Role of the dielectric constants of membrane proteins and channel water in ion permeation

Biophysical Journal

Volumn 84, Issue 5, 2003, Pages 2871-2882

  Baştuǧ, Turgut ^a   Kuyucak, Serdar ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

GLOBULAR PROTEIN; MEMBRANE PROTEIN; WATER;

ARTICLE; DIELECTRIC CONSTANT; ENERGY; ION PERMEABILITY; MATHEMATICAL MODEL; MEMBRANE CHANNEL; MEMBRANE PERMEABILITY;

EID: 0038637798     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)70015-0     Document Type: Article

References (47)

1. Allen, T. W., S. Kuyucak, and S. H. Chung. 1999. The effect of hydrophobic and hydrophilic channel walls on the structure and diffusion of water and ions. J. Chem. Phys. 111:7985-7999.
2. Allen, T. W., S. Kuyucak, and S. H. Chung. 2000. Molecular dynamics estimates of ion diffusion in model hydrophobic and the KcsA potassium channels. Biophys. Chem. 86:1-14.
3. Burykin, A., C. N. Schutz, J. Villa, and A. Warshel. 2002. Simulations of ion current in realistic models of ion channels: the KcsA potassium channel. Proteins. 47:265-280.
4. Chung, S. H., T. W. Allen, M. Hoyles, and S. Kuyucak. 1999. Permeation of ions across the potassium channel: Brownian dynamics studies. Biophys. J. 77:2517-2533.
5. Chung, S. H., T. W. Allen, and S. Kuyucak. 2002. Conducting-state properties of the KcsA potassium channel from molecular and Brownian dynamics simulations. Biophys. J. 82:628-645.
6. Chung, S. H., M. Hoyles, T. W. Allen, and S. Kuyucak. 1998. Study of ionic currents across a model membrane channel using Brownian dynamics. Biophys. J. 75:793-809.
7. Corry, B., T. W. Allen, S. Kuyucak, and S. H. Chung. 2001. Mechanisms of permeation and selectivity in calcium channels. Biophys. J. 80:195-214.
8. Corry, B., S. Kuyucak, and S. H. Chung. 2000. Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus Brownian dynamics. Biophys. J. 78:2364-2381.
9. Crozier, P. S., D. Henderson, R. L. Rowley, and D. D. Busath. 2001. Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics. Biophys. J. 81:3077-3089.
10. + conduction and selectivity. Science. 280:69-77.
11. Edwards, S., B. Corry, S. Kuyucak, and S. H. Chung. 2002. Continuum electrostatics fails to describe ion permeation in the gramicidin channel. Biophys. J. 83:1348-1360.
12. Eisenberg, R. S. 1996. Computing the field in proteins and channels. J. Membr. Biol. 150:1-25.
13. Eisenberg, R. S. 1999. From structure to function in open ionic channels. J. Membr. Biol. 171:1-24.
14. Green, M. E., and J. Lu. 1997. Simulation of water in a small pore: effect of electric field and density. J. Phys. Chem. B. 101:6512-6524.
15. Hoyles, M., S. Kuyucak, and S. H. Chung. 1996. Energy barrier presented to ions by the vestibule of the biological membrane channel. Biophys. J. 70:1628-1642.
16. Hoyles, M., S. Kuyucak, and S. H. Chung. 1998. Solutions of Poisson's equation in channel-like geometries. Comput. Phys. Commun. 115:45-68.
17. Im, W., and B. Roux. 2002. Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. J. Mol. Biol. 322:851-869.
18. Jackson, J. D. 1975. Classical Electrodynamics, 2nd ed. Wiley, New York.
19. Jordan, P. C. 1982. Electrostatic modeling of ion pores. Energy barriers and electric field profiles. Biophys. J. 39:157-164.
20. Jordan, P. C., R. J. Bacquet, J. A. McCammon, and P. Tran. 1989. How electrolyte shielding influences the electrical potential in transmembrane ion channels. Biophys. J. 55:1041-1052.
21. Jordan, P. C., M. B. Partenskii, and V. Dorman. 1997. Electrostatic influences on ion-water correlations in ion channels. Prog. Cell Res. 6:279-293.
