Molecular basis of voltage gating of OmpF porin

Biochemistry and Cell Biology

Volumn 80, Issue 5, 2002, Pages 517-523

  Robertson, Kindal M ^a   Tieleman, D Peter ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

haemolysin; barrels; E. coli; Eyelet region; Porins

Indexed keywords

BIOLOGICAL MEMBRANES; COMPUTER SIMULATION; ESCHERICHIA COLI; PROTEINS;

VOLTAGE GATING;

MOLECULAR BIOLOGY;

PORIN;

ARTICLE; BACTERIAL OUTER MEMBRANE; CALCULATION; CHANNEL GATING; COMPUTER SIMULATION; ELECTRIC POTENTIAL; ESCHERICHIA COLI; GRAM NEGATIVE BACTERIUM; IN VITRO STUDY; MOLECULAR BIOLOGY; NONHUMAN; OUTER MEMBRANE; PASSIVE TRANSPORT; SEQUENCE HOMOLOGY; THEORETICAL STUDY;

ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; ION CHANNEL GATING; PORINS; PROTEIN CONFORMATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0036968478     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o02-145     Document Type: Article

References (45)

1. Arbing, M.A., Hanrahan, J.W., and Coulton, J.W. 2001. Mutagenesis identifies amino acid residues in extracellular loops and within the barrel lumen that determine voltage gating of porin from Haemophilus influenzae type B. Biochemistry, 40: 14 621 - 14 628.
2. Bainbridge, G., Gokce, I., and Lakey, J.H. 1998a. Voltage gating is a fundamental feature of porin and toxin beta-barrel membrane channels. FEBS Lett. 431: 305-308.
3. Bainbridge, G., Mobasheri, H., Armstrong, G.A., Lea, E.J., and Lakey, J.H. 1998b. Voltage-gating of Escherichia coli porin: a cystine-scanning mutagenesis study of loop 3. J. Mol. Biol. 275: 171-176.
4. Bayley, H. 1999. Designed membrane channels and pores. Curr. Opin. Biotechnol. 10: 94-103.
5. Berendsen, H.J.C., Postma, J.P.M., DiNola, A., and J.R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81: 3684-3690.
6. Berendsen, H.J.C., van der Spoel, D., and van Drunen, R. 1995. GROMACS: A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 91: 43-56.
7. Berrier, C., Coulombe, A., Houssin, C., and Ghazi, A. 1992. Fast and slow kinetics of porin channels from Escherichia coli reconstituted into giant liposomes and studied by patch-clamp. FEBS Lett. 306: 251-256.
8. Bjorksten, J., Soares, C.M., Nilsson, O., and Tapia, O. 1994. On the stability and plastic properties of the interior L3 loop in R. capsulatus porin. A molecular dynamics study. Protein Eng. 7: 487-493.
9. Bredin, J., Saint, N., Mallea, M., Emanuelle, D.E., Molle, G., Pages, J.M., and Simonet, V. 2002. Alteration of pore properties of Escherichia coli OmpF induced by mutation of key residues in anti-loop 3 region. Biochem. J. 363: 521-528.
10. Cowan, S.W., Schirmer, T., Rummel, G., Steiert, M., Ghosh, R., Pauptit, R.A., Jansonius, J.N., and Rosenbusch, J.P. 1992. Crystal structures explain functional properties of two E. coli porins. Nature (London), 358: 727-733.
11. Darden, T., York, D., and Pedersen, L. 1993. Particle mesh Ewald: an N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10 089 - 10 092.
12. Delcour, A.H. 1997. Function and modulation of bacterial porins: insights from electrophysiology. FEMS Microbiol. Lett. 151: 115-123.
13. Dutzler, R., Rummel, G., Alberti, S., Hernandez-Alles, S., Phale, P., Rosenbusch, J., Benedi, V., and Schirmer, T. 1999. Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae. Struct. Fold. Des. 7: 425-434.
14. Eppens, E.F., Saint, N., Van Gelder, P., van Boxtel, R., and Tommassen, J. 1997. Role of the constriction loop in the gating of outer membrane porin PhoE of Escherichia coli. FEBS Lett. 415: 317-320.
