An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels

Journal of Molecular Biology

Volumn 340, Issue 2, 2004, Pages 307-318

  Fleishman, Sarel J ^a   Yifrach, Ofer ^b   Ben Tal, Nir ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

correlated mutations; Kv, voltage gated potassium; maximum likelihood; phylogenetic analysis; structural biology; voltage gated potassium channel

Indexed keywords

AMINO ACID; VOLTAGE GATED POTASSIUM CHANNEL;

ACCURACY; ARTICLE; CHANNEL GATING; CORRELATION ANALYSIS; GENE MUTATION; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; SENSITIVITY ANALYSIS; STATISTICAL SIGNIFICANCE;

AEROPYRUM; AEROPYRUM PERNIX;

EID: 2942580743     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.04.064     Document Type: Article

References (63)

1. Sigworth F.J. Voltage gating of ion channels. Quart. Rev. Biophys. 27:1994;1-40
2. Yellen G. The moving parts of voltage-gated ion channels. Quart. Rev. Biophys. 31:1998;239-295
3. Bezanilla F. The voltage sensor in voltage-dependent ion channels. Physiol. Rev. 80:2000;555-592
4. Hille B. Ion Channels of Excitable Membranes. 3rd edit. 2001;Sinauer Associates, Sunderland, MA
5. MacKinnon R. Determination of the subunit stoichiometry of a voltage-activated potassium channel. Nature. 350:1991;232-235
6. Tempel B.L., Papazian D.M., Schwarz T.L., Jan Y.N., Jan L.Y. Sequence of a probable potassium channel component encoded at Shaker locus of Drosophila. Science. 237:1987;770-775
7. Miller C. A charged view of voltage-gated ion channels. Nature Struct. Biol. 10:2003;422-424
8. Papazian D.M., Timpe L.C., Jan Y.N., Jan L.Y. Alteration of voltage-dependence of Shaker potassium channel by mutations in the S4 sequence. Nature. 349:1991;305-310
9. + channel. Nature. 353:1991;752-756
10. + conduction and selectivity. Science. 280:1998;69-77
11. Jiang Y., Lee A., Chen J., Cadene M., Chait B.T., MacKinnon R. The open pore conformation of potassium channels. Nature. 417:2002;523-526
12. Kelly B.L., Gross A. Potassium channel gating observed with site-directed mass tagging. Nature Struct. Biol. 10:2003;280-284
13. + channel. Nature. 423:2003;33-41
14. + channel. Nature. 423:2003;42-48
15. Yifrach O., MacKinnon R. Energetics of pore opening in a voltage-gated K(+) channel. Cell. 111:2002;231-239
16. Schoppa N.E., McCormack K., Tanouye M.A., Sigworth F.J. The size of gating charge in wild-type and mutant Shaker potassium channels. Science. 255:1992;1712-1715
17. + channel. Neuron. 16:1996;1159-1167
18. + channel. Neuron. 16:1996;1169-1177
19. Bezanilla F. Voltage sensor movements. J. Gen. Physiol. 120:2002;465-473
20. Honig B.H., Hubbell W.L. Stability of "salt bridges" in membrane proteins. Proc. Natl Acad. Sci. USA. 81:1984;5412-5416
21. Laine M., Lin M.C., Bannister J.P., Silverman W.R., Mock A.F., Roux B., Papazain D.M. Atomic proximity between S4 segment and pore domain in Shaker potassium channels. Neuron. 39:2003;467-481
22. Lee H.C., Wang J.M., Swartz K.J. Interaction between extracellular Hanatoxin and the resting conformation of the voltage-sensor paddle in Kv channels. Neuron. 40:2003;527-536
23. Cohen B.E., Grabe M., Jan L.Y. Answers and questions from the KvAP structures. Neuron. 39:2003;395-400
24. Gandhi C.S., Clark E., Loots E., Pralle A., Isacoff E.Y. The orientation and molecular movement of a K(+) channel voltage-sensing domain. Neuron. 40:2003;515-525
25. Broomand A., Mannikko R., Larsson H.P., Elinder F. Molecular movement of the voltage sensor in a k channel. J. Gen. Physiol. 122:2003;741-748
26. Sigworth F.J. Potassium channel mechanics. Neuron. 32:2001;555-556
27. Gobel U., Sander C., Schneider R., Valencia A. Correlated mutations and residue contacts in proteins. Proteins: Struct. Funct. Genet. 18:1994;309-317
28. Shindyalov I.N., Kolchanov N.A., Sander C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7:1994;349-358
