Correlated movements of ions and water in a nanochannel

Molecular Simulation

Volumn 35, Issue 1-2, 2009, Pages 13-23

  Haan, M ^a   Gwan, J F ^a   Baumgaertner, A ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

Incommensurability; Ion conduction; Molecular dynamics simulation; Permeation; Potassium channel; Ratchet; Rectification

Indexed keywords

DYNAMICS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULES; NANOFLUIDICS;

INCOMMENSURABILITY; ION CONDUCTION; MOLECULAR DYNAMICS SIMULATION; POTASSIUM CHANNEL; RATCHET; RECTIFICATION;

IONS;

EID: 61549090249     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020802433160     Document Type: Article

References (44)

1. T. Chou and D. Lohse, Entropy-driven pumping in zeolites and biological channels. Phys. Rev. Lett. 82 (1999), pp. 3552-3555.
2. D. Dubbeldam, S. Calero, T.L.M. Maesen, and B. Smit, Incommensurate diffusion in confined systems, Phys. Rev. Lett. 90(2003), 245901.
3. A. Kalra, S. Garde, and G. Hummer, Osmotic water transport through carbon nanotube membranes, Proc. Natl Acad. Sci. USA 100 (2003), pp. 10175-10178.
4. I.-C. Yeh and G. Hummer, Nucleic acid transport through carbon nanotube membranes, Proc. Natl Acad. Sci. 101 (2004), pp. 12177-12182.
5. Y. Fujiyoshia, K. Mitsuoka, B.L. de Groot, A. Philippsen, H. Grubmüller, P. Agre, and A. Engel, Structure and function of water channels, Curr. Opin. Struct. Biol. 12 (2002), pp. 509-515.
6. + selectivity filter. Nature 414 (2001), pp. 37-42.
7. S. Bemeche and B. Roux, A microscopiv view of ion conduction through the k + channel, Proc. Natl Acad. Sci. 100 (2003), pp. 8644-8648.
8. R. Elber, D.P. Chen, D. Rojewska, and R. Eisenberg, Sodium in gramicidin: An example of a permion, Biophys. J. 68 (1995), pp. 906-924.
9. + conduction and selectivity, Science 280 (1998), pp. 69-77.
10. + channel-fab complex at 2.0Å resolution, Nature 414 (2001). pp. 43-48.
11. B. Hille, Ion Channels of Excitable Membranes, 3rd ed., Sinauer Associates Inc., Sunderland, MA, 2001.
12. A.L. Hodgkin and R.D. Keynes, The potassium permeability of a giant nerve fibre, J. Physiol. 128 (1955), pp. 61 -88.
13. T.W. Allen, S. Kuyucak, and S.-H. Chung, Molecular dynamics study of the kcsa potassium channel, Biophys. J. 77 (1999), pp. 2502-2516.
14. + channel in a bilayer membrane, Biophys. J. 78 (2000), pp. 2900-2917.
15. I.H. Shrivastava and M.S.P. Sansom, Simulations of ion permeation through a potassium channel: molecular dynamics of kcsa in a phospholipid bilayer, Biophys. J. 78 (2000), pp. 557-570.
16. S.-H. Chung, T.W. Allen, and S. Kuyucak, Conducting-state properties of the kcsa potassium channel from molecular and brownian dynamics simulations, Biophys. J. 82 (2002), pp. 628-645.
17. S. Kuyucak, O.S. Andersen, and S.-H. Chung, Models of permeation in ion channels. Rep. Prog. Phys. 64 (2001), pp. 1427-1472.
18. B. Roux, T. Allen, S. Berneche, and W. Im, Theoretical and computational models of biological ion channels. Quart. Rev. Biophys. 37 (2004), pp. 15-103.
19. J.C. Wand and D.F. Pickett, One-dimensional models for superionic conductors, J. Chem. Phys. 65 (1976), pp. 5378-5384.
20. J.B. Sokoloff, Ionic order and defect conductivity in the one-dimensional superionic conductor hollandite, Phys. Rev. B 17 (1978), pp. 4843-4849.
21. T. Geisel, Interacting brownian particles and correlations in superionic conductors, Phys. Rev. B 20 (1979), pp. 4294-4302.
