Modeling permeation energetics in the KcsA potassium channel

Biophysical Journal

Volumn 84, Issue 5, 2003, Pages 2814-2830

  Garofoli, S ^a   Jordan, P C ^a,b  

^a BRANDEIS UNIVERSITY   (United States)

^b UNIVERSITÀ DI ROMA LA SAPIENZA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BARIUM ION; CESIUM ION; POTASSIUM CHANNEL; POTASSIUM ION; RUBIDIUM ION; SODIUM ION;

ARTICLE; ENERGY; ION PERMEABILITY; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MEMBRANE PERMEABILITY; MOLECULAR STABILITY; MONTE CARLO METHOD; THERMODYNAMICS;

EID: 0038298804     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)70011-3     Document Type: Article

References (81)

1. Allen, T. W., T. Bastug, S. Kuyucak, and S. H. Chung. 2003. Gramicidin A channel as a test ground for molecular dynamics force fields. Biophys. J. 84:2159-2168.
2. Allen, T. W., A. Bilznyuk, A. P. Rendell, S. Kuyucak, and S. H. Chung. 2000. The potassium channel: structure, selectivity and diffusion. J. Chem. Phys. 112:8191-8204.
3. Allen, T. W., M. Hoyles, S. Kuyucak, and S. H. Chung. 1999a. Molecular and Brownian dynamics study of ion selectivity and conductivity in the potassium channel. Chem. Phys. Lett. 313:358-365.
4. Allen, T. W., S. Kuyucak, and S. H. Chung. 1999b. Molecular dynamics study of the KcsA potassium channel. Biophys. J. 77:2502-2516.
5. Åqvist, J., and V. Luzhkov. 2000. Ion permeation mechanism of the potassium channel. Nature. 404:881-884.
6. + channel in a bilayer membrane. Biophys. J. 77:2517-2533.
7. + channel. Nature. 414:73-77.
8. + channel. Biophys. J. 82:772-780.
9. Beveridge, D. L., and G. W. Schnuelle. 1975. Free energy of a charge distribution in concentric dielectric continua. J. Phys. Chem. 79:2562-2573.
10. Bezanilla, F., and C. M. Armstrong. 1972. Negative conductance caused by entry of sodium and cesium ions into the potassium channels of squid axon. J. Gen. Physiol. 60:588-608.
11. Biggin, P. C., G. R. Smith, I. Shrivastava, S. Choe, and M. S. P. Sansom. 2001. Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations. Biochim. Biophys. Acta. 1510:1-9.
12. Burykin, A., C. N. Schutz, J. Villá, and A. Warshel. 2002. Simulations of ion current in realistic models of ion channels: the KcsA potassium channel. Proteins. 47:265-280.
13. Chung, S. H., T. W. Allen, M. Hoyles, and S. Kuyucak. 1999. Permeation of ions across the potassium channel: Brownian dynamics studies. Biophys. J. 77:2517-2533.
14. Chung, S. H., T. W. Allen, and S. Kuyucak. 2002a. Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations. Biophys. J. 82:628-645.
15. Chung, S. H., T. W. Allen, and S. Kuyucak. 2002b. Modeling diverse range of potassium channels with Brownian dynamics. Biophys. J. 83:263-277.
16. Dauber-Osguthorpe, P., V. A. Roberts, D. J. Osguthorpe, J. Wolff. M. Genest, and A. T. Hagler. 1988. Structure and energetics of ligand binding to proteins: E. coli dihydrofolate reductase-trimethoprim, a drugreceptor system. Proteins: Struc. Func. and Genet. 4:31-47.
17. Dorman, V. L., S. Garofoli, and P. C. Jordan. 1999. Ionic interactions in multiply occupied channels. In Gramicidin and Related Ion-Channel Forming Peptides. Novartis Found. Symp. 225, John Wiley & Sons, Chichester. 153-169.
18. Dorman, V. L., and P. C. Jordan. 2003. Ion-water interaction potentials in the semi-microscopic model. J. Chem. Phys. 118:1333-1340.
19. Dorman, V. L., M. B. Partenskii, and P. C. Jordan. 1996. A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin like channel: the origin of cation selectivity. Biophys. J. 70:121-134.
20. + conduction and selectivity. Science. 280:69-77.
21. Dutzler, R., E. B. Campbell, M. Cadene, B. T. Chait, and R. MacKinnon. 2002. X-ray structure of a CIC chloride channel at 3.0 A reveals the molecular basis of anion selectivity. Nature. 415:287-294.
