A homology model of the pore domain of a voltage-gated calcium channel is consistent with available SCAM data

Journal of General Physiology

Volumn 135, Issue 3, 2010, Pages 261-274

  Bruhova, Iva ^a   Zhorov, Boris S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM CHANNEL N TYPE; VOLTAGE DEPENDENT CALCIUM CHANNEL (P Q TYPE); VOLTAGE-DEPENDENT CALCIUM CHANNEL (P-Q TYPE);

ARTICLE; AUDIOVISUAL EQUIPMENT; CHANNEL GATING; COMPUTER SIMULATION; MONTE CARLO METHOD; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY;

CALCIUM CHANNELS, N-TYPE; COMPUTER SIMULATION; ION CHANNEL GATING; MODELS, STRUCTURAL; MONTE CARLO METHOD; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 77649104603     PISSN: 00221295     EISSN: 15407748     Source Type: Journal    
DOI: 10.1085/jgp.200910288     Document Type: Article

References (50)

1. Ahem, C.A., A.L. Eastwood, D.A. Dougherty, and R. Horn. 2008. Electrostatic contributions of aromatic residues in the local anesthetic receptor of voltage-gated sodium channels. Circ. Res. 102:86-94, doi:10.1161/CIRCRESAHA.107.160663
2. Anderson, P.A., and R.M. Greenberg. 2001. Phylogeny of ion channels: clues to structure and function. Comp. Biochem, Physiol. BBioclmn. Mol Biol 129:17-28. doi:10.1016/Sl096-4959(01)00376-1 (Pubitemid 32397706)
3. Bruhova, I., and B.S. Zhorov. 2007. Monte Carlo-energy minimization of correolide in the Kv1.3 channel: possible role of potassium ion in ligand-receptor interactions. BMC Struct. Biol 7:5. doi:10.1186/1472-6807-7-5 (Pubitemid 46237596)
4. Bruhova, I., D.B. Tikhonov, and B.S. Zhorov. 2008. Access and binding of local anesthetics in the closed sodium channel. Mol. Pharmacol. 74:1033-1045. doi:10.1124/mol.108.049759
5. Catterall, W.A., A.L. Goldin, and S.G. Waxman. 2005. International Union of Pharmacology. XLVII. Nomenclature and structurefunction, relationships of volrage-gated sodium channels. Pharmacol Rev. 57:397-409. doi:10.1124/pr.57.4.4 (Pubitemid 43036431)
6. Cheng, R.C., D.B. Tikhonov, and B.S. Zhorov. 2009. Structural model, for phenylalkylamine binding to L-type calcium, channels. J. Biol Chem. 284:28332-28342. doi:10.1074/jbc.M109.027326
7. Cosconati, S., L. Marinelli, A. Lavecchia, and E. Novellino. 2007. Characterizing the 1,4-dihydropyridines binding interactions in the L-type Ca2+ channel: model construction and docking calculations.J. Med. Chem. 50:1504-1513. doi:10.1021/jm061245a (Pubitemid 46564372)
8. Dewar, M.J., E.G. Zoebisch, E.F. Healy, and J.J. Stewart. 1985. Development, and use of quantum mechanical molecular models. 76. AMI: a new general purpose quantum mechanical. molecular model. J. Am, Cliem. Soc. 107:3902-3909. doi:10.1021/ ja00299a024
9. Doyle, D.A.,J. Morais Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998. The structure of the potassium, channel: molecular basis of K+ conduction and selectivity. Science. 280:69-77. doi:10.11.26/science.280.5360.69
10. Du, Y., J.E. Lee, Y. Nomura, T. Zhang, B.S. Zhorov, and K. Dong. 2009. Identification, of a cluster of residues in transmembrane segment. 6 of domain III of the cockroach sodium, channel essential for the action of pyrethroid insecticides. Biochem, J. 419:377385. doi:10.1042/BJ20082082
11. + channel predict a clockwise arrangement, of the domains. J. Gen. Physiol. 116:679-690. doi:10.1085/jgp.116.5.679
12. Durell, S. R., and H. R. Guy. 2001. A. putative prokaryote voltage-gated Ca(2+) channel, with, only one 6TM motif per subunit. Biochem. Biophys. Res. Commun, 281:741-746. doi:10.1006/bbrc.2001.4408
13. Fozzard, H.A., P.J. Lee, and G.M. Lipkind. 2005. Mechanism of local anesthetic drug action on voltage-gated sodium channels. Curr. Pharm. Des. 11:2671-2686. doi:10.2174/1381612054546833 (Pubitemid 41051877)
