Simulation of MscL gating in a bilayer under stress

Biophysical Journal

Volumn 84, Issue 4, 2003, Pages 2331-2337

  Colombo, Giorgio ^a   Marrink, Siewert Jan ^b   Mark, Alan E ^b  

^a CNR   (Italy)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ION CHANNEL; MEMBRANE PROTEIN; PHOSPHATIDYLCHOLINE; PHOSPHOLIPID;

ARTICLE; BACTERIAL MEMBRANE; BILAYER MEMBRANE; MEMBRANE CONDUCTANCE; MEMBRANE MODEL; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PATCH CLAMP; PROTEIN SECONDARY STRUCTURE;

BACTERIA (MICROORGANISMS); MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS;

EID: 0037382083     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75038-3     Document Type: Article

References (39)

1. Ajouz, B., C. Berrier, M. Besnard, B. Martinac, and A. Ghazi. 2000. Contribution of the different extramembranous domains of the mechanosensitive ion channel MscL to its response to membrane tension. J. Biol. Chem. 275:1015-1022.
2. Ajouz, B., C. Berrier, A. Garrigues, M. Besnard, and E. Ghazi. 1998. Release of thioredoxin via the mechanosensitive channel MscL during osmotic downshock of Escherichia coli cells. J. Biol. Chem. 273:26670-26674.
3. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. Di Nola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
4. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, and J. Hermans. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces. B. Pullman, editor. Reidel, Dordrecht.
5. Berger, O., O. Edholm, and F. Jahnig. 1997. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophys. J. 72:2002-2013.
6. Betanzos, M., C. S. Chiang, H. R. Guy, and S. Sukharev. 2002. A large iris-like expansion of a mechanoselective channel protein induced by membrane tension. Nat. Struct. Biol. 9:704-710.
7. Blount, P., S. I. Sukharev, P. Moe, and C. Kung. 1997. Mechanosensitive channels of E. coli: a genetic and molecular dissection. Biol. Bull. 192:126-127.
8. Blount, P., S. I. Sukharev, P. C. Moe, B. Martinac, and C. Kung. 1999. Mechanosensitive channels of bacteria. In Methods in Enzymology, Vol. 294. M. Conn, editor. Academic Press, London. 458-482.
9. Chang, G., R. H. Spencer, A. T. Lee, M. T. Barclay, and D. C. Rees. 1998. Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel. Science. 282:2220-2226.
10. Elmore, D. E., and D. A. Dougherty. 2001. Molecular dynamics simulations of wild-type and mutant forms of the Mycobacterium tuberculosis MscL channel. Biophys. J. 81:1345-1359.
11. Feenstra, K. A., B. Hess, and H. J. C. Berendsen. 1999. Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems. J. Comput. Chem. 20:786-798.
12. Feenstra, K. A., C. Peter, R. M. Scheek, W. F. van Gunsteren, and A. E. Mark. 2002. A comparison of methods for calculating NMR cross-relaxation rates (NOESY and ROESY intensities) in small peptides. J. Biomol. NMR. 23:181-194.
13. Gullingsrud, J., D. Kosztin, and K. Schulten. 2001. Structural determinants of MscL gating studied by molecular dynamics simulations. Biophys. J. 80:2074-2081.
14. Hamill, O., and D. McBride. 1993. Molecular clues to mechanosensitivity. Biophys. J. 65:17-18.
15. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD - Visual Molecular Dynamics. J. Mol. Graph. 14:33-38.
16. Kong, Y., Y. Shen, T. E. Warth, and J. Ma. 2002. Conformational pathways in the gating of Escherichia coli mechanosensitive channel. Proc. Natl. Acad. Sci. USA. 99:5999-6004.
17. Levina, N., S. Totemeyer, N. R. Stokes, P. Louis, and M. A. Jones. 1999. Protection of Escherichia coli cells against extreme turgor by activation of MscS and MscL mechanosensitive channels: identification of genes required for MscS activity. EMBO J. 18:1730-1737.
