Distinct interactions of Na+ and Ca2+ ions with the selectivity filter of the bacterial sodium channel NaVAb

Biochemical and Biophysical Research Communications

Volumn 430, Issue 4, 2013, Pages 1272-1276

  Ke, Song ^a   Zangerl, Eva Maria ^a   Stary Weinzinger, Anna ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

Bacterial sodium channel; Ca2+ selectivity; Free energy profile; Ion binding sites; Molecular dynamics simulation

Indexed keywords

CALCIUM ION; LEUCINE; SODIUM CHANNEL; SODIUM CHANNEL NAVAB; SODIUM ION; THREONINE; UNCLASSIFIED DRUG;

ARCOBACTER; ARCOBACTER BUTZLERI; ARTICLE; BINDING AFFINITY; BINDING SITE; CALCIUM BINDING; CALCULATION; CHEMICAL INTERACTION; ENERGY; FILTER; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL;

ARCOBACTER; BACTERIAL PROTEINS; CALCIUM; CATIONS, DIVALENT; CATIONS, MONOVALENT; MOLECULAR DYNAMICS SIMULATION; SODIUM; SODIUM CHANNELS;

ARCOBACTER BUTZLERI; BACTERIA (MICROORGANISMS);

EID: 84872838529     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2012.12.055     Document Type: Article

References (35)

1. Catterall W.A. From ionic currents to molecular review mechanisms: the structure and function of voltage-gated sodium channels. Neuron 2000, 26:13-25.
2. Payandeh J., Scheuer T., Zheng N., Catterall W.A. The crystal structure of a voltage-gated sodium channel. Nature 2011, 475:353-358.
3. Payandeh J., El-Din T.M.G., Scheuer T., Zheng N., Catterall W.A. Crystal structure of a voltage-gated sodium channel in two potentially inactivated states. Nature 2012, 486:135-139.
4. Zhang X., Ren W., DeCaen P., Yan C., Tao X., Tang L., et al. Crystal structure of an orthologue of the NaChBac voltage-gated sodium channel. Nature 2012, 486:130-134.
5. McCusker E.C., Bagnéris C., Naylor C.E., Cole A.R., D'Avanzo N., Nichols C.G., et al. Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing. Nat. Commun. 2012, 3:1102.
6. Furini S., Domene C. On conduction in a bacterial sodium channel. PLoS Comput. Biol. 2012, 8:e1002476.
7. Corry B., Thomas M. Mechanism of ion permeation and selectivity in a voltage gated sodium channel. J. Am. Chem. Soc. 2011, 134:1840-1846.
8. Sather W.A., McCleskey E.W. Permeation and selectivity in calcium channels. Annu. Rev. Physiol. 2003, 65:133-159.
9. Dejian R. Sodium leak channels in neuronal excitability and rhythmic behaviors. Neuron 2011, 72:899-911.
10. 2+ channels. Nature 1993, 366:158-161.
11. Heinemann S.H., Terlau H., Stühmer W., Imoto K., Numa S. Calcium channel characteristics conferred on the sodium channel by single mutations. Nature 1992, 356:441-443.
12. Yue L., Navarro B., Ren D., Ramos A., Clapham D.E. The cation selectivity filter of the bacterial sodium channel, NaChBac. J. Gen. Physiol. 2002, 120:845-853.
13. V) protein dissection creates a set of functional pore-only proteins. Proc. Nat. Acad. Sci. 2011, 108:12313.
14. Hess B., Kutzner C., Van Der Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 2008, 4:435-447.
15. Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 2006, 65:712-725.
16. Siu S.W.I., Vácha R., Jungwirth P., Böckmann R.A. Biomolecular simulations of membranes: physical properties from different force fields. J. Chem. Phys. 2008, 128:125103.
17. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79:926-935.
18. Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 1997, 18:1463-1472.
19. Darden T., York D., Pedersen L. Particle Mesh Ewald: an N log (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98. 10089-10089.
20. Joung I.S., Cheatham T.E. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B 2008, 112:9020-9041.
21. Nose S. A unified formulation of the constant temperature molecular-dynamics methods. J. Chem. Phys. 1984, 81:511-519.
22. Hoover W.G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 1985, 31:1695-1697.
23. Martoňák R., Laio A., Parrinello M. Predicting crystal structures: the Parrinello-Rahman method revisited. Phys. Rev. Lett. 2003, 90:75503.
24. Torrie G.M., Valleau J.P. Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem. Phys. Lett. 1974, 28:578-581.
25. Lemkul J.A., Bevan D.R. Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics. J. Phys. Chem. B 2010, 114:1652-1660.
26. Hub J.S., de Groot B.L., van der Spoel D. G_wham-a free weighted histogram analysis implementation including robust error and autocorrelation estimates. J. Chem. Theory Comput. 2010, 6:3713-3720.
27. Carnevale V., Treptow W., Klein M.L. Sodium ion binding sites and hydration in the lumen of a bacterial ion channel from molecular dynamics simulations. J. Phys. Chem. Lett. 2011, 2:2504-2508.
28. Qiu H., Shen R., Guo W. Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations. Biochim. Biophys. Acta (BBA) - Biomembr. 1818, 2012:2529-2535.
29. Boda D., Busath D.D., Henderson D., Sokolowski S. Monte Carlo simulations of the mechanism for channel selectivity: the competition between volume exclusion and charge neutrality. J. Phys. Chem. B 2000, 104:8903-8910.
30. Boda D., Busath D.D., Eisenberg B., Henderson D., Nonner W. Monte Carlo simulations of ion selectivity in a biological Na channel: charge-space competition. Phys. Chem. Chem. Phys. 2002, 4:5154-5160.
31. Boda D., Varga T., Henderson D., Busath D.D., Nonner W., Gillespie D., et al. Monte Carlo simulation study of a system with a dielectric boundary: application to calcium channel selectivity. Mol. Simul. 2004, 30:89-96.
32. Corry B., Chung S.H. Mechanisms of valence selectivity in biological ion channels. Cell. Mol. Life Sci. 2006, 63:301-315.
33. + channels with the same EEEE motif in their selectivity filters confer opposite metal selectivity. Phys. Chem. Chem. Phys. 2012, 14:12451-12456.
34. + for model ion channel selectivity filters: determinants of ion selectivity. J. Phys. Chem. B 2012, 116:10703-10714.
35. Koneshan S., Rasaiah J.C., Lynden-Bell R.M., Lee S.H. Solvent structure, dynamics, and ion mobility in aqueous solutions at 25°C. J. Phys. Chem. B 1998, 102:4193-4204.