Determinants of water permeability through nanoscopic hydrophilic channels

Biophysical Journal

Volumn 96, Issue 3, 2009, Pages 925-938

  Portella, Guillem ^a   De Groot, Bert L ^a  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GRAMICIDIN A; ION CHANNEL; PEPTIDE; WATER;

ARTICLE; DENSITY; DIFFUSION COEFFICIENT; HYDROPHILICITY; MEMBRANE PERMEABILITY; MOLECULAR DYNAMICS; MOLECULAR SIZE; MOLECULAR STABILITY; OSMOSIS; WATER PERMEABILITY; CELL MEMBRANE PERMEABILITY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DIFFUSION; METABOLISM; NANOTECHNOLOGY; POROSITY;

CELL MEMBRANE PERMEABILITY; DIFFUSION; ION CHANNELS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NANOTECHNOLOGY; OSMOSIS; PEPTIDES; POROSITY; WATER;

EID: 61549089671     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.09.059     Document Type: Article

References (65)

1. Agre, P. 2004. Aquaporin water channels (Nobel Lecture). Angew. Chem. Int. Ed. 43:4278-4290.
2. Jensen, P.H., and D. Keller, 2006. Membrane for filtering of water. Patent number WO 2006/122566.
3. Cornell, B. A., V. L. Braach-Maksvytis, L. G. King, P. D. Osman, B. Raguse, et al. 1997. A biosensor that uses ion-channel switches. Nature. 387:580-583.
4. Hirano, A., M. Wakabayashi, Y. Matsuno, and M. Sugawara. 2003. A single-channel sensor based on gramicidin controlled by molecular recognition at bilayer lipid membranes containing receptor. Biosens. Bioelectron. 18:973-983.
5. Futaki, S., Y. J. Zhang, T. Kiwada, I. Nakase, T. Yagami, et al. 2004. Gramicidin-based channel systems for the detection of protein-ligand interaction. Bioorg. Med. Chem. 12:1343-1350.
6. Borisenko, V., Z. Zhang, and G. A. Woolley. 2002. Gramicidin derivatives as membrane-based pH sensors. Biochim. Biophys. Acta. 1558:26-33.
7. Koeppe, R. E., and O. S. Anderson. 1996. Engineering the gramicidin channel. Annu. Rev. Biophys. Biomol. Struct. 25:231-258.
8. Banghart, M. R., M. Volgraf, and D. Trauner. 2006. Engineering light- gated ion channels. Biochemistry. 45:15129-15141.
9. Ghadiri, M. R., J. R. Granja, R. A. Milligan, D. E. McRee, and N. Khazanovich. 1993. Self-assembling organic nanotubes based on a cyclic peptide architecture. Nature. 366:324-327.
10. Ghadiri, M. R., J. R. Granja, and L. K. Buehler. 1994. Artificial trans- membrane ion channels from self-assembling peptide nanotubes. Nature. 369:301-304.
11. Motesharei, K., and M. Ghadiri. 1997. Diffusion-limited size-selective ion sensing based on SAM-supported peptide nanotubes. J. Am. Chem. Soc. 119:11306-11312.
12. Braha, O., B. Walker, S. Cheley, J. J. Kasianowicz, L. Song, et al. 1997. Designed protein pores as components for biosensors. Chem. Biol. 4:497-505.
13. Finkelstein, A. 1987. Water Movement Through Lipid Bilayers, Pores, and Plasma Membranes. Wiley & Sons, New York.
14. Pappenheimer, J. R. 1953. Passage of molecules through capillary walls. Physiol. Rev. 33:387-432.
15. Paganelli, C. V., and A. K. Solomon. 1957.The rate of exchange of tritiated water across the human red cell membrane. J. Gen. Physiol. 41:259-277.
16. Saparov, S. M., J. R. Pfeifer, L. Al-Momani, G. Portella, B. L. de Groot, et al. 2006. Mobility of a one-dimensional confined file of water molecules as a function of file length. Phys. Rev. Lett. 96:148101.
17. Portella, G., P. Pohl, and B. L. de Groot. 2007. Invariance of single-file water mobility in gramicidin-like peptidic pores as function of pore length. Biophys. J. 92:3930-3937.
18. Levitt, D. G. 1973. Dynamics of a single-file pore: non-Fickian behavior. Phys. Rev. A. 8:3050-3054.
19. Richards, P. M. 1977. Theory of one-dimensional hopping conductivity and diffusion. Phys. Rev. B. 16:1393-1409.
20. Alexander, S., and P. Pincus. 1978. Diffusion of labeled particles on one-dimensional chains. Phys. Rev. B. 18:2011-2012.
21. Fedders, P. A. 1978. Two-point correlation functions for a distinguishable particle hopping on a uniform one-dimensional chain. Phys. Rev. B. 17:40-46.
22. Levitt, D. G. 1973. Kinetics of diffusion and convection in 3.2 A pores. Biophys. J. 13:186-206.
23. Allen, T., S. Kuyucak, and S. H. Chung. 1999. The effect of hydrophobic and hydrophilic channel walls on the structure and diffusion of water and ions. J. Chem. Phys. 111:7985-7999.
24. Hummer, G., J. C. Rasaiah, and J. P. Noworyta. 2001. Water conduction through the hydrophobic channel of a carbon nanotube. Nature. 414:188-190.
25. de Groot, B. L., D. P. Tieleman, P. Pohl, and H. Grubmuller. 2002. Water permeation through gramicidin A: desformylation and the double helix; a molecular dynamics study. Biophys. J. 82:2934-2942.
26. Allen, R., S. Melchionna, and J. P. Hansen. 2002. Intermittent permeation of cylindrical nanopores by water. Phys. Rev. Lett. 89:175502.
27. Beckstein, O., and M. S. Sansom. 2003. Liquid-vapor oscillations of water in hydrophobic nanopores. Proc. Natl. Acad. Sci. USA. 100:7063-7068.
28. Kalra, A., S. Garde, and G. Hummer. 2003. Osmotic water transport through carbon nanotube membranes. Proc. Natl. Acad. Sci. USA. 100:10175-10180.