22. H.U. Beyeler, L. Pietronero, and S. Strässler, Configurational model for a one-dimensional ionic conductor, Phys. Rev. B 22 (1980), pp. 2988-3000.
23. M. Weiss and F.-J. Elmer, Dry friction in the frenkel-kontorova- tomlinson model: static properties, Phys. Rev. B 53 (1996), p. 7539.
24. Y. Michiue and M. Watanabe, Atomistic simulation study of k-hollandìte: Ionic correlation and dynamics of the linearly disordered solid, Phys. Rev. B 59 (1999X pp. 11298-11302.
25. J. Piasecki, R.J. Allen, and J.-P. Hansen, Kinetic models of ion transport through a nanopore, Phys. Rev. E 70 (2004), 021105.
26. H. Lu, J. Li, X. Gong, R. Wan, L. Zeng, and H. Fang, Water permeation and wavelike density distributions inside narrow nanochannels, Phys. Rev. B 77 (2008), p. 174115.
27. J J.F. Gwan and A. Baumgaertner, Cooperative transport in a potassium ion channel, J. Chem. Phys. 127 (2007), p. 045103.
28. J.F. Gwan and A. Baumgaertner, Ion transport in a nanochannel, J. Comput. Theor. Nanosci. 4 (2007), pp. 50-56.
29. + selectivity filter: Charge balance and coupling of the ion binding to a protein confoπnatìonal clmnge undelie high conduction rates, J. Mol. Biol. 333 (2003), pp. 965-975.
30. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, Comparsion of simple potential functions for simulating liquid water, J. Chem. Phys. 79 (1983), pp. 926-935.
31. D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheatham, W.S. Ross, C. Simmerling, T. Darden, K.M. Merz, R.V. Stanton, A. Cheng et al., AMBER 5.Ü, University of California, San Francisco, 1997.
32. M. Haan, Simulations of a biological ion channel, MSc thesis, University Duisburg-Essen, Duisburg, Germany, 2007.
33. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, and J.R. Haak, Molecular dynamics with coupling to an external hath, J. Chem. Phys. 81 (1984), pp. 3684-3690.
34. S.J. Weiner, P.A. Kollman, D.T. Nguyen, and D.A. Case, An all atom force field for simulations of proteins and nucleic acids, J. Comp. Chem. 7 (1986), pp. 230-252.
35. A. Onufriev, D. Bashford, and D.A. Case, Modification of the generalized horn model suitable for macromolecules, J. Phys. Chem. B 104 (2000), pp. 3712-3720.
36. J. Srinivasan, M.W. Trevathan, P. Beroza, and D.A. Case, Application of a pairwise generalized born model to proteins and nucleic acids: inclusion of salt effects, Theor. Chem. Ace. 101 (1999), pp. 426-434.
37. J. Frenkel and T. Kontorova, On the theory of plastic deformation and twinning, J. Phys. (Moscow) 1 (1939), pp. 137-149.
38. R. Feynman, R. Leighton, and M. Sands, The Feyman Lectures on Physics, Vol. 1, Addison Wesley, Reading, MA, 1963.
39. R.D. Vale and F. Oosawa, Protein motors and maxwell's demons: Does mechanochemical transductìon Involve a thermal ratchet? Adv. Biophys. 26 (1990), pp. 97-134.
40. A. Adjari and J. Prost, Mouvement induit par un potentiel periodique de basse svmetrie: dielectrophorese pulsee, CR. Acad. Sci. Paris II 315 (1992), pp. 1635-1639.
41. M.O. Magnasco, Forced thermal ratchets, Phys. Rev. Lett. 71 (1993), pp. 1477-1480.
42. R.D. Astumian, Thermodynamics and kinetics of a hrownian motor. Science 276 (1997), pp. 917 - 922.
43. P. Reimann and P. Hänggi, Introduction to the physics of hrownian motors, Appl. Phys. A 75 (2002), pp. 169-178.
44. P.W. Anderson, Concepts in solids: Lectures on the Theory of Solids, 2nd ed., W.A. Benjamin, Reading, MA, 1971.