Dynamic Properties of Na+ Ions in Models of Ion Channels: a Molecular Dynamics Study

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 1998 Nov 25

PMID 9826599

Citations 14

Authors

G R Smith

M S Sansom

Affiliations

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Abstract

We present simulation results for the effective diffusion coefficients of a sodium ion in a series of model ion channels of different diameters and hydrophobicities, including models of alamethicin, a leucine-serine peptide, and the M2 helix bundle of the nicotinic acetylcholine receptor. The diffusion coefficient, which in the simulations has a value of 0.15(2) A2ps-1 in bulk water, is found to be reduced to as little as 0.02(1) A2ps-1 in the narrower channels, and to about 0.10(5) A2ps-1 in wider channels such as the nicotinic acetylcholine receptor. It is anticipated that this work will be useful in connection with calculations of channel conductivity using such techniques as the Poisson-Nernst-Planck equation, Eyring rate theory, or Brownian dynamics.

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References

Urry D . The gramicidin A transmembrane channel: a proposed pi(L,D) helix. Proc Natl Acad Sci U S A. 1971; 68(3):672-6. PMC: 389014. DOI: 10.1073/pnas.68.3.672. View

Chen D, Xu L, Tripathy A, Meissner G, Eisenberg B . Permeation through the calcium release channel of cardiac muscle. Biophys J. 1997; 73(3):1337-54. PMC: 1181034. DOI: 10.1016/S0006-3495(97)78167-0. View

Jordan P . Electrostatic modeling of ion pores. Energy barriers and electric field profiles. Biophys J. 1982; 39(2):157-64. PMC: 1328927. DOI: 10.1016/S0006-3495(82)84503-7. View

Fox Jr R, Richards F . A voltage-gated ion channel model inferred from the crystal structure of alamethicin at 1.5-A resolution. Nature. 1982; 300(5890):325-30. DOI: 10.1038/300325a0. View

Cooper K, Jakobsson E, Wolynes P . The theory of ion transport through membrane channels. Prog Biophys Mol Biol. 1985; 46(1):51-96. DOI: 10.1016/0079-6107(85)90012-4. View

Wallace B . Structure of gramicidin A. Biophys J. 1986; 49(1):295-306. PMC: 1329637. DOI: 10.1016/S0006-3495(86)83642-6. View

Hucho F, Oberthur W, Lottspeich F . The ion channel of the nicotinic acetylcholine receptor is formed by the homologous helices M II of the receptor subunits. FEBS Lett. 1986; 205(1):137-42. DOI: 10.1016/0014-5793(86)80881-x. View

Skerra A, Brickmann J . Simulation of voltage-driven hydrated cation transport through narrow transmembrane channels. Biophys J. 1987; 51(6):977-83. PMC: 1330031. DOI: 10.1016/S0006-3495(87)83425-2. View

Jakobsson E, Chiu S . Stochastic theory of ion movement in channels with single-ion occupancy. Application to sodium permeation of gramicidin channels. Biophys J. 1987; 52(1):33-45. PMC: 1329981. DOI: 10.1016/S0006-3495(87)83186-7. View

10.

Lear J, Wasserman Z, Degrado W . Synthetic amphiphilic peptide models for protein ion channels. Science. 1988; 240(4856):1177-81. DOI: 10.1126/science.2453923. View

11.

Chiu S, Jakobsson E . Stochastic theory of singly occupied ion channels. II. Effects of access resistance and potential gradients extending into the bath. Biophys J. 1989; 55(1):147-57. PMC: 1330449. DOI: 10.1016/S0006-3495(89)82786-9. View

12.

Nicholson L, Teng Q, Cross T . Solid-state nuclear magnetic resonance derived model for dynamics in the polypeptide backbone of the gramicidin A channel. J Mol Biol. 1991; 218(3):621-37. DOI: 10.1016/0022-2836(91)90706-c. View

13.

Villarroel A, Herlitze S, Koenen M, Sakmann B . Location of a threonine residue in the alpha-subunit M2 transmembrane segment that determines the ion flow through the acetylcholine receptor channel. Proc Biol Sci. 1991; 243(1306):69-74. DOI: 10.1098/rspb.1991.0012. View

14.

Roux B, Karplus M . Ion transport in a model gramicidin channel. Structure and thermodynamics. Biophys J. 1991; 59(5):961-81. PMC: 1281331. DOI: 10.1016/S0006-3495(91)82311-6. View

15.

Chiu S, Jakobsson E, Subramaniam S, McCammon J . Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophys J. 1991; 60(1):273-85. PMC: 1260057. DOI: 10.1016/S0006-3495(91)82049-5. View

16.

Bertrand D, Devillers-Thiery A, Revah F, Galzi J, Hussy N, Mulle C . Unconventional pharmacology of a neuronal nicotinic receptor mutated in the channel domain. Proc Natl Acad Sci U S A. 1992; 89(4):1261-5. PMC: 48429. DOI: 10.1073/pnas.89.4.1261. View

17.

Cohen B, Labarca C, Czyzyk L, Davidson N, Lester H . Tris+/Na+ permeability ratios of nicotinic acetylcholine receptors are reduced by mutations near the intracellular end of the M2 region. J Gen Physiol. 1992; 99(4):545-72. PMC: 2219204. DOI: 10.1085/jgp.99.4.545. View

18.

Cowan S, Schirmer T, Rummel G, Steiert M, Ghosh R, Pauptit R . Crystal structures explain functional properties of two E. coli porins. Nature. 1992; 358(6389):727-33. DOI: 10.1038/358727a0. View

19.

Gutman M, Tsfadia Y, Masad A, Nachliel E . Quantitation of physical-chemical properties of the aqueous phase inside the phoE ionic channel. Biochim Biophys Acta. 1992; 1109(2):141-8. DOI: 10.1016/0005-2736(92)90077-y. View

20.

Galzi J, Devillers-Thiery A, Hussy N, Bertrand S, Changeux J, Bertrand D . Mutations in the channel domain of a neuronal nicotinic receptor convert ion selectivity from cationic to anionic. Nature. 1992; 359(6395):500-5. DOI: 10.1038/359500a0. View