18. Lide, D. R. editor. 1992. Handbook of Chemistry and Physics, CRC Press LLC, Boca Raton, FL. 1991-1992.
19. Martinac, B. 1993. Thermodynamics of Membrane Receptors and Channels. Ellis Horwood series in chemical engineering. CRC Press LLC, Boca Raton, FL.
20. Moe, P. C., G. Levin, and P. Blount. 2000. Correlating a protein structure with function of a bacterial mechanosensitive channel. J. Biol. Chem. 40:31121-31127.
21. Oakley, A. J., B. Martinac, and M. C. J. Wilce. 1999. Structure and function of the bacterial mechanosensitive channel of large conductance. Protein. Sci. 8:1915-1921.
22. Ou, X., P. Blount, R. J. Hoffman, and C. Kung. 1998. One face of a transmembrane helix is crucial in mechanosensitive channel gating. Proc. Natl. Acad. Sci. USA. 95:11471-11475.
23. Perozo, E., D. M. Cortes, P. Sompornpisut, and B. Martinac. 2002a. Open channel structure of MscL and the gating mechanism of mechanosensitive channels. Nature. 418:942-948.
24. Perozo, E., A. Kloda, D. M. Cortes, and B. Martinac. 2002b. Physical principles underlying the transduction of bilayer deformation forces during mechanoselective channel gating. Nat. Struct. Biol. 9:696-703.
25. Sachs, F. 1991. Mechanical transduction by membrane ion channels: a mini review. Mol. Cell. Biochem. 104:57-60.
26. Shrivastava, I. H., D. P. Tieleman, P. C. Biggin, and M. S. P. Sansom. 2002. K+ versus Na+ ions in a K channel selectivity filter: a simulation study. Biophys. J. 83:633-645.
27. Spencer, R. H., G. Chang, and D. C. Rees. 1999. Feeling the pressure: structural insights into a gated mechanosensitive ion channel. Curr. Opin. Struct. Biol. 9:448-454.
28. Sukharev, S. I., P. Blount, B. Martignac, and C. Kung. 1997. Mechanosensitive channels of Escherichia coli: the MscL gene, protein, and activities. Annu. Rev. Physiol. 59:633-657.
29. Sukharev, S. I., P. Blount, B. Martinac, F. R. Blattner, and C. Kung. 1994. A large conductance mechanosensitive channel in E. coli encoded by MscL alone. Nature. 368:265-268.
30. Sukharev, S. I., S. R. Durell, and H. R. Guy. 2001. Structural models of MscL gating mechanism. Biophys. J. 81:917-936.
31. Sukharev, S. I., W. J. Sigurdson, C. Kung, and F. Sachs. 1999. Energetic and spatial parameters for gating of the bacterial large conductance mechanosensitive channel, MscL. J. Gen. Physiol. 113:525-539.
32. Tieleman, D. P., and H. J. C. Berendsen. 1998. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys. J. 74:2786-2801.
33. Tieleman, D. P., H. Leontiadou, A. E. Mark, and S. J. Marrink. 2002. Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. J. Am. Chem. Soc. In press.
34. van der Spoel, D., R. van Drunen, and H. J. C. Berendsen. 1994. GROningen MAchine for Chemical Simulations. Department of Biophysical Chemistry, BIOSON Research Institute, Nijenborgh 4, NL-9717 AG Groningen. E-mail to gromacs@chem.rug.nl.
35. van Gunsteren, W. F., S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi. 1996. Biomolecular Simulation: The GROMOS96 Manual and User Guide. vdf Hochschulverlag, ETH Zurich, Switzerland.
36. van Gunsteren, W. F., X. Daura, and A. E. Mark. 1998. GROMOS forcefield. In Encyclopedia of Computational Chemistry, Vol. 2. P. von Rague Scheleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer, III, and P. R. Schriener, editors Wiley and Sons, Chichester, USA. 1211-1216.
37. Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
38. Yoshimura, K., A. Batiza, and C. Kung. 2001. Chemically charging the pore constriction opens the mechanosensitive channel MscL. Biophys. J. 80:2198-2206.
39. Yoshimura, K., A. Batiza, M. Schroeder, P. Blount, and C. Kung. 1999. Hydrophilicity of a single residue within MscL correlates with increased channel mechanosensitivity. Biophys. J. 77:1960-1972.