14. ílockerman, G.H., B.Z. Peterson, B.D.Johnson, and W.A. Catterall. 1997. Molecular determinants of drug binding and action on L-type calcium channels. Annu. Rev. Pharmacol. Toxicol. 37:361396. doi:10.1146/annurev. pharmtox.37.1.361
15. Huber, I., E. Wappl, A. Herzog, J. Mitterdorfer, H. Glossmann, T. Langer, and J. Striessnig. 2000. Conserved Ca2+-antagonistbinding properties and putative folding structure of a recombinant high-affinity dihydropyridine- binding domain. Biocliem. J. 347:829-836. doi:10.1042/0264-6021:3470829 (Pubitemid 30260975)
16. Jiang, Y., A. Lee, J. Chen, V. Ruta, M. Cadene, B.T. Chait, and R. MacKinnon. 2003. X-ray structure of a voltage-dependent K+ channel. Nature. 423:33-41. doi:10.1038/nature01580
17. Karlin, A., and M.H. Akabas. 1998. Substituted-cysteine accessibility method. Methods Enzymol 293:123-145. doi:10.1016/ S0076-6879(98)93011-93017
18. Klein, H., L. Garneau, U. Banderali, M. Simoes, L. Parent, and R. Sauvé. 2007. Structural determinants of the closed KCa3.1 channel pore in relation to channel gating: results from a substituted cysteine accessibility analysis. J. Gen. Physiol. 129:299-315. doi:10.1085/jgp.200609726 (Pubitemid 46506981)
19. Lazaiidis, T., and M. Karplus. 1999. Effective energy function for proteins in solution. Proteins. 35:1.33-152. doi:10.1002/(SICI) 10970134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
20. Li, Z., and H.A. Scheraga. 1987. Monte Carlo-minimization approach, to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA.84:6611 -6615. doi:1.0.1073/pn.as.84.19.6611.
21. Lipkind, G.M., and H.A. Fozzard. 2003. Molecular modeling of interactions of dihydropyridines and phenylalkylamines with the inner pore of the L-type Ca2+ channel. Mol. Pharmacol. 63:499-511. doi:10.1124/mol.63.3.499
22. Lipkind, G.M., and H.A. Fozzard. 2005. Molecular modeling of local, anesthetic drug binding by voltage-gated sodium channels. Mol. Pharmacol. 68:1611-1622. (Pubitemid 41654345)
23. Liu, Y., M. Holmgren, M.E. Jurman, and G. Yellen. 1997. Gated access to the pore of a voltage-dependent K-I- channel. Neuron. 19:1.75-184. doi:10.1016/S0896-6273(00)80357-8 (Pubitemid 27333003)
24. Long, S.B., E.B. Campbell, and R. Mackinnon. 2005. Crystal structure of a mammalian voltage-dependent Shaker family K+ channel. Science. 309:897-903. doi:10.1126/science.1116269
25. Long, S.B., X. Tao, E.B. Campbell, and R. MacKinnon. 2007. Atomic structure of a voltage-dependent K+ channel in a lipid membranelike environment. Nature. 450:376-382. doi:10.1038/nature06265
26. Lu,T,B.Nguyen,X.Zhang,andJ.Yang.1999.ArchitectureofaK+channel, innerporerevealedbystoichiometriccovalentmodification.Neuron.22:571-580.doi:10. 1016/S0896-6273(00)80711-4(Pubitemid29159855)
27. O'Reilly, A.O., B.P. Khambay, M.S. Williamson, L.M. Field, B.A. Wallace, and T.G. Davies. 2006. Modelling insecticide-binding sites in the voltage-gated sodium channel. Biochem. J. 396:255-263. doi:10.1042/BJ20051925 (Pubitemid 43837241)
28. Pathak, M.M., V. Yarov-Yarovoy, G. Agarwal, B. Roux, P. Barth, S. Kohout, F. Tombola, and E.Y Isacoff. 2007. Closing in on the resting state of the Shaker K.(+) channel. Neuron. 56:124-140. doi:10.1016/j.neuron.2007.09.023
29. Phillips, L.R., D. Enkvetchakul, and C.G. Nichols. 2003. Gating dependence of inner pore access in inward rectifier K(+) channels. Neuron. 37:953-962. doi:10.1016/S0896-6273(03)00155-7 (Pubitemid 36398300)
30. + as permeant ions. J. Gen. Physiol. 94:1-21. doi:10.1085/jgp.94.l.l
31. Prod'hom, B., D. Pietrobon, and P. Hess. 1987. Direct measurement, of proton transfer rates to a group controlling the dihydropyridinesensitive Ca2+channel. Nature. 329:243-246. doi:l0.1038/329243a0
