Ions and blockers in potassium channels: Insights from free energy simulations

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1747, Issue 1, 2005, Pages 109-120

  Luzhkov, V B ^a   Aqvist J ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Blocking; Free energy calculation; Ion transport; KcsA; Molecular dynamics; Potassium channel

Indexed keywords

POTASSIUM CHANNEL BLOCKING AGENT; POTASSIUM ION; VOLTAGE GATED POTASSIUM CHANNEL;

COMBINATORIAL CHEMISTRY; CONFORMATION; CRYSTAL STRUCTURE; ENERGY; ENERGY TRANSFER; ION TRANSPORT; IONIZATION; MEMBRANE PERMEABILITY; MOLECULAR MODEL; PRIORITY JOURNAL; REVIEW; SIMULATION; STRUCTURE ANALYSIS; THERMODYNAMICS; X RAY ANALYSIS;

EID: 12844254389     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2004.10.006     Document Type: Article

References (72)

1. B. Hille Ionic Channels of Excitable Membranes 1992 Sinauer Associates Sunderland, MA
2. F.M. Ashcroft Ion Channels and Disease 2000 Academic Press San Diego
3. A.L. Hodgkin, and R.D. Keynes The potassium permeability of a giant nerve fibre J. Physiol. (Lond.) 128 1955 61 88
4. B. Hille, and W. Schwarz Potassium channels as multi-ion single-file pores J. Gen. Physiol. 72 1978 409 442
5. O. Pongs, N. Kecskemethy, R. Müller, I. Krah-Jentgens, A. Baumann, H.H. Kiltz, I. Canal, S. Llamazares, and A. Ferrus Shaker encodes a family of putative potassium channel proteins in the nervous system of Drosophila EMBO J. 7 1988 1087 1096
6. H. Schrempf, O. Schmidt, R. Kümmerlen, S. Hinnah, D. Müller, M. Betzler, T. Steinkamp, and R. Wagner A prokaryotic potassium ion channel with two predicted transmembrane segments from Streptomyces lividans EMBO J. 14 1995 5170 5178
7. R. MacKinnon Determination of the subunit stoichiometry of a voltage-activated potassium channel Nature 350 1991 232 235
8. O. Pongs Structure-function studies on the pore of potassium channels J. Membr. Biol. 136 1993 1 8
9. C. Miller An overview of the potassium channel family Genome Biol. 1 2000 0004.1 0004.5
10. + channels in open, closed, and inactivated conformations J. Struct. Biol. 121 1998 263 284
11. + conduction and selectivity Science 280 1998 69 77
12. C.L. Brooks III, M. Karplus, and B. Montgomery Pettitt Proteins: a theoretical perspective of dynamics, structure, and thermodynamics Advances in Chemical Physics vol. LXXI 1988 John Wiley and Sons New York
13. W.F. van Gunsteren, and H.J.C. Berendsen Computer-simulations of molecular dynamics-methodology, applications, and perspectives in chemistry Angew. Chem., Int. Ed. Engl. 29 1990 992 1023
14. A. Warshel Computer Modeling of Chemical Reactions in Enzymes and in Solutions 1991 Wiley New York
15. Y. Jiang, and R. MacKinnon The barium site in a potassium channel by X-ray crystallography J. Gen. Physiol. 115 2000 269 272
16. + channel-Fab complex at 2.0 Å resolution Nature 414 2001 43 48
17. Y. Jiang, A. Lee, J. Chen, M. Cadene, B.T. Chait, and R. MacKinnon Crystal structure and mechanism of a calcium-gated potassium channels Nature 417 2002 515 522
18. + channels Nature 423 2003 33 41
19. + channel and its structural implications Nature 403 2000 321 325
20. P. Kollman Free energy calculations: applications to chemical and biological phenomena Chem. Rev. 93 1993 2395 2417
21. B.O. Bransdal, F. Österberg, M. Almlöf, I. Feierberg, V.B. Luzhkov, and J. Åqvist Free energy calculations and ligand binding Adv. Protein Chem. 66 2003 123 158
22. R.W. Zwanzig J. Chem. Phys 22 1954 1420 1426
23. J.P. Valleau, and G.M. Torrie A guide for Monte Carlo for statistical mechanics B.J. Berne Statistical Mechanics, Part A. 1977 Plenum Press 169 194
24. S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules: 1. Method J. Comput. Chem. 13 1992 1011 1021
25. B. Roux The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 91 1995 275 282
26. P. Läuger Ion transport through pores: a rate-theory analysis Biochim. Biophys. Acta 311 1973 423 441
27. K. Cooper, E. Jacobsson, and P. Wolynes The theory of ion transport through membrane channels Prog. Biophys. Mol. Biol. 46 1985 51 96
28. E.M. McCleskey Calcium channel permeation: a field in flux J. Gen. Physiol. 113 1999 765 772
29. W. Nonner, D.P. Chen, and B. Eisenberg Progress and prospects in permeation J. Gen. Physiol. 113 1999 773 782
30. + channel Biochemistry 38 1999 8599 8604
31. + channel: electrostatic stabilization of monovalent cations Science 285 1999 100 102
32. T. Allen, S. Kuyucak, and S.-H. Chung Molecular dynamics study of the KcsA channel Biophys. J. 77 1999 2502 2516
33. J. Åqvist, and V. Luzhkov Ion permeation mechanism of the potassium channel Nature 404 2000 881 884
34. V.B. Luzhkov, and J. Åqvist A computational study of ion binding and protonation states in the KcsA potassium channel Biochim. Biophys. Acta 1481 2000 360 370
