Ion selectivity in the KcsA potassium channel from the perspective of the ion binding site

Biophysical Journal

Volumn 96, Issue 6, 2009, Pages 2138-2145

  Dixit, Purushottam D ^a   Merchant, Safir ^a   Asthagiri, D ^a  

^a Johns Hopkins University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OXYGEN; POTASSIUM CHANNEL; SODIUM; POTASSIUM; WATER;

ARTICLE; CALCULATION; MATHEMATICAL ANALYSIS; NORMAL DISTRIBUTION; THERMODYNAMICS; ALGORITHM; BINDING COMPETITION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION;

ALGORITHMS; BINDING SITES; BINDING, COMPETITIVE; COMPUTER SIMULATION; MODELS, MOLECULAR; NORMAL DISTRIBUTION; OXYGEN; POTASSIUM; POTASSIUM CHANNELS; SODIUM; THERMODYNAMICS; WATER;

EID: 65949103611     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2008.12.3917     Document Type: Article

References (33)

1. Latorre, R., and C. Miller. 1983. Conduction and selectivity in potassium channels. J. Membr. Biol. 71:11-30.
2. + conduction and selectivity. Science. 280:69-77.
3. Allen, T. W., A. Bliznyuk, A. P. Rendell, S. Kuyucak, and S. H. Chung. 2000. The potassium channel: structure, selectivity and diffusion. J. Chem. Phys. 112:8191-8204.
4. + selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations. Biochim. Biophys. Acta. 1548:194-202.
5. Noskov, S. Y., S. Bernéche, and B. Roux. 2004. Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature. 431:830-834.
6. + channel-Fab complex at 2.0 A° resolution. Nature. 414:43-48.
7. Noskov, S. Y., and B. Roux. 2006. Ion selectivity in potassium channels. Biophys. Chem. 124:279-291.
8. Noskov, S. Y., and B. Roux. 2007. Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels. J. Gen. Physiol. 129:135-143.
9. Varma, S., and S. B. Rempe. 2007. Tuning ion coordination architectures to enable selective partitioning. Biophys. J. 93:1093-1099.
10. Thomas, M., D. Jayatilaka, and B. Corry. 2007. The predominant role of coordination number in potassium channel selectivity. Biophys. J. 93:2635-2643.
11. + channels is due to topological control of the permeant ion's coordinated state. Proc. Natl. Acad. Sci. USA. 104:9260-9265.
12. Asthagiri, D., L. R. Pratt, and M. E. Paulaitis. 2006. Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity. J. Chem. Phys. 125:024701.
13. Hummer, G., L. R. Pratt, and A. E. Garcia. 1997. Multistate Gaussian model for electrostatic solvation free energies. J. Am. Chem. Soc. 119:8523-8527.
14. Widom, B. 1982. Potential-distribution theory and the statistical mechanics of fluids. J. Phys. Chem. 86:869-872.
15. Beck, T. L., M. E. Paulaitis, and L. R. Pratt. 2006. The Potential Distribution Theorem and Models of Molecular Solutions. Cambridge University Press, Cambridge, UK.
16. Pratt, L. R., and D. Asthagiri. 2007. Potential distribution methods and free energy models of molecular solutions. In Free Energy Calculations: Theory and Applications in Chemistry and Biology, Vol. 86, Chapt. 9, of Springer Series in Chemical Physics. C. Chipot and A. Pohorille, editors. Springer, New York.
17. Kubo, R. 1962. Generalized cumulant expansion method. J. Phys. Soc. Jpn. 17:1100-1120.
18. Stillinger, F. H., and T. A. Weber. 1982. Hidden structures in liquids. Phys. Rev. A. 25:978-989.
19. Deng, Y., and B. Roux. 2008. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. J. Chem. Phys. 128:115103.
20. Azzalini, A. 1985. A class of distributions which includes the normal ones. Scand. J. Stat. 12:171-178.
21. MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
22. Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, et al. 1999. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
23. Humphrey, W., A. Dalke, and K. Schulten. 1996. VMD - visual molecular dynamics. J. Mol. Graph. 14:33-38.
24. + channel in a bilayer membrane. Biophys. J. 78:2900-2917.
25. Jorgensen, W., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
26. Neria, E., S. Fischer, and M. Karplus. 1996. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105:1902-1921.
27. Martyna, G. J., D. J. Tobias, and M. L. Klein. 1994. Constant pressure molecular dynamics algorithms. J. Chem. Phys. 101:4177-4189.
28. Feller, S. E., Y. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation: the Langevin piston method. J. Chem. Phys. 103:4613-4621.
29. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
30. Tieleman, D. P., P. C. Biggin, G. R. Smith, and M. S. P. Sansom. 2001. Simulation approaches to ion channel structure-function relationships. Q. Rev. Biophys. 34:473-561.
31. + in a K channel selectivity filter: a simulation study. Biophys. J. 83:633-645.
32. Asthagiri, D., S. Merchant, and L. R. Pratt. 2008. Role of attractive methane-water interactions in the potential of mean force between methane molecules in water. J. Chem. Phys. 128:244512.
33. Hummer, G., and A. Szabo. 1996. Calculation of free-energy differences from computer simulations of initial and final states. J. Chem. Phys. 105:2004-2010.