22. Fisher, W., J. Brickmann, and P. Läuger. 1981. Molecular dynamics study of ion transport in transmembrane protein channels. Biophys. Chem. 13:105-116.
23. French, R. J., and J. B. Wells. 1977. Sodium ions as blocking agents and charge carriers in the potassium channel of squid giant axon. J. Gen. Physiol. 70:707-724.
24. Fu, D., A. Libson, L. J. W. Miercke, C. Weitzman, P. Nollert, J. Krucinski, and R. M. Stroud. 2000. Structure of a glycerol-conducting channel and the basis for its selectivity. Science. 290:481-486.
25. Garofoli, S., G. Miloshevsky, V. L. Dorman, and P. C. Jordan. 2002. Permeation energetics in a model potassium channel. In Ion Channels from Atomic Resolution to Functional Genomics. Novartis Found Symp 245, John Wiley & Sons, Chichester. 109-122.
26. Grunwald, E. 1996. Thermodynamics of Molecular Species. Wiley-Interscience, New York.
27. + channel. FEBS Lett. 477:37-42.
28. + channels. Science. 251:942-944.
29. + channels: functional asymmetries and sidedness of proton activation. J. Gen. Physiol. 114:551-559.
30. rd Ed. Sinauer Associates, Inc., Sunderland, MA.
31. Hille, B., and W. Schwartz. 1978. Potassium channels as multi-ion single-file pores. J. Gen. Physiol. 72:409-442.
32. Hille, B., C. M. Armstrong, and R. MacKinnon. 1999. Ion channels: from idea to reality. Nat. Med. 5:1105-1109.
33. Hodgkin, A., and R. Keynes. 1955. The potassium permeability of a giant nerve fibre. J. Physiol. 121:61-88.
34. Hol, W. G., P. T. Van Duijnen, and H. J. Berendsen. 1978. The alpha-helix dipole and the properties of proteins. Nature. 273:443-446.
35. Hummer, G., L. R. Pratt, and A. E. Garcia. 1996. Free energy of ionic hydration. J. Phys. Chem. 100:1206-1215.
36. Hyun, J. K., and T. Ichiye. 1997. Understanding the bom radius via computer simulations and theory. J. Phys. Chem. B. 101:3596-3604.
37. Jackson, J. D. 1962. Classical Electrodynamics. Wiley, New York.
38. Jiang, Y., and R. MacKinnon. 2000. The barium site in a potassium channel by X-ray crystallography. J. Gen. Physiol. 115:269-272.
39. Jiang, Y., A. Lee, J. Chen, M. Cadene, B. T. Chait, and R. MacKinnon. 2002. The open pore conformation of potassium channels. Nature. 417:523-526.
40. Jordan, P. C. 2002. Unclogging a pipe: potassium channel pinball. Biophys. J. 83:2-4.
41. Kabsch, W., and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22:2577-2637.
42. Lee, W. K., and P. C. Jordan. 1984. Molecular dynamics simulation of cation motion in water-filled gramicidin-like pores. Biophys. J. 46:805-819.
43. Lee, F. S., and A. Warshel. 1992. A local reaction field method for fast evaluation of long range electrostatic interactions in molecular simulations. J. Chem. Phys. 97:3100-3107.
44. LeMasurier, M., L. Heginbotham, and C. Miller. 2001. KcsA: it's a potassium channel. J. Gen. Physiol. 118:303-313.
45. Luzhkov, V., and J. Åqvist. 2000. A computational study of ion binding and protonation states in the KcsA potassium channel. Biochim. Biophys. Acta. 1481:360-370.
46. + selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations. Biochim. Biophys. Acta. 1548:194-202.
47. + channels. Science. 250:276-279.
48. Miller, C. 2001. See potassium run. Nature. 414:23-24.
49. Miloshevsky, G., and P. C. Jordan. 2002. Deconstructing permeation energetics in a model potassium channel selectivity filter. Biophys. J. 82:199a.
50. + selectivity filter. Nature. 414:37-42.
51. Murata, K., K. Mitsuoka, T. Hirai, T. Walz, P. Agre, J. B. Heymann, A. Engel, and Y. Fujiyoshi. 2000. Structural determinants of water permeation through aquaporin-1. Science. 407:599-605.
52. 2+ activated potassium channel. J. Gen. Physiol. 92:549-567.
53. + channel. J. Gen. Physiol. 92:569-586.
54. Partenskii, M. B., M. Cai, and P. C. Jordan. 1991. A dipolar chain model for the electrostatics of transmembrane ion channels. Chem. Phys. 153: 125-131.