35. I.H. Shrivastara, and M.S.P. Sansom Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer Biophys. J. 78 2000 557 570
36. T.W. Allen, A. Bliznyuk, A.P. Rendell, S. Kuyucak, and S.-H. Chung The potassium channel: structure, selectivity and diffusion J. Chem. Phys. 112 2000 8191 8204
37. + channel in a bilayer membrane Biophys. J. 78 2000 2900 2917
38. + channel Nature 414 2001 73 77
39. C. Domene, and M.S.P. Sansom Potassium channel, ions, and water: simulation studies based on the high-resolution X-ray structure of KcsA Biophys. J. 85 2003 2787 2800
40. M. Compoint, P. Carloni, C. Ramseyer, and C. Girardet Molecular dynamics study of the KcsA channel at 2.0 Å resolution: stability and concerted motions within the pore Biochim. Biophys. Acta 1661 2004 26 39
41. A. Burykin, C.N. Schutz, J. Villa, and A. Warshel Simulation of ion current in realistic models of ion channels: the KcsA potassium channel Proteins 47 2002 265 280
42. K.M. Ranatunga, I.H. Shrivastara, G.R. Smith, and M.S.P. Sansom Side-chain ionization states in a potassium channel Biophys. J. 80 2001 1210 1219
43. + channel Biophys. J. 82 2002 772 780
44. S. Braun-Sand, and A. Warshel Electrostatics of proteins: principles, models, and applications J. Buchner T. Kiefhaber Protein Folding Handbook 2005 Wiley-VCH Weinheim in press
45. + channel J. Gen. Physiol. 92 1988 569 586
46. + permeability J. Gen. Physiol. 114 1999 365 376
47. + ion binding site in Shaker K channels J. Gen. Physiol. 117 2001 373 383
48. M. Zhou, J.H. Morais-Cabral, S. Mann, and R. MacKinnon Potassium channel receptor site for the inactivation gate and quaternary amine inhibitors Nature 411 2001 657 661
49. W.F. van Gunsteren, and H.J.C. Berendsen Groningen Molecular Simulation (Gromos) Library Manual 1987 Biomos B.V Groningen, The Netherlands
50. W.L. Jorgensen, and J. Tirado-Rieves The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 110 1988 1657 1666
51. J. Wu Microscopic model for selective permeation in ion channels Biophys. J. 60 1991 238 251
52. A. Burykin, M. Kato, and A. Warshel Exploring the origin of the ion selectivity of the KcsA potassium channel Proteins 52 2003 412 426
53. + selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations Biochim. Biophys. Acta 1548 2001 194 202
54. M. LeMasurier, L. Heginbotham, and C. Miller KcsA: it's a potassium channel J. Gen. Physiol. 118 2001 303 313
55. + channels from Streptomycins lividans: functional assymmetries and sidedness of proton activation J. Gen. Physiol. 114 1999 551 560
56. V.B. Luzhkov, and J. Åqvist Mechanisms of tetraethylammonium ion block in the KcsA potassium channel FEBS Lett. 495 2001 191 196
57. V.B. Luzhkov, F. Österberg, P. Acharya, J. Chattopadhyaya, and J. Åqvist Computational and NMR study of quaternary ammonium ion conformations in solution Phys. Chem. Chem. Phys. 4 2002 4640 4647
58. + channels by tetralkylammonium ions FEBS Lett. 554 2003 159 164
59. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, and A.J. Olson Automated docking using a Lamarchian genetic algorithm and an empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662
60. J. Åqvist, C. Medina, and J.-E. Samuelsson A new method for predicting binding affinity in computer-aided drug design Protein Eng. 7 1994 385 391
61. M. Almlöf, B.O. Brandsdal, and J. Åqvist Binding affinity prediction with different force fields: examination of the linear interaction energy method J. Comput. Chem. 25 2004 1242 1254
62. D. Meuser, H. Splitt, R. Wagner, and H. Schrempf Exploring the open pore of the potassium channel from Streptomyces lividans FEBS Lett. 462 1999 447 452
63. + channels. Functional asymmetries and sidedness of proton activation J. Gen. Physiol. 114 1999 551 559
64. + channels by TEA: results from molecular dynamics simulations of the KcsA channel J. Gen. Physiol. 118 2001 207 216
65. + channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles Biophys. J. 83 2002 2595 2609
66. V.B. Luzhkov, J. Nilsson, P. Århem, and J. Åqvist Computational modelling of the open-state Kv1.5 channel block by bupivacaine Biochim. Biophys. Acta 1652 2003 35 51
67. + channels defined by high-affinity metal bridges Nature 428 2004 864 868
68. M.S.P. Sansom, I.H. Shrivastava, K.M. Ranatunga, and G.R. Smith Simulations of ion channels-watching ions and water move TIBS 25 2000 368 374
69. D.P. Tieleman, P.C. Biggin, G.R. Smith, and M.S.P. Sansom Simulation approaches to ion channel structure-function relationships Q. Rev. Biophys. 34 2001 473 561
70. B. Roux Theoretical and computational models of ion channels Curr. Opin. Struct. Biol. 12 2002 182 189
71. M.S.P. Sansom, I.H. Shrivastava, J.N. Bright, J. Tate, C.E. Capener, and P.C. Biggin Potassium channels: structures, models, simulations Biochim. Biophys. Acta 1565 2002 294 307
72. P.L. Yeagle Membrane protein structure Biochim. Biophys. Acta 1565 2002 143