Ion channel gates: Comparative analysis of energy barriers

European Biophysics Journal

Volumn 38, Issue 4, 2009, Pages 347-354

  Tai, Kaihsu ^a   Haider, Shozeb ^a,b   Grottesi, Alessandro ^a,c   Sansom, Mark S P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF LONDON   (United Kingdom)

^c CASPUR   (Italy)

Author keywords

Electrostatics; Gate; Ion channel; Model; Simulation

Indexed keywords

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; DATABASES, GENETIC; HYDROPHOBICITY; ION CHANNEL GATING; LEUCINE; MODELS, MOLECULAR; POTASSIUM CHANNELS, INWARDLY RECTIFYING; PROTEIN CONFORMATION; RECEPTORS, NICOTINIC; STATIC ELECTRICITY;

BACTERIA (MICROORGANISMS);

EID: 62949137785     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-008-0377-x     Document Type: Article

References (59)

1. TW Allen OS Andersen B Roux 2004 On the Importance of atomic fluctuations, protein flexibility, and solvent in ion permeation J Gen Physiol 124 679 690 10.1085/jgp.200409111
2. S Amiri K Tai O Beckstein PC Biggin MSP Sansom 2005 The a7 nicotinic acetylcholine receptor: molecular modelling, electrostatics, and energetics Mol Membr Biol 22 151 162 10.1080/09687860500063340
3. A Anishkin S Sukharev 2004 Water dynamics and dewetting transitions in the small mechanosensitive channel MscS Biophys J 86 2883 2895
4. Archer SL, Rusch NJ (2001) Potassium channels in cardiovascular biology. Kluwer Academic/Plenum Publishers, New York, p 899
5. Ashcroft FM (2000) Ion channels and disease. Academic Press, San Diego
6. NA Baker D Sept S Joseph MJ Holst JA McCammon 2001 Electrostatics of nanosystems: application to microtubules and the ribosome Proc Natl Acad Sci USA 98 10037 10041 10.1073/pnas.181342398
7. O Beckstein MSP Sansom 2003 Liquid-vapor oscillations of water in hydrophobic nanopores Proc Natl Acad Sci USA 100 7063 7068 10.1073/pnas. 1136844100
8. O Beckstein MSP Sansom 2004 The influence of geometry, surface character and flexibility on the permeation of ions and water through biological pores Phys Biol 1 42 52 10.1088/1478-3967/1/1/005
9. O Beckstein MSP Sansom 2006 A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor Phys Biol 3 147 159 10.1088/1478-3975/3/2/007
10. O Beckstein PC Biggin MSP Sansom 2001 A hydrophobic gating mechanism for nanopores J Phys Chem B 105 12902 12905 10.1021/jp012233y
11. O Beckstein PC Biggin PJ Bond JN Bright C Domene A Grottesi J Holyoake MSP Sansom 2003 Ion channel gating: insights via molecular simulations FEBS Lett 555 85 90 10.1016/S0014-5793(03)01151-7
12. O Beckstein K Tai MSP Sansom 2004 Not ions alone: barriers to ion permeation in nanopores and channels J Am Chem Soc 126 14694 14695 10.1021/ja045271e
13. H Berman K Henrick H Nakamura 2003 Announcing the worldwide protein data bank Nat Struct Biol 10 980 10.1038/nsb1203-980
14. D Boda W Nonner M Valiskó D Henderson B Eisenberg D Gillespie 2007 Steric selectivity in Na channels arising from protein polarization and mobile side chains Biophys J 93 1960 1980 10.1529/biophysj.107.105478
15. + channels is due to topological control of the permanent ion's coordinated state Proc Natl Acad Sci USA 104 9260 9265 10.1073/pnas.0700554104
16. D Buchera S Raugei L Guidoni M Dal Peraro U Rothlisberger P Carloni ML Klein 2006 Polarization effects and charge transfer in the KcsA potassium channel Biophys Chem 124 292 301 10.1016/j.bpc.2006.04.008
17. G Chang RH Spencer AT Lee MT Barclay DC Rees 1998 Structure of the MscL homolog from Mycobacterium tuberculosis: a gated mechanosensitive ion channel Science 282 2220 2226 10.1126/science.282.5397.2220
18. SH Chung TW Allen S Kuyucak 2002 Modeling diverse range of potassium channels with brownian dynamics Biophys J 83 263 277
19. JF Cordero-Morales LG Cuello E Perozo 2006 Voltage-dependent gating at the KcsA selectivity filter Nat Struct Mol Biol 13 319 322 10.1038/nsmb1070
20. JF Cordero-Morales LG Cuello YX Zhao V Jogini DM Cortes B Roux E Perozo 2006 Molecular determinants of gating at the potassium-channel selectivity filter Nat Struct Mol Biol 13 311 318 10.1038/nsmb1069
21. B Corry 2004 Theoretical conformation of the closed and open states of the acetylcholine receptor channel Biochim Biophys Acta 1663 2 5 10.1016/j.bbamem.2004.02.006
22. TJ Dolinsky JE Nielsen JA McCammon NA Baker 2004 PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations Nucleic Acids Res 32 W665 W667 10.1093/nar/gkh381
23. DA Doyle 2004 Structural themes in ion channels Eur Biophys J 33 175 179 10.1007/s00249-003-0382-z
24. + conduction and selectivity Science 280 69 77 10.1126/science.280. 5360.69
25. S Edwards B Corry S Kuyucak S-H Chung 2002 Continuum electrostatics fails to describe ion permeation in the gramicidin channel Biophys J 83 1348 1360