22. Kuyucak, S., O. S. Andersen, and S. H. Chung. 2001. Models of permeation in ion channels. Rep. Prog. Phys. 64:1427-1472.
23. Kuyucak, S., M. Hoyles, and S. H. Chung. 1998. Analytical solutions of Poisson's equation for realistic geometrical shapes of membrane ion channels. Biophys. J. 74:22-36.
24. Levitt, D. G. 1978. Electrostatic calculations for an ion channel. I. Energy and potential profiles and interactions between ions. Biophys. J. 22:209-219.
25. Levitt, D. G. 1986. Interpretation of biological ion channel flux data reaction-rate versus continuum theory. Annu. Rev. Biophys. Biophys. Chem. 15:29-57.
26. Mashl, R. J., Y. Tang, J. Schnitzer, and E. Jakobsson. 2001. Hierarchical approach to predicting permeation in ion channels. Biophys. J. 81:2473-2483.
27. + selectivity filter. Nature. 414:37-42.
28. Moy, G., B. Corry, S. Kuyucak, and S. H. Chung. 2000. Tests of continuum theories as models of ion channels. I. Poisson-Boltzmann theory versus Brownian dynamics. Biophys. J. 78:2349-2363.
29. Nakamura, H. 1996. Roles of electrostatic interactions in proteins. Q. Rev. Biophys. 29:1-90.
30. Parsegian, A. 1969. Energy of an ion crossing a low dielectric membrane: solutions to four relevant electrostatic problems. Nature. 221:844-846.
31. Partenskii, M. B., and P. C. Jordan. 1992. Theoretical perspectives on ion-channel electrostatics: continuum and microscopic approaches. Q. Rev. Biophys. 25:477-510.
32. Pitera, J. W., M. Falta, and W. F. van Gunsteren. 2001. Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature. Biophys. J. 80:2546-2555.
33. Roux, B., S. Bernéche, and W. Im. 2000. Ion channels, permeation, and electrostatics: insight into the function of KcsA. Biochemistry. 39: 13295-13306.
34. + channel: electrostatic stabilization of monovalent cations. Science. 285:100-102.
35. Sansom, M. S. P., G. R. Smith, C. Adcock, and P. C. Biggin. 1997. The dielectric properties of water within model transbilayer pores. Biqphys. J. 73:2404-2415.
36. Schirmer, T., and P. S. Phale. 1999. Brownian dynamics simulation of ion flow through porin channels. J. Mol. Biol. 294:1159-1167.
37. Schutz, C. N., and A. Warshel. 2001. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins. 44: 400-417.
38. Simonson, T. 1998. Dielectric constant of cytochrome c from simulations in a water droplet including all electrostatic interactions. J. Am. Chem. Soc. 120:4875-4876.
39. Simonson, T., and C. L. Brooks, 3rd.1996. Charge screening and the dielectric constant of proteins: insights from molecular dynamics. J. Am. Chem. Soc. 118:8452-8458.
40. - ions in ion channel models. Biophys. Chem. 79:129-151.
41. Smith, P. E., R. M. Brunne, A. E. Mark, and W. F. van Gunsteren. 1993. Dielectric properties of trypsin inhibitor and lysozyme calculated from molecular dynamics simulations. J. Phys. Chem. 97:2009-2014.
42. Smythe, W. R. 1968. Static and Dynamic Electricity, 3rd ed. McGraw Hill, New York.
43. Suenaga, A., Y. Komeiji, M. Uebayasi, T. Meguro, M. Saito, and I. Yamato. 1998. Computational observation of an ion permeation through a channel protein. Biosci. Rep. 18:39-48.
44. Tian, F., and T. A. Cross. 1999. Cation transport: an example of structural based selectivity. J. Mol. Biol. 285:1993-2003.
45. Tieleman, D. P., and H. J. C. Berendsen. 1998. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys. J. 74:2786-2801.
46. Tieleman, D. P., P. C. Biggin, G. R. Smith, and M. S. P. Sansom. 2001. Simulation approaches to ion channel structure-function relationships. Q. Rev. Biophys. 34:473-561.
47. + channel-Fab complex at 2.0 Å resolution. Nature. 414:43-48.