Permeation of ions across the potassium channel: Brownian dynamics studies

Biophysical Journal

Volumn 77, Issue 5, 1999, Pages 2517-2533

  Chung, Shin Ho ^a   Allen, Toby W ^a   Hoyles, Matthew ^a   Kuyucak, Serdar ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONYL DERIVATIVE; POTASSIUM CHANNEL;

ARTICLE; CRYSTALLOGRAPHY; DIELECTRIC CONSTANT; DIPOLE; ELECTRIC POTENTIAL; ELECTRICITY; ION TRANSPORT; MATHEMATICAL ANALYSIS; MEMBRANE CHANNEL; MOLECULAR DYNAMICS;

EID: 0032708637     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(99)77087-6     Document Type: Article

References (43)

1. Allen, T. W., S. Kuyucak, and S. H. Chung. 1999a. Molecular dynamics study of the KcsA potassium channel. Biophys. J. 77:000-000.
2. Allen, T. W., S. Kuyucak, and S. H. Chung. 1999b. The effect of hydrophobic and hydrophilic channel walls on the structure and diffusion of water and ions. J. Chem. Phys. (in press).
3. Bek, S., and E. Jakobsson. 1994. Brownian dynamics study of a multiplyoccupied cation channel: application to understanding permeation in potassium channel. Biophys. J. 66:1028-1038.
4. Bockris, J. O'M., and A. K. N. Reddy. 1970. Modern Electrochemistry, Vol. 1. Plenum Press, New York.
5. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization and dynamic calculations. J. Comp. Chem. 4:187-217.
6. Chiu, S.-W., and E. Jakobsson. 1989. Stochastic theory of singly occupied ion channels. II. Effects of access resistance and potential gradients extending into the bath. Biophys. J. 55:147-157.
7. Chiu, S.-W., J. A. Novotny, and E. Jakobsson. 1993. The nature of ion and water barrier crossings in a simulated ion channel. Biophys. J. 64: 98-108.
8. Chung, S. H., M. Hoyles, T. Allen, and S. Kuyucak. 1998. Study of ionic currents across a model membrane channel using Brownian dynamics. Biophys. J. 75:793-809.
9. +-selective channel from sarcoplasmic reticulum. J. Gen. Physiol. 76:425-446.
10. + conduction and selectivity. Science. 280:69-73.
11. Hol, W. G. J., P. T. van Duijnen, and H. J. C. Berendsen. 1978. The α-helix dipole and the properties of protein. Nature. 273:443-446.
12. Hoyles, M., S. Kuyucak, and S. H. Chung. 1996. Energy barrier presented to ions by the vestibule of the biological membrane channel. Biophys. J. 70:1628-1642.
13. Hoyles, M., S. Kuyucak, and S. H. Chung. 1998a. Computer simulation of ion conductance in membrane channels. Phys. Rev. E. 58:3654-3661.
14. Hoyles, M., S. Kuyucak, and S. H. Chung. 1998b. Solutions of Poisson's equation in channel-like geometries. Comput. Phys. Comm. 115:45-68.
15. Jakobsson, E., and S.-W. Chiu. 1987. Stochastic theory of singly occupied ion channels. Biophys. J. 52:33-46.
16. Jordan, P. C. 1981. Energy barriers for passage of ions through channels. Exact solution of two electrostatic problems. Biophys. Chem. 13: 203-212.
17. Jordan, P. C. 1982. Electrostatic modeling of ion pores. Energy barriers and electric field profiles. Biophys. J. 39:157-164.
18. Jordan, P. C. 1983. Electrostatic modeling of ion pores. II. Effects attributable to the membrane dipole potential. Biophys. J. 41:189-195.
19. Kuyucak, S., M. Hoyles, and S. H. Chung. 1998. Analytical solutions of Poisson's equation for realistic geometrical shapes of membrane ion channels. Biophys. J. 74:22-36.
20. Levitt, D. G. 1978a. Electrostatic calculations for an ion channel. I. Energy and potential profiles and interactions between ions. Biophys. J. 22: 209-219.