26. A Fiser R Kinh Gian Do A Sali 2000 Modeling of loops in protein structures Protein Sci 9 1753 1773
27. E Gouaux R MacKinnon 2005 Principles of selective ion transport in channels and pumps Science 310 1461 1465 10.1126/science.1113666
28. S Haider S Khalid S Tucker FM Ashcroft MSP Sansom 2007 Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study Biochemistry 46 3643 3652 10.1021/bi062210f
29. RJC Hilf R Dutzler 2008 X-ray structure of a prokaryotic pentameric ligand-gated ion channel Nature 452 375 379 10.1038/nature06717
30. Hille B (2001) Ionic channels of excitable membranes, 3rd edn. Sinauer Associates Inc, Sunderland
31. J Holyoake C Domene JN Bright MSP Sansom 2003 KcsA closed and open: modelling and simulation studies Eur Biophys J 33 238 246
32. AL Hopkins CR Groom 2002 The druggable genome Nat Rev Drug Discov 1 727 730 10.1038/nrd892
33. W Humphrey A Dalke K Schulten 1996 VMD - visual molecular dynamics J Mol Graph 14 33 38 10.1016/0263-7855(96)00018-5
34. I Ivanov X Cheng SM Sine JA McCammon 2007 Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family J Am Chem Soc 129 8217 8224 10.1021/ja070778l
35. F Jeanmougin JD Thompson M Gouy DG Higgins TJ Gibson 1998 Multiple sequence alignment with clustal X Trends Biochem Sci 23 403 405 10.1016/S0968-0004(98)01285-7
36. + channels J Mol Biol 354 272 288 10.1016/j.jmb.2005.09.031
37. Y Kong Y Shen TE Warth J Ma 2002 Conformational pathways in the gating of Escherichia coli mechanosensitive channel Proc Natl Acad Sci USA 99 5999 6004 10.1073/pnas.092051099
38. A Kuo JM Gulbis JF Antcliff T Rahman ED Lowe J Zimmer J Cuthbertson FM Ashcroft T Ezaki DA Doyle 2003 Crystal structure of the potassium channel KirBac1.1 in the closed state Science 300 1922 1926 10.1126/science.1085028
39. AL Kuo C Domene LN Johnson DA Doyle C Venien-Bryan 2005 Two different conformational states of the KirBac3.1 potassium channel revealed by electron crystallography Structure 13 1463 1472 10.1016/j.str.2005.07.011
40. R MacKinnon 2003 Potassium channels FEBS Lett 555 62 65 10.1016/S0014-5793(03)01104-9
41. R MacKinnon SL Cohen A Kuo A Lee BT Chait 1998 Structural conservation in prokaryotic and eukaryotic potassium channels Science 280 106 109 10.1126/science.280.5360.106
42. 2+-selective channel Curr Opin Struct Biol 16 432 438 10.1016/j.sbi.2006.06.006
43. AB Mamonov RD Coalson A Nitzan MG Kurnikova 2003 The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents Biophys J 84 3646 3661
44. M Nishida M Cadene BT Chait R MacKinnon 2007 Crystal structure of a Kir3.1-prokaryotic Kir channel chimera EMBO J 26 4005 4015 10.1038/sj.emboj. 7601828
45. SY Noskov B Roux 2006 Ion selectivity in potassium channels Biophys Chem 124 279 291 10.1016/j.bpc.2006.05.033
46. SY Noskov S Bernèche B Roux 2004 Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands Nature 431 830 834 10.1038/nature02943
47. A Rashin B Honig 1985 Reevaluation of the Born model of ion hydration J Phys Chem 89 5588 10.1021/j100272a006
48. R Roth D Gillespie W Nonner R Eisenberg 2008 Bubbles, gating, and anaesthetics in ion channels Biophys J 94 4282 4298 10.1529/biophysj.107.120493
49. B Roux K Schulten 2004 Computational studies of membrane channels Structure 12 1343 1351 10.1016/j.str.2004.06.013
50. B Roux T Allen S Berneche W Im 2004 Theoretical and computational models of biological ion channels Q Rev Biophys 37 15 103 10.1017/S0033583504003968
51. A Sali TL Blundell 1993 Comparative protein modeling by satisfaction of spatial restraints J Mol Biol 234 779 815 10.1006/jmbi.1993.1626
52. YF Shen YF Kong JP Ma 2002 Intrinsic flexibility and gating mechanism of the potassium channel KcsA Proc Natl Acad Sci USA 99 1949 1953 10.1073/pnas.042650399
53. +-conducting channel Nature 440 570 574 10.1038/nature04508
54. IH Shrivastava I Bahar 2006 Common mechanism of pore opening shared by five different potassium channels Biophys J 90 3929 3940 10.1529/biophysj.105. 080093
55. OS Smart JG Neduvelil X Wang BA Wallace MSP Sansom 1996 Hole: a program for the analysis of the pore dimensions of ion channel structural models J Mol Graph 14 354 360 10.1016/S0263-7855(97)00009-X
56. DP Tieleman PC Biggin GR Smith MSP Sansom 2001 Simulation approaches to ion channel structure-function relationships Q Rev Biophys 34 473 561 10.1017/S0033583501003729
57. D van der Spoel E Lindahl B Hess G Groenhof AE Mark HJ Berendsen 2005 GROMACS: fast, flexible, and free J Comput Chem 26 1701 1718 10.1002/jcc.20291
58. TB Woolf DM Zuckerman N Lua H Jang 2004 Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics J Mol Graph Model 22 359 368 10.1016/j.jmgm.2003.12.003
59. FH Yu V Yarov-Yarovoy GA Gutman WA Catterall 2005 Overview of molecular relationships in the voltage-gated ion channel superfamily Pharmacol Rev 57 387 395 10.1124/pr.57.4.13