Gauging of the PhoE channel by a single freely diffusing proton

Biophysical Journal

Volumn 83, Issue 6, 2002, Pages 2987-3000

  Bransburg Zabary, Sharron ^a   Nachliel, Esther ^a   Gutman, Menachem ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

8 HYDROXYPYRENE 1,2,3 TRISULFONATE; ION CHANNEL; PROTON; SULFONIC ACID DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL MEMBRANE; CALCULATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIFFUSION; ELECTRICITY; ESCHERICHIA COLI; MICELLE; MOLECULE; NONHUMAN;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0036929207     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(02)75305-8     Document Type: Article

References (55)

1. Agmon, N. 1983. Transient kinetics of chemical reactions with bounded diffusion perpendicular to the reaction coordinate: Intramolecular processes with slow conformational changes. J. Chem. Phys. 78:6947-6959.
2. Bauer, K., P. Van Der Ley, R. Benz, and J. Tommassen. 1988. The Pho-controlled outer membrane porin PhoE does not contain specific binding sites for phosphate or polyphosphates. J. Biol. Chem. 263:13046-13053.
3. Benz, R., R. Darveau, and R. Hancock. 1984. Outer-membrane protein PhoE from Escherichia coli forms anion-selective pores in lipid-bilayer membranes. Eur. J. Biochem. 140:319-324.
4. Benz, R., A. Schmid, P. Van Der Ley, and J. Tommassen. 1989. Molecular basis of porin selectivity: Membrane experiments with Ompc-PhoE and Ompf-PhoE hybrid proteins of Escherichia coli K-12. Biochim. Biophys. Acta. 981:8-14.
5. Berrier, C., M. Besnard, and A. Ghazi. 1997. Electrophysiological characteristics of the PhoE porin channel from Escherichia coli: Implications for the possible existence of a superfamily of ion channels. J. Membr. Biol. 156(2):105-115.
6. Bransburg-Zabary, S., E. Nachliel, and M. Gutman. 2002. A fast in silico simulation of ion flux through the large-pore channel protein. Biophys. J. 83:3001-3011.
7. Breed, J. R., I. D. Kerr, and M. S. P. Sansim. 1996. Molecular dynamics simulations of water within models of ion channels. Biophys. J. 70:1643-1661.
8. Cohen, B., and D. Huppert. 2001. Evidence for a continuous transition from nonadiabatic to adiabatic proton transfer dynamics in protic solvents. J. Phys. Chem. 105:2988-2990.
9. Cohen, B., D. Huppert, K. M. Solntsev, Y. Tsfadia, E. Nachliel, and M. Gutman. 2002. Excited state proton transfer in reversed micelles. J. Am. Chem. Soc. 124:7539-7547.
10. Crozier, P., R. Rowley, N. Holladay, D. Henderson, and D. Busath. 2001. Molecular dynamics simulation of continuous current flow through a model biological membrane channel. Phys. Rev. Lett. 86:2467-2470.
11. Dennis. S., C. Camacho, and S. Vajda. 2000. Continuum electrostatic analysis of preferred solvation sites around proteins in solution. Proteins. 38:176-188.
12. Eppens, E., N. Nouwen, and J. Tommassen. 1997a. Folding of a bacterial outer-membrane protein during passage through the periplasm. EMBO J. 16:4295-4301.
13. Eppens, E., N. Saint, P. Vangelder, R. Vanboxtel, and J. Tommassen. 1997b. Role of the constriction loop in the gating of outer-membrane porin PhoE of Escherichia coli. FEBS Lett. 415:317-320.
14. Fischer, W., M. Pitkeathly, B. Wallace, L. Forrest, G. Smith, and M. Sansom. 2000. Transmembrane peptide Nb of influenza B: A simulation, structure, and conductance study. Biochemistry. 39:12708-12716.