21. Levitt, D. G. 1978b. Electrostatic calculations for an ion channel, n. Kinetic behavior of the gramicidin A channel. Biophys. J. 22:221-248.
22. Li, S. C., M. Hoyles, S. Kuyucak, and S. H. Chung. 1998. Brownian dynamics study of ion transport in the vestibule of membrane channels. Biophys. J. 74:37-47.
23. Lynden-Bell, R. M., and J. C. Rasaiah. 1996. Mobility and solvation of ions in channels. J. Chem. Phys. 105:9266-9280.
24. Pauling, L, 1942. The Nature of the Chemical Bond. Cornell University Press, Ithaca, NY.
25. Press, W. H., B. P. Flannery, S. A. Teukolsky, and W. T. Vetterling. 1989. Numerical Recipes. Cambridge University Press, Cambridge.
26. Rae, J. L., R. A. Levis, and R. S. Eisenberg. 1988. Ionic channels in ocular epithelia. In Ion Channels, Vol. 1. T. Narahashi, editor. Plenum Press, New York. 283-327.
27. Roux, B., and M. Karplus. 1991a. Ion transport in a model gramicidin channel: structure and thermodynamics. Biophys. J. 59:961-981.
28. Roux, B., and M. Karplus. 1991b. Ion transport in a gramicidin-like channel: dynamics and mobility. J. Phys. Chem. 95:4856-4868.
29. Sankararamakrishnan, R., C. Adcock, and M. S. P. Sansom. 1996. The pore domain of the nicotinic acetylcholine receptor: molecular modeling, pore dimensions, and electrostatics. Biophys. J. 71:1659-1671.
30. Sansom, M. S. P., I. D. Breed, and R. Sankararamakrishnan. 1996. Water in channel-like cavities: structure and dynamics. Biophys. J. 70: 693-702.
31. Sansom, M. S. P., G. R. Smith, C. Adcock, and P. C. Biggin. 1997. The dielectric properties of water within model transbilayer pores. Biobpphys. J. 73:2404-2415.
32. Schrempf, H., O. Schmidt, R. Kümmerlen, S. Hinnah, D. Müller, M. Betzler, T. Steinkamp, and R. Wagner. 1995. A prokaryotic potassium ion channel with two predicted transmembrane segment from Steptomyces lividans. EMBO J. 14:5170-5178.
33. Singh, C., R. Sankararamakrishnan, S. Subramaniam, and E. Jakobsson. 1996. Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel. Biophys. J. 71:2276-2288.
34. + ions in models of ion channels: a molecular dynamics study. Biophys. J. 75:2767-2782.
35. Stillinger, F. H., and A. Rahman. 1974. Improved simulation of liquid water by molecular dynamics. J. Chem. Phys. 60:1545-1557.
36. 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 palmitoyloleoylphsophtidylcholine bilayer. Biophys. J. 74: 2786-2801.
37. Toyoshima, C., and N. Unwin. 1988. Ion channel of acetylcholine receptor reconstructed from images of postsynaptic membranes. Nature. 336: 247-250.
38. Unwin, N. 1989. The structure of ion channels in membranes of excitable cells. Neuron. 3:665-676.
39. van Gunsteren, W. F., H. J. C. Berendsen, and J. A. Rullmann. 1981. Stochastic dynamics for molecules with constraints: Brownian dynamics of n-alkanes. Mol. Phys. 44:69-95.
40. van Gunsteren, W. F., and H. J. C. Berendsen. 1982. Algorithms for Brownian dynamics. Mol. Phys. 45:637-647.
41. Vasudevan, S., L. Premkumar, S. Stowe, P. W. Gage, H. Reiländer, and S. H. Chung. 1992. Muscarinic acetylcholine receptor produced in recombinant baculovirus infected Sf9 insect cells couples with endogenous G-protein to activate ion channels. FEBS Lett. 311:7-11.
42. Weast, R. C., editor. 1983. CRC Handbook of Chemistry and Physics. CRC Press, Boca Raton, FL. D-171.
43. Zhang, L., H. T. Davis, D. M. Kroll, and H. S. White. 1995. Molecular dynamics simulations of water in a spherical cavity. J. Phys. Chem. 99:2878-2884.