32. Ren, D., B. Navarro, H. Xu, L. Yue, Q. Shi, and D.E. Clapham. 2001. A prokaryotk voltage-gated sodium channel. Science. 294:2372-2375. doi:10.1126/science.1065635
33. Santarelli, V.P., A.L. Eastwood, D.A. Dougherty, R. Horn, and C.A. Ahem. 2007. A cation-pi interaction, discriminates among sodium channels that are either sensitive or resistant to tetrodotoxin block. J. Biol. Chem. 282:8044-8051. doi:10.1074/jbc.M611334200
34. Shafrir, Y, S.R. Durell, and H.R. Guy. 2008. Models of the structure and gating mechanisms of the pore domain, of the NaChBac ion. channel. Biophys. J. 95:3650-3662. doi:10.1529/biophysj.108.135327
35. Stary, A., Y Shafrir, S. Hering, P. Wolschann, and H.R. Guy. 2008. Structural model of the Ca(V) 1.2 pore. Channels (Austin). 2:210-215.
36. Sunami, A., A. Tracey, I.W. Glaaser, G.M. Lipkind, D.A. Hanck, and H.A. Fozzard. 2004. Accessibility of mid-segment domain IV S6 residues of the voltage-gated Na+ channel to methariethiosulfonate reagents. J. Physiol. 561:403-413. doi:10.1113/jphysiol.2004.067579 (Pubitemid 39646531)
37. Tikhonov, D.B. 2007. Ion channels of glutamate receptors: structural modeling. Mol. Membr. Biol 24:135-147. doi: 10.1080/ 09687860601008806
38. Tikhonov, D.B., and B.S. Zhorov. 2005. Modeling P-loops domain of sodium channel: homology with potassium channels and interaction with ligands. Biophys. J. 88:184-197. doi:10.1529/ biophysj.104.048173
39. Tikhonov, D.B., and B.S. Zhorov. 2007. Sodium channels: ionic model of slow inactivation and state-dependent, drug binding. Biophys. J. 93:1557-1570.
40. Tikhonov, D.B., and B.S. Zhorov. 2008. Molecular modeling of benzodiazepine binding in the L-type calcium channel. J. Biol Chem. 283:17594-17604. doi:10.1074/jbc.M800141200
41. Tikhonov, D.B., and B.S. Zhorov. 2009. Structural model, for dihydropyridine binding to L-type calcium channels. J. Biol. Chem. 284:19006-19017. doi:10.1074/jbc.M109.011296
42. Tikhonov, D.B., I. Bruhova, and B.S. Zhorov. 2006. Atomic determinants of state-dependent block of sodium channels by charged local anesthetics and benzocaine. FEBS Lett. 580:6027-6032. doi:10.1016/j.febslet.2006.10.035
43. Wang, S.Y., J. Mitchell, D.B. Tikhonov, B.S. Zhorov, and G.K. Wang. 2006. How batrachotoxin modifies the sodium channel permeation pathway: computer modeling and site-directed mutagenesis. Mol. Pharmacol. 69:788-795. doi.:10.1124/mol.106 .022368
44. Weiner, S.J., P.A. Kollman, DA. Case, U.C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner. 1984. A new force-field for molecular mechanical simulation of nucleic-acids and proteins. J. Am. Chem. Soc. 106:765-784, doi:10.1021/ja00315a051.
45. Weiner, S.J., P.A. Kollman, D.T. Nguyen, and D.A. Case. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comput Chem. 7:230-252. doi:10.1002/jcc.540070216
46. Xiu, X., N.L. Puskar, J.A. Shanata, H.A. Lester, and D.A. Dougherty. 2009. Nicotine binding to brain receptors requires a strong cationpi interaction. Nature. 458:534-537. doi:10.1038/nature07768
47. 2+ channel. J. Gen. Physiol. 126:193-204, doi:10 .1085/jgp.200509292
48. Zhorov, B.S., and D.B. Tikhonov. 2004. Potassium, sodium, calcium and glutamate-gated channels: pore architecture and ligand action. J. Neurochem. 88:782-799.
49. Zhorov, B.S., E.V. Folkman, and V.S. Ananthanarayanan, 2001, Homology model of dihydropyridine receptor: implications for L-type Ca(2+) channel modulation by agonists and antagonists. Arch, Biocliem. Biophys. 393:22-41, doi: 10.1006/abbi.2001.2484
50. Zong, Y., S.K. Mazmanian, O. Schneewind, and S.V. Narayana. 2004. The structure of sonase B, a cysteine transpeptidase that tethers surface protein to the Staphylococcus aureus cell wall. Structure. 12:105-112. doi:10.1016/j.str.2003.11.021 (Pubitemid 38114810)