Volume exclusion in calcium selective channels

Biophysical Journal

Volumn 94, Issue 9, 2008, Pages 3486-3496

  Boda, Dezso' ^a,b   Nonner, Wolfgang ^c   Henderson, Douglas ^d   Eisenberg, Bob ^a   Gillespie, Dirk ^a  

^a RUSH MEDICAL COLLEGE   (United States)

^b UNIVERSITY OF PANNONIA   (Hungary)

^c UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^d Brigham Young University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; CALCIUM CHANNEL;

ARTICLE; BIOLOGICAL MODEL; METABOLISM; MONTE CARLO METHOD; SENSITIVITY AND SPECIFICITY;

CALCIUM; CALCIUM CHANNELS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; SENSITIVITY AND SPECIFICITY;

EID: 43649092750     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.122796     Document Type: Article

References (42)

1. Hille, B. 2001. Ionic Channels of Excitable Membranes. Sinauer Associates, Sunderland, MA.
2. Almers, W., E. McCleskey, and P. Palade. 1984. Non-selective cation conductance in frog muscle membrane blocked by micromolar external calcium ions. J. Physiol. 353:565-583.
3. Almers, W., and E. McCleskey. 1984. Non-selective conductance in calcium channels of frog muscle: calcium selectivity in a single-file pore. J. Physiol. 353:585-608.
4. 2+ interactions. Neuron. 15:1121-1132.
5. 2+ channels. Nature. 366:158-161.
6. Sather, W., and E. McCleskey. 2003. Permeation and selectivity in calcium channels. Annu. Rev. Physiol. 65:133-159.
7. Nonner, W., L. Catacuzzeno, and B. Eisenberg. 2000. Binding and selectivity in L-type Ca channels: a mean spherical approximation. Biophys. J. 79:1976-1992.
8. Nonner, W., D. Gillespie, D. Henderson, and B. Eisenberg. 2001. Ion accumulation in a biological calcium channel: effects of solvent and confining pressure. J. Phys. Chem. B. 105:6427-6436.
9. Boda, D., W. Nonner, M. Valiskó, D. Henderson, B. Eisenberg, and D. Gillespie. 2007. Steric selectivity in Na channels arising from protein polarization and mobile side chains. Biophys. J. 93:1960-1980.
10. + channel: charge-space competition. Phys. Chem. Chem. Phys. 4:51545160.
11. Barker, J., and D. Henderson. 1976. What is "liquid"? Understanding the states of matter. Rev. Mod. Phys. 48:587-671.
12. Gillespie, D. 2008. Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study. Biophys. J. 94:1169-1184.
13. Gillespie, D., L. Xu, Y. Wang, and G. Meissner. 2005. (De)constructing the ryanodine receptor: modeling ion permeation and selectivity of the calcium release channel. J. Phys. Chem. B. 109:15598-15610.
14. Boda, D., D. Henderson, and D. Busath. 2002. Monte Carlo study of the selectivity of calcium channels: improved geometrical mode. Mol. Phys. 100:2361-2368.
15. Boda, D., D. Henderson, and D. Busath. 2001. Monte Carlo study of the effect of ion and channel size on the selectivity of a model calcium channel. J. Phys. Chem. B. 105:11574-11577.
16. Boda, D., D. Busath, D. Henderson, and S. Sokolowski. 2000. Monte Carlo simulations of the mechanism of channel selectivity: the competition between volume exclusion and charge neutrality. J. Phys. Chem. B. 104:8903-8910.
17. Boda, D., M. Valiskó, B. Eisenberg, W. Nonner, D. Henderson, and D. Gillespie. 2007. The combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel. Phys. Rev. Lett. 98:168102.
18. Boda, D., M. Valiskó, B. Eisenberg, W. Nonner, D. Henderson, and D. Gillespie. 2006. The effect of protein dielectric coefficient on the ionic selectivity of a calcium channel. J. Chem. Phys. 125:034901.
