., J. Breed, G. R. Smith, and M. S. P. Sansom. 1997. A novel method for structure-based predictions of ion channel conductance properties. Biophys. J. 72:1109-1126.
22. Smondyrev, A. M., and M. L. Berkowitz. 1999a. Molecular dynamics simulation of fluorination effects on a phospholipid bilayer. J. Chem. Phys. 111:9864-9870.
23. Smondyrev, A. M., and M. L. Berkowitz. 1999b. United atom force field for phospholipid membranes. Constant pressure molecular dynamics simulation of DPPC/water system. J. Comp. Chem. 20:531-545.
24. Smondyrev, A. M., and G. A. Voth. 2002. Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane. Biophys. J. 82:1460-1468.
25. + channel. Protein Sci. 10:2241-2250.
26. Wang, C., R. A. Lamb, and L. H. Pinto. 1995. Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. Biophys. J. 69:1363-1371.
27. Wang, C., K. Takeuchi, L. H. Pinto, and R. A. Lamb. 1993. Ion channel activity of influenza A virus M2 protein: chracterization of the amantadine block. J. Virol. 67:5585-5594.
28. Zhong, Q., T. Husslein, P. B. Moore, D. M. Newns. P. Pattnaik. and M. L. Klein. 1998. The M2 channel of influenza A virus: a molecular dynamics study. FEBS Lett. 434:265-271.