29. Kass I., Horovitz A. Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins: Struct. Funct. Genet. 48:2002;611-617
30. Oliveira L., Paiva A.C., Vriend G. Correlated mutation analyses on very large sequence families. Chembiochem. 3:2002;1010-1017
31. Valencia A., Pazos F. Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12:2002;368-373
32. Lockless S.W., Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science. 286:1999;295-299
33. Suel G.M., Lockless S.W., Wall M.A., Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nature Struct. Biol. 10:2003;59-69
34. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:1997;555-556
35. Miyata T., Miyazawa S., Yasunaga T. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12:1979;219-236
36. Dayhoff M.O., Schwartz R.M., Orcutt B.C. Dayhoff M.O. Atlas of Protein Sequence and Structure. A model of evolutionary change in proteins. 1979;353-358 National Biomedical Research Foundation, Washington, DC
37. Shannon C.E. A mathematical theory of communication. Bell Syst. Tech. J. 27:1948;379-423. 623-656
38. Bradley E., Tibshirani R. An Introduction to the Bootstrap. 1993;Chapman & Hall, New York
39. Lebart L., Morineau A., Warwick K.M. Multivariate Descriptive Statistical Analysis. 1984;Wiley, New York
40. Hong K.H., Miller C. The lipid-protein interface of a Shaker K(+) channel. J. Gen. Physiol. 115:2000;51-58
41. + channel. Neuron. 25:2000;411-423
42. + channel can be trapped in the open state by an intersubunit metal bridge. Neuron. 21:1998;617-621
43. del Camino D., Yellen G. Tight steric closure at the intracellular activation gate of a voltage-gated K(+) channel. Neuron. 32:2001;649-656
44. Labro A.J., Raes A.L., Bellens I., Ottschytsch N., Snyders D.J. Gating of shaker-type channels requires the flexibility of S6 caused by prolines. J. Biol. Chem. 278:2003;50724-50731
45. + channel selectivity filter by mutant cycle-based structure analysis. Neuron. 16:1996;131-139
46. Li-Smerin Y., Hackos D.H., Swartz K.J. alpha-helical structural elements within the voltage-sensing domains of a K(+) channel. J. Gen. Physiol. 115:2000;33-50
47. + channel. Nature Struct. Biol. 7:2000;309-311
48. Santacruz-Toloza L., Huang Y., John S.A., Papazian D.M. Glycosylation of shaker potassium channel protein in insect cell culture and in Xenopus oocytes. Biochemistry. 33:1994;5607-5613
49. Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425
50. Schmidt H.A., Strimmer K., Vingron M., von Haeseler A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 18:2002;502-504
51. + channels. J. Gen. Physiol. 120:2002;663-676
52. + channel. J. Gen. Physiol. 113:1999;415-423
53. Carter P.J., Winter G., Wilkinson A.J., Fersht A.R. The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell. 38:1984;835-840
54. Perozo E. Structure and packing orientation of transmembrane segments in voltage-dependent channels. Lessons from perturbation analysis. J. Gen. Physiol. 115:2000;29-32
55. Lu Z., Klem A.M., Ramu Y. Ion conduction pore is conserved among potassium channels. Nature. 413:2001;809-813
56. Smith-Maxwell C.J., Ledwell J.L., Aldrich R.W. Uncharged S4 residues and cooperativity in voltage-dependent potassium channel activation. J. Gen. Physiol. 111:1998;421-439
57. Dutzler R., Campbell E.B., MacKinnon R. Gating the selectivity filter in ClC chloride channels. Science. 300:2003;108-112
58. Bairoch A., Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acids Res. 28:2000;45-48
59. Eddy S.R. Hidden Markov models. Curr. Opin. Struct. Biol. 6:1996;361-365
60. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:1994;4673-4680
61. Pupko T., Bell R.E., Mayrose I., Glaser F., Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics. 18:2002;S71-S77
62. Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950
63. Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524