Effects of the protonation state of the EEEE motif of a bacterial Na +-channel on conduction and pore structure

Biophysical Journal

Volumn 106, Issue 10, 2014, Pages 2175-2183

  Furini, Simone ^a   Barbini, Paolo ^a   Domene, Carmen ^b  

^a UNIVERSITY OF SIENA   (Italy)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTON; SODIUM; SODIUM CHANNEL;

CHEMISTRY; ELECTROPHYSIOLOGY; METABOLISM; MOLECULAR DYNAMICS; POROSITY; PROBABILITY; PROTEIN MOTIF;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; ELECTROPHYSIOLOGICAL PROCESSES; MOLECULAR DYNAMICS SIMULATION; POROSITY; PROBABILITY; PROTONS; SODIUM; SODIUM CHANNELS;

EID: 84901246379     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.04.005     Document Type: Article

References (30)

1. K. Charalambous, and B.A. Wallace NaChBac: the long lost sodium channel ancestor Biochemistry 50 2011 6742 6752
2. J. Payandeh, and T. Scheuer W.A. Catterall The crystal structure of a voltage-gated sodium channel Nature 475 2011 353 358
3. X. Zhang, and W. Ren N. Yan Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel Nature 486 2012 130 134
4. E.C. McCusker, and C. Bagneris B.A. Wallace Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing Nature Comm. 3 2012 1102 10.1038/ncomms2077
5. S.H. Heinemann, and H. Terlau S. Numa Calcium channel characteristics conferred on the sodium channel by single mutations Nature 356 1992 441 443
6. V. Carnevale, W. Treptow, and M.L. Klein Sodium ion binding sites and hydration in the lumen of a bacterial ion channel from molecular dynamics simulations J. Phys. Chem. Lett 2 2011 2504 2508
7. H. Qiu, R. Shen, and W. Guo Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations Biochim. Biophys. Acta 1818 2012 2529 2535
8. 2+ ions with the selectivity filter of the bacterial sodium channel Na(V)Ab Biochem. Biophys. Res. Commun. 430 2013 1272 1276
9. B. Corry, and M. Thomas Mechanism of ion permeation and selectivity in a voltage gated sodium channel J. Am. Chem. Soc. 134 2012 1840 1846
10. S. Furini, and C. Domene On conduction in a bacterial sodium channel PLOS Comput. Biol. 8 2012 e1002476
11. L. Stock, and L. Delemotte M.L. Klein Conduction in a biological sodium selective channel J. Phys. Chem. B 117 2013 3782 3789
12. M.B. Ulmschneider, and C. Bagnéris B.A. Wallace Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel Proc. Natl. Acad. Sci. USA 110 2013 6364 6369
13. 2+ selectivity in the bacterial voltage-gated sodium channel NavAb PeerJ 1 2013 e16
14. + permeation in the bacterial sodium channel Na(V)Ab Proc. Natl. Acad. Sci. USA 110 2013 11331 11336
15. + channel J. Am. Chem. Soc. 130 2008 3389 3398
16. W. Humphrey, A. Dalke, and K. Schulten VMD: visual molecular dynamics J. Mol. Graph. 14 1996 33 38
17. C. Domene, and S. Furini M.H. Jo Examining Ion Channel Properties Using Free-Energy Methods Methods in Enzymology 2009 Academic Press New York 155 177
18. J.C. Phillips, and R. Braun K. Schulten Scalable molecular dynamics with NAMD J. Comput. Chem. 26 2005 1781 1802
19. A.D. MacKerell, and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
20. W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
21. G.J. Martyna, D.J. Tobias, and M.L. Klein Constant-pressure molecular-dynamics algorithms J. Chem. Phys. 101 1994 4177 4189
22. S.E. Feller, and Y.H. Zhang B.R. Brooks Constant pressure molecular dynamics simulation: the Langevin piston method J. Chem. Phys. 103 1995 4613 4621
23. U. Essmann, and L. Perera L.G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 1995 8577 8593
24. S. Miyamoto, and P.A. Kollman Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water molecules J. Comput. Chem. 13 1992 952 962
25. + channel Proc. Natl. Acad. Sci. USA 100 2003 8644 8648
26. C.J.R. Illingworth, S. Furini, and C. Domene Computational studies on polarization effects and selectivity in K+ channels J. Chem. Theory Comput. 6 2010 3780 3792
27. + conduction in selective and nonselective ion channels via molecular dynamics simulations Biophys. J. 105 2013 1737 1745
28. 2+ selectivity of a voltage-gated calcium channel Nature 505 2014 56 61
29. C. Boiteux, I. Vorobyov, and T.W. Allen Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel Proc. Natl. Acad. Sci. USA 111 2014 3454 3459
30. M.O. Jensen, and V. Jogini D.E. Shaw Atomic-level simulation of current-voltage relationships in single-file ion channels J. Gen. Physiol. 141 2013 619 632