Permeation energetics in a model potassium channel

Novartis Foundation Symposium

Volumn 245, Issue , 2002, Pages 109-126

  Garofoli, Stefano ^a   Miloshevsky, Gennady ^a   Dorman, Vladimir L ^a   Jordan, Peter C ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POTASSIUM; POTASSIUM CHANNEL;

ANIMAL; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PERMEABILITY; REVIEW; THERMODYNAMICS;

ANIMALS; BINDING SITES; MODELS, MOLECULAR; PERMEABILITY; POTASSIUM; POTASSIUM CHANNELS; THERMODYNAMICS;

EID: 0036355576     PISSN: None     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (35)

1. Antosiewicz J, McCammon JA, Gilson MK 1994 Prediction of pH-dependent properties of proteins. J Mol Biol 238:415-436
2. Åqvist J, Luzhkov V 2000 Ion permeation mechanism of the potassium channel. Nature 404:881-884
3. + channel in a bilayer membrane. Biophys J 78:2900-2917
4. Biggin PC, Smith GR, Shrivastava I, Choe S, Sansom MSP 2001 Potassium and sodium ions in a potassium channel studied by molecular dynamics simulations. Biochim Biophys Acta 1510:1-9
5. Chang G, Spencer RH, Lee AT, Barclay MT, Rees DC 1998 Structure of the McsL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel. Science 282:2220-2226
6. Chiu SW, Jakobsson E, Subramaniam S, McCammon JA 1991 Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. Biophys J 60:273-285
7. Chung S-H, Allen TW, Hoyles M, Kuyucak S 1999 Permeation of ions across the potassium channel: Brownian dynamics studies. Biophys J 77:2517-2533
8. Dorman VL, Partenskii MB, Jordan PC 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
9. Dorman VL, Garofoli S, Jordan PC 1999 Ionic interactions in multiply occupied channels. In: Gramicidin and related ion-channel forming peptides. Wiley, Chichester, (Novartis Found Symp 225) p 153-169
10. + conduction and selectivity. Science 280:69-77
11. Fu D, Libson A, Miercke LJ et al 2000 Structure of a glycerol-conducting channel and the basis of its selectivity. Science 290:481-486
12. a calculations. Biophys J 71:138-147
13. Grunwald E 1997 Thermodynamics of molecular species. Wiley-Interscience, New York
14. + channel. FEBS Lett 477:37-42
15. + channels: functional asymmetries and sidedness of proton activation. J Gen Physiol 114:551-560
16. Hille B 1992 Ionic channels of excitable membranes, 2nd edn. Sinauer Associates, Sunderland, MA
17. Hille B, Schwartz W 1978 Potassium channels as multi-ion single-file pores. J Gen Physiol 72:409-442
18. Jakobsson E, Chiu SW 1987 Stochastic theory of ion movement in channels with single-ion occupancy. Application to sodium permeation of gramicidin channels. Biophys J 52:33-45
19. Jiang Y, MacKinnon R 2000 The barium site in a potassium channel by X-ray crystallography. J Gen Physiol 115:269-272
20. Jordan P 2002 Ionic energetics in narrow channels. In: Layton H (ed) Proceedings of the IMA Workshop on Membrane Transport and Renal Physiology. Springer-Verlag, New York, in press
21. Murata K, Mitsuoka K, Hirai T et al 2000 Structural determinants of water permeation through aquaporin-1. Nature 407:599-605
22. + channel. J Gen Physiol 92:569-586
23. Partenskii MB, Jordan PC 1992 Theoretical perspectives on ion channel electrostatics. Continuum and microscopic approaches. Q Rev Biophys 24:477-510
24. Partenskii MB, Dorman V, Jordan PC 1994 Influence of a channel-forming peptide on energy barriers to ion permeation, viewed from a continuum dielectric perspective. Biophys J 67:1429-1438
25. Reiss H, Heller A 1985 The absolute potential of the standard hydrogen electrode: A new estimate. J Phys Chem 89:4207-4213
26. Roux B, Yu H-A, Karplus M 1990 Molecular basis for the Born model of ion solvation. J Phys Chem 94:4683-4688
27. Roux B, Karplus M 1994 Molecular dynamics simulations of the gramicidin channel. Annu Rev Biophys Biomol Struct 23:731-761
28. Roux B, Karplus M 1995 Potential energy function for cation-peptide interactions: An ab initio study. J Comp Chem 16:690-704
29. + channel: electrostatic stabilization of monovalent cations. Science 285:100-102
30. Sansom MS, Smith GR, Adcock C, Biggin PC 1997 The dielectric properties of water within model transbilayer pores. Biophys J 73:2404-2415
31. Shrivastava IH, Sansom MS 2000 Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. Biophys J 78:557-570
32. Tissandier MD, Cowan KA, Feng WY et al 1998 The proton's absolute enthalpy and Gibbs free energy of solvation from cluster-ion solvation data. J Phys Chem A 102:7787-7794
33. Wallace B 1999 X-ray crystallographic structures of gramicidin and their relation to the Streptomyces lividans potassium channel structure. In: Gramicidin and related ion-channel forming peptides. Wiley, Chichester (Novartis Found Symp 225) p 23-37
34. Woolf TB, Roux B 1997 The binding of sodium in the gramicidin A channel: comparison of molecular dynamics with solid-state NMR data. Biophys J 72:1930-1945
35. Zhang L, Davis HT, Kroll DM, White HS 1995 Molecular dynamics simulation of water in a spherical cavity. J Chem Phys 99:2878-2884