Structure and Dynamics of One-dimensional Ionic Solutions in Biological Transmembrane Channels

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 1987 Jun 1

PMID 2440485

Citations 13

Authors

A Skerra

J Brickmann

Affiliations

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Abstract

The structure and dynamics of solvated alkali metal cations in transmembrane channels are treated using the molecular dynamics simulation technique. The simulations are based on a modified Fischer-Brickmann model (Fischer, W., and J. Brickmann, 1983, Biophys. Chem., 18:323-337) for gramicidin A-type channels. The trajectories of all particles in the channel as well as two-dimensional pair correlation functions are analyzed. It is found from the analysis of the stationary simulation state that one-dimensional solvation complexes are formed and that the number of water molecules in the channel varies for different alkali metal cations.

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References

Wallace B . Ion-bond forms of the gramicidin a transmembrane channel. Biophys J. 2009; 45(1):114-6. PMC: 1435275. DOI: 10.1016/S0006-3495(84)84131-4. View

Mackay D, Berens P, Wilson K, Hagler A . Structure and dynamics of ion transport through gramicidin A. Biophys J. 1984; 46(2):229-48. PMC: 1435037. DOI: 10.1016/S0006-3495(84)84016-3. View

Kappas U, Fischer W, Polymeropoulos E, Brickmann J . Solvent effects in ionic transport through transmembrane protein channels. J Theor Biol. 1985; 112(3):459-64. DOI: 10.1016/s0022-5193(85)80014-x. View

Fischer W, Brickmann J, Lauger P . Molecular dynamics study of ion transport in transmembrane protein channels. Biophys Chem. 1981; 13(2):105-16. DOI: 10.1016/0301-4622(81)80009-9. View

Naik V, Krimm S . Vibrational analysis of the structure of crystalline gramicidin a. Biophys J. 2009; 45(1):109-12. PMC: 1435265. DOI: 10.1016/S0006-3495(84)84129-6. View

Wallace B, Veatch W, BLOUT E . The effects of lipid environment, ion-binding and chemical modifications on the structure of the gramicidin transmembrane channel. Biophys J. 2009; 37(1):197-9. PMC: 1329122. DOI: 10.1016/S0006-3495(82)84667-5. View

Dwivedi A, Krimm S . Vibrational analysis of peptides, polypeptides, and proteins. XVIII. Conformational sensitivity of the alpha-helix spectrum: alpha I- and alpha II-poly(L-alanine). Biopolymers. 1984; 23(5):923-43. DOI: 10.1002/bip.360230509. View

Fischer W, Brickmann J . Ion-specific diffusion rates through transmembrane protein channels. A molecular dynamics study. Biophys Chem. 1983; 18(4):323-37. DOI: 10.1016/0301-4622(83)80045-3. View

Polymeropoulos E, Brickmann J . Molecular dynamics of ion transport through transmembrane model channels. Annu Rev Biophys Biophys Chem. 1985; 14:315-30. DOI: 10.1146/annurev.bb.14.060185.001531. View

10.

Rosenberg P, Finkelstein A . Interaction of ions and water in gramicidin A channels: streaming potentials across lipid bilayer membranes. J Gen Physiol. 1978; 72(3):327-40. PMC: 2228537. DOI: 10.1085/jgp.72.3.327. View

11.

Urry D . A molecular theory of ion-conductng channels: a field-dependent transition between conducting and nonconducting conformations. Proc Natl Acad Sci U S A. 1972; 69(6):1610-4. PMC: 426759. DOI: 10.1073/pnas.69.6.1610. View

12.

Myers V, Haydon D . Ion transfer across lipid membranes in the presence of gramicidin A. II. The ion selectivity. Biochim Biophys Acta. 1972; 274(2):313-22. DOI: 10.1016/0005-2736(72)90179-4. View

13.

Finkelstein A, Andersen O . The gramicidin A channel: a review of its permeability characteristics with special reference to the single-file aspect of transport. J Membr Biol. 1981; 59(3):155-71. DOI: 10.1007/BF01875422. View

14.

Brickmann J, Fischer W . Entropy effects on the ion-diffusion rate in transmembrane protein channels. Biophys Chem. 1983; 17(3):245-58. DOI: 10.1016/0301-4622(83)87007-0. View

15.

Rosenberg P, Finkelstein A . Water permeability of gramicidin A-treated lipid bilayer membranes. J Gen Physiol. 1978; 72(3):341-50. PMC: 2228543. DOI: 10.1085/jgp.72.3.341. View