15. Groves, J., S. G. Boxer, and H. M. Maconnell. 2000. Lateral reorganization of fluid lipid membranes in response to the electric field produced by a buried charge. J. Phys. Chem. 104:11409-11415.
16. Gutman, M., D. Huppert, and E. Nachliel. 1982a. Kinetic studies of proton transfer in the microenvironment of a binding site. Eur. J. Biochem. 121:637-642.
17. Gutman, M., and E. Nachliel. 1990. The dynamic aspects of proton transfer processes. Biochim. Biophys. Acta. 1015:391-414.
18. Gutman, M., E. Nachliel, and D. Huppert. 1982b. Direct measurement of proton transfer as a probing reaction for the microenvironment of the apomyoglobin heme-binding site. Eur. J. Biochem. 125:175-181.
19. Gutman, M., E. Nachliel, and S. Kiryati. 1992a. Dynamic studies of proton diffusion in mesoscopic heterogeneous matrix: The interbilayer space between phospholipids membranes. Biophys. J. 63:281-290.
20. Gutman, M., E. Nachliel, and S. Moshiach. 1989. Dynamics of proton diffusion within the hydration layer of phospholipid membrane. Biochemistry. 28:2936-2940.
21. Gutman, M., Y. Tsfadia, A. Masad, and E. Nachliel. 1992b. Quantitation of physical-chemical properties of the aqueous phase inside the PhoE ionic channel. Biochim. Biophys. Acta. 1109:141-148.
22. Holst, M., R. Kozack, F. Saied, and S. Subramaniam. 1994. Treatment of electrostatic effects in proteins: Multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation. Proteins. 18:231-245.
23. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
24. Huppert, D. E., M. Gutman, and E. Nachliel. 1982. The effect of water activity on the rate constant of proton dissociation. J. Am. Chem. Soc. 104:6944-6953.
25. Jakobsson, E. 1998. Using theory and simulation to understand permeation and selectivity in ion channels. Methods. 14:342-351.
26. Jap, B., P. Walian, and K. Gehring. 1991. Structural architecture of an outer membrane channel as determined by electron crystallography. Nature. 350:167-170.
27. Jordan, P. 1982. Electrostatic modeling of ion pores-energy barriers and electric field profile. Biophys. J. 39:157-164.
28. Karshikoff, A., V. Spassov, S. Cowan, R. Ladenstein, and T. Schirmer. 1994. Electrostatic properties of two porin channels from Escherichia coli. J. Mol. Biol. 240:372-384.
29. Koebnik, R., K. Locher, and P. Vangelder. 2000. Structure and function of bacterial outer membrane proteins: Barrels in a nutshell. Mol. Microbiol. 37:239-253.
30. Krissinel, E., and N. Agmon. 1996. Spherical symmetric diffusion problem. J. Comp. Chem. 17:1085-1098.
31. Kurnikova, M., R. Coalson, P. Graf, and A. Nitzan. 1999. A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel. Biophys. J. 76:642-656.
32. Li, H., H. Sui, S. Ghanshani, S. Lee, P. Walian, C. Wu, K. Chandy, and B. Jap. 1998. 2-Dimensional crystallization and projection structure of Kcsa potassium channel. J. Mol. Biol. 282:211-216.
33. Marino, M., M. Galvano, A. Cambria, F. Polticelli, and A. Desideri. 1995. Modeling the three-dimensional structure and the electrostatic potential field of two Cu, Zn superoxide dismutase variants from tomato leaves. Protein Eng. 8:551-556.
34. Oberoi, H., and N. Allewell. 1993. Multigrid solution of the nonlinear Poisson-Boltzmann equation and calculation of titration curves. Biophys. J. 65:48-55.
35. Pellequer, J., and S. Chen. 1997. Does conformational free energy distinguish loop conformations in proteins? Biophys. J. 73:2359-2375.
