Models of the structure and gating mechanisms of the pore domain of the NaChBac ion channel

Biophysical Journal

Volumn 95, Issue 8, 2008, Pages 3650-3662

  Shafrir, Yinon ^a   Durell, Stewart R ^a   Guy, H Robert ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; MUTANT PROTEIN; NACHBAC PROTEIN, BACTERIA; PROTEIN SUBUNIT; SODIUM CHANNEL;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BACILLUS; CHANNEL GATING; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BACILLUS; BACTERIAL PROTEINS; COMPUTER SIMULATION; CONSERVED SEQUENCE; ION CHANNEL GATING; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTANT PROTEINS; MUTATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; SEQUENCE ALIGNMENT; SODIUM CHANNELS;

EID: 56049102613     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.135327     Document Type: Article

References (36)

1. 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.
2. + channel in a lipid membrane-like environment. Nature. 450:376-382.
3. + channel. Science. 309:897-903.
4. Clayton, G. M., S. Altieri, L. Heginbotham, V. M. Unger, and J. H. Morais-Cabral. 2008. Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel. Proc. Natl. Acad. Sci. USA. 105:1511-1515.
5. Anderson, P. A., and R. M. Greenberg. 2001. Phylogeny of ion channels: clues to structure and function. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 129:17-28.
6. Ren, D., B. Navarro, H. Xu, L. Yue, Q. Shi, and D. E. Clapham. 2001. A prokaryotic voltage-gated sodium channel. Science. 294:2372-2375.
7. Ishibashi, K., M. Suzuki, and M. Imai. 2000. Molecular cloning of a novel form (two-repeat) protein related to voltage-gated sodium and calcium channels. Biochem. Biophys. Res. Commun. 270:370-376.
8. 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.
9. Yue, L., B. Navarro, D. Ren, A. Ramos, and D. E. Clapham. 2002. The cation selectivity filter of the bacterial sodium channel, NaChBac. J. Gen. Physiol. 120:845-853.
10. Zhao, Y., T. Scheuer, and W. A. Catterall. 2004. Reversed voltage-dependent gating of a bacterial sodium channel with proline substitutions in the S6 transmembrane segment. Proc. Natl. Acad. Sci. USA. 101:17873-17878.
11. + channels: a molecular switch for electrical signaling. Neuron. 41:859-865.
12. + channel-Fab complex at 2.0 Å resolution. Nature. 414:43-48.
13. Shrivastava, I. H., S. R. Durell, and H. R. Guy. 2004. A model of voltage gating developed using the KvAP channel crystal structure. Biophys. J. 87:2255-2270.
14. Brooks, B. R., R. E. Bruccoleri, B. D. Olafsin, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
15. Van Der, S. D., E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. Berendsen. 2005. GROMACS: fast, flexible, and free. J. Comput. Chem. 26:1701-1718.
16. Pettersen, E. F., T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin. 2004. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 25:1605-1612.
17. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
18. + channels. Soc. Gen. Physiol. Ser. 50:1-16.
19. Burley, S. K., and G. A. Petsko. 1985. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science. 229:23-28.
20. Richardson, J., R. Blunck, P. Ge, P. R. Selvin, F. Bezanilla, D. M. Papazian, and A. M. Correa. 2006. Distance measurements reveal a common topology of prokaryotic voltage-gated ion channels in the lipid bilayer. Proc. Natl. Acad. Sci. USA. 103:15865-15870.
21. 2+ channel. J. Gen. Physiol. 126:193-204.
22. Kloczkowski, A., K. L. Ting, R. L. Jernigan, and J. Garnier. 2002. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins. 49:154-166.
23. Deane, C. M., F. H. Allen, R. Taylor, and T. L. Blundell. 1999. Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid. Protein Eng. 12:1025-1028.
24. Stary, A., Y. Shafrir, S. Hering, P. Wolschann, and H. R. Guy. 2008. Structural models of the Cav1.2 pore. Channels. 2:210-215.
25. + channel revealed by cysteine mutagenesis. Neuron. 16:1037-1047.
26. Perez-Garcia, M. T., N. Chiamvimonvat, E. Marban, and G. F. Tomaselli. 1996. Structure of the sodium channel pore revealed by serial cysteine mutagenesis. Proc. Natl. Acad. Sci. USA. 93:300-304.
27. Tsushima, R. G., R. A. Li, and P. H. Backx. 1997. Altered ionic selectivity of the sodium channel revealed by cysteine mutations within the pore. J. Gen. Physiol. 109:463-475.
28. Yamagishi, T., M. Janecki, E. Marban, and G. F. Tomaselli. 1997. Topology of the P segments in the sodium channel pore revealed by cysteine mutagenesis. Biophys. J. 73:195-204.
29. Yamagishi, T., R. A. Li, K. Hsu, E. Marban, and G. F. Tomaselli. 2001. Molecular architecture of the voltage-dependent Na channel: functional evidence for alpha helices in the pore. J. Gen. Physiol. 118:171-182.
30. Koch, S. E., I. Bodi, A. Schwartz, and G. Varadi. 2000. Architecture of Ca(2+) channel pore-lining segments revealed by covalent modification of substituted cysteines. J. Biol. Chem. 275:34493-34500.
31. 2+ channel. J. Biol. Chem. 275:31778-31785.
32. Beyl, S., E. N. Timin, A. Hohaus, A. Stary, M. Kudrnac, R. H. Guy, and S. Hering. 2007. Probing the architecture of an L-type calcium channel with a charged phenylalkylamine: evidence for a widely open pore and drug trapping. J. Biol. Chem. 282:3864-3870.
33. Hockerman, 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. 37:361-396.
34. 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. Biochem. Biophys. 393:22-41.
35. 2+ channel. Mol. Pharmacol. 63:499-511.
36. Peterson, B. Z., and W. A. Catterall. 2006. Allosteric interactions required for high-affinity binding of dihydropyridine antagonists to Ca(V)1.1 channels are modulated by calcium in the pore. Mol. Pharmacol. 70:667-675.