Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands

Nature

Volumn 431, Issue 7010, 2004, Pages 830-834

  Noskov, Sergei Yu ^a,c   Bernéche, Simon ^b   Roux, Benoît ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b UNIVERSITY OF BASEL   (Switzerland)

^c INSTITUTE OF SOLUTION CHEMISTRY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANES; COMPUTER SIMULATION; ELECTROSTATICS; FLEXIBLE STRUCTURES; MOLECULAR DYNAMICS; POTASSIUM; PROTEINS;

ION CONDUCTION; ION SELECTIVITY; IONIC BALANCE; TRANSMEMBRANES;

IONS;

CARBONYL DERIVATIVE; COORDINATION COMPOUND; ION; LIGAND; MEMBRANE PROTEIN; POTASSIUM CHANNEL; POTASSIUM ION; PROTEIN KCSA; SODIUM ION; UNCLASSIFIED DRUG;

BIOCHEMISTRY;

ARTICLE; CELL MEMBRANE; DIFFUSION; ELECTRICITY; ENERGY TRANSFER; ION CONDUCTANCE; ION TRANSPORT; MOLECULAR DYNAMICS; MOLECULAR SIZE; POTASSIUM TRANSPORT; PRIORITY JOURNAL; PROTEIN STRUCTURE; THERMODYNAMICS;

BACTERIAL PROTEINS; BINDING SITES; CATIONS; ELECTROSTATICS; ION CHANNEL GATING; LIGANDS; MODELS, MOLECULAR; OXYGEN; POTASSIUM; POTASSIUM CHANNELS; SODIUM; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 7244251461     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature02943     Document Type: Article

References (32)

1. Hille, B., Armstrong, C. M. & MacKinnon, R. Ion channels: From idea to reality. Nature Med. 5, 1105-1109 (1999).
2. Zaccai, G. How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288, 1604-1609 (2000).
3. Karplus, M. & Petsko, G. A. Molecular dynamics simulations in biology. Nature 347, 631-639 (1990).
4. Eisenman, G. Cation selective electrodes and their mode of operation. Biophys. J. 2, 259-323 (1962).
5. + conduction and selectivity. Science 280, 69-77 (1998).
6. + selectivity filter. Nature 414, 37-42 (2001).
7. + channel-Fab complex at 2.0 Å resolution. Nature 414, 43-48 (2001).
8. Eisenman, G. & Horn, R. Ion selectivity revisited: the role of kinetic and equilibrium processes in ion permeation through channels. J. Membr. Biol. 76, 197-225 (1983).
9. Latorre, R. & Miller, C. Conduction and selectivity in potassium channels. J. Membr. Biol. 71, 11-30 (1983).
10. Hille, B. Ion Channels of Excitable Membranes 3rd edn (Sinauer, Sunderland, Massachusetts, 2001).
11. + channel. J. Gen. Physiol. 92, 569-596 (1988).
12. LeMasurier, M., Heginbotham, L. & Miller, C. KscA: it's a potassium channel. J. Gen. Physiol. 118, 303-314 (2001).
13. + channel of known structure. J. Gen. Physiol. 120, 323-325 (2002).
14. Pauling, L. Nature of the Chemical Bond and Structure of Molecules and Crystals 3rd edn (Cornell Univ. Press, Ithaca, 1960).
15. Allen, T. W., Andersen, O. S. & Roux, B. On the importance of atomic fluctuations, protein flexibility and solvent in ion permeation. J. Gen. Physiol. (in the press).
16. Åqvist, J. & Luzhkov, V. Ion permeation mechanism of the potassium channel. Nature 404, 881-884 (2000).
17. + selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations. Biochim. Biophys. Acta 1548, 194-202 (2001).
18. Allen, T. W., Bliznyuk, A., Rendell, A. P., Kyuucak, S. & Chung, S. H. The potassium channel: Structure, selectivity and diffusion. J. Chem. Phys. 112, 8191-8204 (2000).
19. + channel. Nature 414, 73-77 (2001).
20. + channel. Proc. Natl Acad. Sci. USA 100, 8644-8648 (2003).
21. + ions in a K channel selectivity filter: A simulation study. Biophys. J. 83, 633-645 (2002).
22. + channe. Biochemistry 38, 8599-8604 (1999).
23. +. Biophys. J. 80, 2704-2714 (2001).
24. + selectivity filter: Charge balance and coupling of ion binding to a protein conformational change underlie high conduction rates. J. Mol. Biol. 333, 965-975 (2003).
25. Yamashita, M. M., Wesson, L., Eisenman, G. & Eisenberg, D. Where metal ions bind in proteins. Proc. Natl Acad. Sci USA 87, 5648-5652 (1990).
26. Åqvist, J., Alvarez, O. & Eisenman, G. Ion-selective properties of a small ionophore in methanol studied by free energy perturbation simulations. J. Phys. Chem. 96, 10019-10025 (1992).
27. + by valinomycin in methanol. J. Am. Chem. Soc. 117, 779-791 (1995).
28. MacKerell, A. D. J. et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616 (1998).
29. Weeks, J. D., Chandler, D. & Andersen, H. C. Role of repulsive forces in determining the equilibrium structure of simple liquids. J. Chem. Phys. 54, 5237-5247 (1971).
30. + channel with backbone mutations in the selectivity filter. Nature Neurosci. 4, 239-246 (2001).
31. Heinemann, S. H., Terlau, H., Stuhmer, W., Imoto, K. & Numa, S. Calcium channel characteristics conferred on the sodium channel by single mutations. Nature 356, 441-443 (1992).
32. Brooks, B. R. et al. CHARMM: a program for macromolecular energy minimization and dynamics calculations. Comput. Chem. 4, 187-217 (1983).