55. Partenskii, M. B., V. Dorman, and P. C. Jordan. 1994. Influence of a channel-forming peptide on energy barriers to ion permeation, viewed from a continuum dielectric perspective. Biophys. J. 67:1429-1438.
56. Partenskii, M. B., V. L. Dorman, and P. C. Jordan. 1998. Membrane stability under electrical stress. A non-local electroelastic treatment. J. Chem. Phys. 109:10361-10371.
57. Partenskii, M. B., and P. C. Jordan. 1992a. Theoretical perspectives on ion channel electrostatics. Continuum and microscopic approaches. Q. Rev. Biophys. 24:477-510.
58. Partenskii, M. B., and P. C. Jordan. 1992b. Nonlinear dielectric behavior of water in transmembrane ion channels: ion energy barriers and the channel dielectric constant. J. Phys. Chem. 96:3906-3910.
59. rd Ed. Cornell University, Ithaca, NY.
60. Pethig, R. 1979. Dielectric and Electronic Properties of Biological Materials. John Wiley & Sons, Inc., Chichester.
61. Pliego, J. R., Jr., and J. M. Riveros. 2000. On the calculation of the absolute solvation free energy of ionic species: application of the extrapolation method to the hydroxide ion in aqueous solution. J. Phys. Chem. B. 104:5155-5160.
62. Ranatunga, K. M., I. H. Shrivastava, G. R. Smith, and M. S. P. Sansom. 2001. Side-chain ionization states in a potassium channel. Biophys. J. 80:1210-1219.
63. Randles, J. E. B. 1956. The real hydration energies of ions. Trans. Faraday Soc. 52:1573-1581.
64. Reiss, H., and A. Heller. 1985. The absolute potential of the standard hydrogen electrode: a new estimate. J. Phys. Chem. 89:4207-4213.
65. Roux, B., and M. Karplus. 1995. Potential energy function for cationpeptide interactions: an ab initio study. J. Comput. Chem. 16:690-704.
66. + channel: electrostatic stabilization of monovalent cations. Science. 285:100-102.
67. Roux, B., H.-A. Yu, and M. Karplus. 1990. Molecular basis for the Born model of ion solvation. J. Phys. Chem. 94:4683-4688.
68. Schutz, C. N., and A. Warshel. 2001. What are the dielectric "constants" of proteins and how to validate electrostatic models. Proteins. 44:400-417.
69. Sherry, H. S. 2003. Ion exchange, In Handbook of Zeolite Science and Technology, S. M. Auerbach, K. A. Carrado, and P. K. Dutta, editors. Marcel Dekker, New York. In press.
70. Shrivastava, I. H., and M. S. P. Sansom. 2000. Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. Biophys. J. 78:557-570.
71. + ions in a K channel selectivity filter: a simulational study. Biophys. J. 83:633-645.
72. Sui, H., B. G. Han, J. K. Lee, P. Walian, and B. K. Jap. 2002. Structural basis of water-specific transport through AQP1 water channel. Nature. 414:872-878.
73. Tawa, G. J., I. A. Topol, S. K. Burt, R. A. Caldwell, and A. A. Rashin. 1998. Calculation of the aqueous solvation free energy of the proton. J. Chem. Phys. 109:4852-4863.
74. Tembe, B. L., and J. A. McCammon. 1984. Ligand-receptor interactions. Comput. Chem. 8:281-283.
75. Tissandier, M. D., K. A. Cowan, W. Y. Feng, E. Gundlach, M. H. Cohen, A. D. Earhart, J. V. Coe, and T. R. Tuttle. 1998. The proton's absolute enthalpy and Gibbs free energy of solvation from cluster-ion solvation data. J. Phys. Chem. A. 102:7787-7794.
76. Warshel, A., and A. Papazyan. 1998. Electrostatic effects in macro-molecules: fundamental concepts and practical modeling. Curr. Opin. Struct. Biol. 8:211-217.
77. + channels of bovine chromaffin cells. J. Gen. Physiol. 84:157-186.
78. + channels by external cations. J. Gen. Physiol. 84:187-199.
79. + channel. Science. 251:939-942.
80. Zhang, L., H. T. Davis, D. M. Kroll, and H. S. White. 1995. Molecular dynamics simulation of water in a spherical cavity. J. Chem. Phys. 99:2878-2884.
81. + channel-Fab complex at 2.0 Å resolution. Nature. 414:43-48.