Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length

Biophysical Journal

Volumn 92, Issue 11, 2007, Pages 3930-3937

  Portella, Guillem ^a   Pohl, Peter ^b   De Groot, Bert L ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b JOHANNES KEPLER UNIVERSITY LINZ   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

GRAMICIDIN; PEPTIDE; WATER;

ARTICLE; ATOM; BINDING SITE; ENERGY TRANSFER; EXPERIMENTATION; HYDROPHILICITY; MOLECULAR DYNAMICS; MONTE CARLO METHOD; NANOTECHNOLOGY; OSMOSIS; SOLVATION; THERMODYNAMICS; WATER FLOW; WATER PERMEABILITY;

EID: 34250334738     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.102921     Document Type: Article

References (42)

1. de Groot, B. L., and H. Grubmüller. 2001. Water permeation across biological membranes: mechanism and dynamics of Aquaporin-1 and GlpF. Science. 294:2353-2357.
2. Corry, B., and S. H. Chung. 2006. Mechanisms of valence selectivity in biological ion channels. Cell. Mol. Life Sci. 63:301-315.
3. Roux, B., and K. Schulten. 2004. Computational studies of membrane channels. Structure. 12:1343-1351.
4. + channels. Annu. Rev. Biophys. Biomol. Struct. 34:153-171.
5. Futaki, S., Y. J. Zhang, T. Kiwada, I. Nakase, T. Yagami, S. Oiki, and Y. Sugiura. 2004. Gramicidin-based channel systems for the detection of protein-ligand interaction. Bioorg. Med. Chem. 12:1343-1350.
6. Hummer, G., J. C. Rasaiah, and J. P. Noworyta. 2001. Water conduction through the hydrophobic channel of a carbon nanotube. Nature. 414:188-190.
7. Beckstein, O., and M. S. Sansom. 2003. Liquid-vapor oscillations of water in hydrophobic nanopores. Proc. Natl. Acad. Sci. USA. 100:7063-7068.
8. + translocation along the single-file water chain in the gramicidin A channel. Biophys. J. 71:19-39.
9. Saparov, S. M., J. R. Pfeifer, L. Al-Momani, G. Portella, B. L. deGroot, U. Koert, and P. Pohl. 2006. Mobility of a one-dimensional confined file of water molecules as a function of file length. Phys. Rev. Lett. 96:148101.
10. Finkelstein, A., and P. Rosenberg. 1979. Single-file transport: implications for ion and water movement through gramicidin A channels. Membr. Transp. Processes. 3:77-88.
11. Finkelstein, A. 1987. Water movement through lipid bilayers, pores, and plasma membranes. Wiley & Sons, New York.
12. de Groot, B. L., D. P. Tieleman, P. Pohl, and H. Grubmüller. 2002. Water permeation through gramicidin A: desformylation and the double helix; a molecular dynamics study. Biophys. J. 82:2934-2942.
13. Zhu, F. Q., E. Tajkhorshid, and K. Schulten. 2004. Theory and simulation of water permeation in aquaporin-1. Biophys. J. 86:50-57.
14. Lomize, A. L., V. I. Orekhov, and A. S. Arsen'ev. 1992. Refinement of the spatial structure of the gramicidin A ion channel. Bioorg. Chim. 18:182-200.
15. Townsley, L. E., W. A. Tucker, S. Sham, and J. F. Hinton. 2001. Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles. Biochemistry. 40:11676-11686.
16. Ketchem, R. R., B. Roux, and T. A. Cross. 1997. High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure. 5:1655-1669.
17. dePlanque, M. R. R., J. A. W. Kruijtzer, R. M. J. Liskamp, D. Marsh, D. V. Greathouse, R. E. Koeppe, B. deKruijff, and J. A. Killian. 1999. Different membrane anchoring positions of tryptophan and lysine in synthetic transmembrane alpha-helical peptides. J. Biol. Chem. 274:20839-20846.
18. Jude, A. R., D. V. Greathouse, R. E. Koeppe, L. L. Providence, and O. S. Andersen. 1999. Modulation of gramicidin channel structure and function by the aliphatic "spacer" residues 10, 12, and 14 between the tryptophans. Biochemistry. 38:1030-1039.
19. Reithmeier, R. A. F. 1995. Characterization and modeling of membrane-proteins using sequence-analysis. Curr. Opin. Struct. Biol. 5:491-500.
20. Galbraith, T. P., and B. A. Wallace. 1998. Phospholipid chain length alters the equilibrium between pore and channel forms of gramicidin. Faraday Discuss. 111:159-164.
21. Chiu, S.-W., S. Subramaniam, and E. Jakobsson. 1999. Simulation study of the gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanism of water transport. Biophys. J. 76:1939-1950.
22. Kaminski, G. A., R. A. Friesner, J. Tirado-Rives, and W. L. Jorgensen. 2001. Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B. 105:6474-6487.
23. Jorgensen, W. L., D. S. Maxwell, and J. Tirado-Rives. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-11236.
24. 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.
25. 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. D. Reidel Publishing Company, Dordrecht, The Netherlands.
26. Lindahl, E., B. Hess, and D. Van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. (Online). 7:306-317.
27. Van der Spoel, D., E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen. 2005. GROMACS: fast, flexible and free. J. Comput. Chem. (Online). 26:1701-1718.
28. Darden, T., D. York, and L. Pedersen. 1993. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
29. Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. 1995. A smooth particle mesh Ewald potential. J. Chem. Phys. 103:8577-8592.
30. Miyamoto, S., and P. A. Kollman. 1992. SETTLE: an analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comput. Chem. 13:952-962.
31. Hess, B., H. Bekker, H. J. C. Berendsen, and J. G. E. M. Fraaije. 1997. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18:1463-1472.
32. Berendsen, H. J. C., J. P. M. Postma, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
33. Zhu, F., E. Tajkhorshid, and K. Schulten. 2004. Collective diffusion model for water permeation through microscopic channels. Phys. Rev. Lett. 93:224501.
34. Chou, T. 1998. How fast do fluids squeeze through microscopic single-file pores? Phys. Rev. Lett. 80:85-88.
35. Chou, T. 1999. Kinetics and thermodynamics across single-file pores: solute permeability and rectified osmosis. J. Chem. Phys. 110:606-615.
36. Hernandez, J. A., and J. Fischbarg. 1992. Kinetic analysis of water transport though a single-file pore. J. Gen. Physiol. 99:645-662.
37. Berezhkovskii, A., and G. Hummer. 2002. Single-file transport of water molecules through a carbon nanotube. Phys. Rev. Lett. 89:064503.
38. Kalra, A., S. Garde, and G. Hummer. 2003. Osmotic water transport through carbon nanotube membranes. Proc. Natl. Acad. Sci. USA. 100:10175-10180.
39. Saparov, S. M., Y. N. Antonenko, R. E. Koeppe II, and P. Pohl. 2000. Desformylgramicidin: a model channel with an extremely high water permeability. Biophys. J. 79:2526-2534.
40. Pohl, P. 2004. Combined transport of water and ions through membrane channels. Biol. Chem. 385:921-926.
41. Pfeifer, J. R., P. Reiss, and U. Koert. 2006. Crown ether-gramicidin hybrid ion channels: dehydration-assisted ion selectivity. Angew. Chem. Ind. Ed. 45:501-504.
42. Longuet-Higgins, H. C., and G. Austin. 1966. The kinetics of osmotic transport through pores of molecular dimensions. Biophys. J. 6:217-224.