29. Tarek, M., B. Maigret, and C. Chipot. 2003. Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers. Biophys. J. 85:2287-2298.
30. Beckstein, O., and M. S. P. Sansom. 2004. The influence of geometry, surface character, and flexibility on the permeation of ions and water through biological pores. Phys. Biol. 1:42-52.
31. Rasaiah, J. C., S. Garde, and G. Hummer. 2008. Water in nonpolar confinement: from nanotubes to proteins and beyond. Annu. Rev. Phys. Chem. 59:713-740.
32. Fang, H., R. Wan, X. Gong, H. Lu, and S. Li. 2008. Dynamics of single- file water chains inside nanoscale channels: physics, biological significance and applications. J. Phys. D Appl. Phys. 41:103002.
33. Dzubiella, J., and J. -P. Hansen. 2005. Electric-field-controlled water and ion permeation of a hydrophobic nanopore. J. Chem. Phys. 122:234706.
34. Freites, J. A., D. J. Tobias, and S. H. White. 2006. A voltage-sensor water pore. Biophys. J. 91:L90-L92.
35. Li, J., X. Gong, H. Lu, D. Li, H. Fang, et al. 2007. Electrostatic gating of a nanometer water channel. Proc. Natl. Acad. Sci. USA. 104:3687-3692.
36. Kaminski, G. A., R. A. Friesner, J. Tirado-Rives, and W. L. Jorgensen. 2001. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B. 105:6474-6487.
37. 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.
38. 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.
39. Lindahl, E., B. Hess, and D. Van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7:306-317.
40. Van der Spoel, D., E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, et al. 2005. GROMACS: fast, flexible and free. J. Comput. Chem. 26:1701-1718.
41. 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.
42. Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, et al. 1995. A smooth particle mesh Ewald potential. J. Chem. Phys. 103:8577-8592.
43. 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.
44. 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.
45. 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.
46. Smart,O. S.,J. G. Neduvelil,X. Wang, B. A. Wallace, and M. S. P. Sansom. 1996. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14:354-360.
47. de Groot, B. L., and H. Grubmuller. 2005. The dynamics and energetics of water permeation and proton exclusion in aquaporins. Curr. Opin. Struct. Biol. 15:176-183.
48. Zhu, F., E. Tajkhorshid, and K. Schulten. 2004. Theory and simulation of water permeation in aquaporin-1. Biophys. J. 86:50-57.
49. Zhu, F., E. Tajkhorshid, and K. Schulten. 2004. Collective diffusion model for water permeation through microscopic channels. Phys. Rev. Lett. 93:224501.
50. Beckstein, O., K. Tai, and M. S. P. Sansom. 2004. Not ions alone: barriers to ion permeation in nanopores and channels. J. Am. Chem. Soc. 126:14694-14695.
51. Noon, W. H., K. D. Aumann, R. E. Smalley, and J. Ma. 2002. Helical ice-sheets inside carbon nanotubes in the physiological condition. Chem. Phys. Lett. 355:445-448.
52. Chou, T. 1998. How fast do fluids squeeze through microscopic single- file pores? Phys. Rev. Lett. 80:85-88.
53. Longuet-Higgins, H. C., and G. Austin. 1966. The kinetics of osmotic transport through pores of molecular dimensions. Biophys. J. 6:217-224.
54. Saparov, S. M., and P. Pohl. 2004. Beyond the diffusion limit: Water flow through the empty bacterial potassium channel. Proc. Natl. Acad. Sci. USA. 101:4805-4809.
55. Dani, J. A., and D. G. Levitt. 1981. Water transport and ion-water interaction in the gramicidin channel. Biophys. J. 35:501-508.
56. Hahn, K., J. Karger, and V. V. Kukla. 1996. Single-file diffusion observation. Phys. Rev. Lett. 76:2762-2765.
57. Zhu, F., E. Tajkhorshid, and K. Schulten. 2002. Pressure-induced water transport in membrane channels studied by molecular dynamics. Bio- phys.J. 83:154-160.
58. Hashido, M., M. Ikeguchi, and A. Kidera. 2005. Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF. FEBS Lett. 579:5549-5552.
59. Jensen, M. Ø., and O. G. Mouritsen. 2006. Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF. Biophys. J. 90: 2270-2284.
60. Levitt, D. G. 1974. A new theory of transport for cell membrane pores. I. General theory and application to red cell. Biochim. Biophys. Acta. 373:115-131.
61. Hernandez, J. A., and J. Fischbarg. 1992. Kinetic analysis of water transport though a single-file pore. J. Gen. Physiol. 99:645-662.
62. Berezhkovskii, A., and G. Hummer. 2002. Single-file transport of water molecules through a carbon nanotube. Phys. Rev. Lett. 89:064503.
63. Pohl, P., and S. M. Saparov. 2000. Solvent drag across gramicidin channels demonstrated by microelectrodes. Biophys. J. 78:2426-2434.
64. Engel, A., and H. Stahlberg. 2002. Aquaglyceroporins: Channel Proteins with a Conserved Core, Multiple Functions and Variable Surfaces., Vol. 215. International Review ofCytology. Academic Press, New York., 75-104.
65. Saparov, S. M., S. P. Tsunoda, and P. Pohl. 2005. Proton exclusion by an aquaglyceroprotein: a voltage clamp study. Biol. Cell. 97: 545-550.