19. Corry, B., T. Allen, S. Kuyucak, and S. Chung. 2001. Mechanisms of permeation and selectivity in calcium channels. Biophys. J. 80:195-214.
20. Krishnamurthy, V., and S. Chung. 2007. Large-scale dynamical models and estimation for permeation in biological membrane ion channels. Proc. IEEE. 95:853-880.
21. Corry, B., and S. Chung. 2006. Mechanisms of valence selectivity in biological ion channels. Cell. Mol. Life Sci. 63:301-315.
22. Corry, B., T. Vora, and S. Chung. 2006. Electrostatic basis of valence selectivity in cationic channels. Biochim. Biophys. Acta. 1711:72-86.
23. Corry, B., M. Hoyles, T. Allen, M. Walker, S. Kuyucak, and S. Chung. 2002. Reservoir boundaries in Brownian dynamics simulations of ion channels. Biophys. J. 82:1975-1984.
24. Im, W., S. Seefeld, and B. Roux. 2000. A grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys. J. 79:788-801.
25. Guàrdia, E., and J. Padró. 1996. On the influence of ionic charge on the mean force potential of ion pairs in water. J. Chem. Phys. 104:7219-7222.
26. - ion pairs in water: mean force potentials by constrained molecular dynamics. J. Chem. Phys. 95:2823-2831.
27. Guàrdia, E., R. Rey, and J. Padró. 1991. Potential of mean force by constrained molecular dynamics: a sodium chloride ion-pair in water. Chem. Phys. 155:187-195.
28. Lyubartsev, A., and A. Laaksonen. 1995. Calculation of the effective interaction potentials from radial distribution functions: a reverse Monte Carlo approach. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 52:3730-3737.
29. Chung, S., T. Allen, M. Hoyles, and S. Kuyucak. 1999. Permeation of ions across the potassium channel: Brownian dynamics studies. Biophys. J. 77:2517-2533.
30. Fawcett, W. 1999. Thermodynamic parameters for the solvation of monatomic ions in water. J. Phys. Chem. B. 103:11181-11185.
31. Shannon, R., and C. Previtt. 1969. Effective ionic radii in oxides and fluorides. Acta Crystallogr. B. 25:925-946.
32. Valleau, J., and L. Cohen. 1980. Primitive model electrolytes. I. Grand canonical Monte Carlo computations. J. Chem. Phys. 72:5935-5941.
33. Gibbs, J. 1948. Elementary Principles of Statistical Mechanics. Yale University Press, New Haven, CT.
34. Malasics, A. D., D. Gillespie, and D. Boda. 2008. Simulating prescribed particle densities in the grand canonical ensemble using iterative algorithms. J. Chem. Phys. In press.
35. Hoyles, M., S. Kuyucak, and S. Chung. 1998. Solutions of Poisson's equation in channel-like geometries. Comput. Phys. Commun. 115:45-68.
36. Boda, D., D. Gillespie, W. Nonner, D. Henderson, and B. Eisenberg. 2004. Computing induced charges in in homogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 69:046702.
37. Kostyuk, P., S. Mironov, and Y. Shuba. 1983. Two ion-selective filters in the calcium channel of the somatic membrane of mollusk neurons. J. Membr. Biol. 76:83-93.
38. 2+. Voltage and concentration dependence of calcium entry into the pore. J. Gen. Physiol. 88:321-347.
39. Fukushima, A., and S. Hagiwara. 1985. Currents carried by monova-lent cations through calcium channels in mouse neoplastic B lymphocytes. J. Physiol. 358:255-284.
40. Nonner, W., D. Chen, and B. Eisenberg. 1998. Anomalous mole fraction effect, electrostatics, and binding in ionic channels. Biophys. J. 74:2327-2334.
41. Polo-Parada, L., and S. Korn. 1997. Block of N-type calcium channels in chick sensory neurons by external sodium. J. Gen. Physiol. 109: 693-702.
42. Yang, Y., D. Henderson, and D. Busath. 2003. Applied-field molecular dynamics study of a model calcium channel selectivity filter. J. Chem. Phys. 118:4213-4220.