36. Phale, P., A. Philippsen, C. Widmer, V. Phale, J. Rosenbusch, and T. Schirmer. 2001. Role of charged residues at the Ompf porin channel constriction probed by mutagenesis and simulation. Biochemistry. 40:6319-6325.
37. Pines, E. D. 1989. Salt effect in photoacids quantum yield measurements: Demonstration of the geminate recombination role in the deprotonation reactions. J. Am. Chem. Soc. 111:4096-4097.
38. Pines, E., D. Huppert, and N. Agmon. 1988. Geminate recombination in excited-state proton transfer reaction: Numerical solution of the Debye-Smoluchowski equation with back-reaction boundary conditions. J. Chem. Phys. 88:5620-5630.
39. Polozov, R., T. Dzhelyadin, A. Sorokin, N. Ivanova, V. Sivozhelezov, and S. Kamzolova. 1999. Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences. J. Biomol. Struct. Dyn. 16:1135-1143.
40. Rand, R., N. Fuller, V. Parsegian, and D. Rau. 1988. Variation in hydration forces between neutral phospholipid bilayers: Evidence for hydration attraction. Biochemistry. 27:7711-7722.
41. Riter, R. E., P. E. Reu, and N. E. Levinger. 1998. Impact of counterions on water motion in aerosol reverse micelles. J. Am. Chem. Soc. 120:6062-6067.
42. Rochel, S., E. Nachliel, D. Huppert, and M. Gutman. 1990. Proton dissociation dynamics in the aqueous layer of multilamellar phospholipid vesicles. J. Membr. Biol. 118:225-232.
43. Samartzidou, H., and A. Delcour. 1999. Distinct sensitivities of Ompf and PhoE porins to charged modulators. FEBS Lett. 444:65-70.
44. Sandberg, L., and O. Edholm. 1997. Pk-A calculations along a bacteriorhodopsin molecular dynamics trajectory. Biophys. Chem. 65:189-204.
45. Schirmer, T., and P. Phale. 1999. Brownian dynamics simulation of ion flow through porin channels. J. Mol. Biol. 294:1159-1167.
46. Shimoni, E., Y. Tsfadia, E. Nachliel, and M. Gutman. 1993. Gaugement of the inner space of the apomyoglobin's heme binding site by a single free diffusing proton. I. Proton in the cavity. Biophys. J. 64:472-479.
47. Sitkoff, D., N. Ben-Tal, and B. Honig. 1996. Calculation of alkane to water solvation free energies using continuum solvent model. J. Phys. Chem 100:2744-2752.
48. Sitkoff, D., D. Lockhart, K. Sharp, and B. Honig. 1994. Calculation of electrostatic effects at the amino-terminus of an alpha-helix. Biophys. J. 67:2251-2260.
49. Smart, O., J. Breed, G. Smith, and M. Sansom. 1997. A novel method for structure-based prediction of ion channels. Biophys. J. 72:1109-1126.
50. Struyve, M., J. Visser, H. Adriaanse, R. Benz, and J. Tommassen. 1993. Topology of PhoE porin: The "eyelet" region. Mol. Microbiol. 7:131-140.
51. Sutcliffe, J., R. Blumenthal, A. Walter, and J. Foulds. 1983. Escherichia coli outer membrane protein K is a porin. J. Bacteriol. 156:867-872.
52. Szabo, A., R. Zwanzig, and N. Agmon. 1988. Diffusion-controlled reactions with mobile traps. Phys. Rev. Lett. 61:2496-2499.
53. Tieleman, D., and H. Berendsen. 1998. A molecular dynamics study of the pores formed by Escherichia coli. Biophys J. 74:2786-2801.
54. Vangelder, P., M. Steiert, M. Elkhattabi, J. Rosenbusch, and J. Tommassen. 1996. Structural and functional characterization of a His-tagged PhoE pore protein of Escherichia coli. Biochem. Biophys. Res. Commun. 229:869-875.
55. Watanabe, M., J. Rosenbusch, T. Schirmer, and M. Karplus. 1997. Computer simulations of the Ompf porin from the outer membrane of Escherichia coli. Biophys. J. 72:2094-2102.