A computational study of ion binding and protonation states in the KcsA potassium channel

Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology

Volumn 1481, Issue 2, 2000, Pages 360-370

  Luzhkov, Victor B ^a   Åqvist, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Free energy perturbation; Ion binding; KcsA; Molecular dynamics; Potassium channel; Protonation states

Indexed keywords

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTALLOGRAPHY; ION PERMEABILITY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; POTASSIUM CHANNEL; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTON TRANSPORT;

BINDING SITES; CATIONS; COMPUTER SIMULATION; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; POTASSIUM; POTASSIUM CHANNELS; PROTONS; SUPPORT, NON-U.S. GOV'T; THERMODYNAMICS;

EID: 0034730689     PISSN: 01674838     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4838(00)00183-7     Document Type: Article

References (24)

1. B. Hille, Ionic Channels of Excitable Membranes, Sinauer Associates, Sunderland, MA, 1992.
2. Hodgkin A.L., Keynes R.D. The potassium permeability of a giant nerve fibre. J. Physiol. 128:1955;61-88.
3. Hille B., Schwarz W. Potassium channels as multi-ion single-file pores. J. Gen. Physiol. 72:1978;409-442.
4. + conduction and selectivity. Science. 280:1998;69-77.
5. + channel. Nature. 404:2000;881-884.
6. + channel. Biochemistry. 38:1999;8599-8604.
7. + channel: electrostatic stabilization of monovalent cations. Science. 285:1999;100-102.
8. Allen T.W., Kuyucak S., Chung S.-H. Molecular dynamics study of the KcsA potassium channel. Biophys. J. 77:1999;2502-2516.
9. Shrivastava I.H., Sansom M.S.P. Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. Biophys. J. 78:2000;557-570.
10. Allen T.W., Bliznyuk A., Rendell A.P., Kuyucak S., Chung S.-H. The potassium channel: structure, selectivity and diffusion. J. Chem. Phys. 112:2000;8191-8204.
11. Marelius J., Kolmodin K., Feierberg I., Åqvist J. Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J. Mol. Graph. Mod. 16:1999;213-225.
12. W.F. van Gunsteren, H.J.C. Berendsen, Groningen Molecular Simulation (GROMOS) Library Manual, Biomos B.V., Groningen, The Netherlands, 1987.
13. Åqvist J. Ion-water interaction potentials derived from free energy perturbation simulations. J. Phys. Chem. 94:1990;8021-8024.
14. Lee F.S., Warshel A. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J. Chem. Phys. 97:1992;3100-3107.
15. King G., Warshel A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91:1989;3647-3661.
16. Warshel A., Sussman F., King G. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry. 25:1986;8368-8372.
17. Kollman P. Free energy calculations: application to chemical and biological phenomena. Chem. Rev. 93:1993;2395-2417.
18. Sternberg M.J.E., Hayes F.R.F., Russel A.J., Thomas P.G., Fersht A.R. Prediction of electrostatic effects of engineering of protein charges. Nature. 330:1987;86-88.
19. Warshel A., Åqvist J. Electrostatic energy and macromolecular function. Annu. Rev. Biophys. Biophys. Chem. 20:1991;267-298.
20. Ponder J.W., Richards F.M. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. J. Mol. Biol. 193:1987;775-791.
21. + by gramicidin A. Biophys. J. 56:1989;171-182.
22. Cuello L.G., Peroso E. A network of charges in the extracellular surface of KcsA contributes to oligomeric stability. Biophys. J. 78:(1 part 2):2000;398A-398A.
23. Eisenman G., Horn R. Ion selectivity revisited: the role of kinetic and equilibrium processes in ion permeation through channels. J. Membr. Biol. 76:1983;197-225.
24. Miller C. Ionic hopping defended. J. Gen. Physiol. 113:1999;783-787.