15. Faraldo-Gomez, J.D., Smith, G.R., and Sansom, M.S.P. 2002. Setting up and optimization of membrane protein simulations. Eur. Biophys. J. 31: 217-227.
16. Hille, B. 2002. Ionic channels of excitable membranes. 3rd ed. Sinauer Associates Inc., Sunderland, Mass.
17. Hirsch, A., Breed, J., Saxena, K., Richter, O.M., Ludwig, B., Diederichs, K., and Welte, W. 1997. The structure of porin from Paracoccus denitrificans at 3.1 Å resolution. FEBS Lett. 404: 208-210.
18. Im, W., Seefeld, S., and Roux, B. 2000. A grand canonical Monte Carlo - Brownian dynamics algorithm for simulating ion channels. Biophys. J. 79: 788-801.
19. Jeanteur, D., Schirmer, T., Fourel, D., Simonet, V., Rummel, G., Widmer, C., Rosenbusch, J.P., Pattus, F., and Pages, J.M. 1994. Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 91: 10 675 - 10 679.
20. Karshikoff, A., Spassov, V., Cowan, S.W., Ladenstein, R., and Schirmer, T. 1994. Electrostatic properties of two porin channels from Escherichia coli. J. Mol. Biol. 240: 372-384.
21. Koebnik, R., Locher, K.P., and Van Gelder, P. 2000. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol. Microbiol. 37: 239-253.
22. Kreusch, A., Neubuser, A., Schiltz, E., Weckesser, J., and Schulz, G.E. 1994. Structure of the membrane channel porin from Rhodopseudomonas blastica at 2.0 Å resolution. Protein Sci. 3: 58-63.
23. Kuyucak, S., Andersen, O.S., and Chung, S.-H. 2001. Models of permeation in ion channels. Rep. Prog. Phys. 64: 1427-1472.
24. Lou, K., Saint, N., Prilipov, A., Rummel, G., Benson, S.A., Rosenbusch, J.P., and Schirmer, T. 1996. Structural and functional characterization of OmpF porin mutants selected for larger pore size. J. Biol. Chem. 271: 20 669 - 20 675.
25. Lindahl, E., Hess, B., van der Spoel, D. 2001. GROMACS 3.0: a package for molecular stimulation and trajectory analysis. J. Mol. Model. 7 (8): 306-317.
26. Muller, D.J., and Engel, A. 1999. Voltage and pH-induced channel closure of porin OmpF visualized by atomic force microscopy. J. Mol. Biol. 285: 1347-1351.
27. Nikaido, H. 1994. Porins and specific diffusion channels in bacterial outer membranes. J. Biol. Chem. 269: 3905-3908.
28. Phale, P.S., Schirmer, T., Prilipov, A., Lou, K.L., Hardmeyer, A., and Rosenbusch, J.P. 1997. Voltage gating of Escherichia coli porin channels: role of the constriction loop. Proc. Natl. Acad. Sci. U.S.A. 94: 6741-6745.
29. Phale, P.S., Philippsen, A., Widmer, C., Phale, V.P., Rosenbusch, J.P., and Schirmer, T. 2001. Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation. Biochemistry, 40: 6319-6325.
30. Philippsen, A., Im, W., Engel, A., Schirmer, T., Roux, B., and Muller, D.J. 2002. Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. Biophys. J. 82: 1667-1676.
31. Robertson, K.M., and Tieleman, D.P. 2002. Orientation and interactions of dipolar molecules during transport through OmpF porin. FEBS Lett. In press.
32. Roux, B. 2002. Theoretical and computational models of ion channels. Curr. Opin. Struct. Biol. 12: 182-189.
33. Saint, N., Lou, K.L., Widmer, C., Luckey, M., Schirmer, T., and Rosenbusch, J.P. 1996. Structural and functional characterization of OmpF porin mutants selected for larger pore size. II. Functional characterization. J. Biol. Chem. 271: 20 676 - 20 680.
34. Samartzidou, H., and Delcour, A.H. 1998. E. coli PhoE porin has an opposite voltage-dependence to the homologous OmpF. EMBO J. 17: 93-100.
35. Schirmer, T. 1998. General and specific porins from bacterial outer membranes. J. Struct. Biol. 121: 101-109.
36. Schirmer, T., and Phale, P.S. 1999. Brownian dynamics simulation of ion flow through porin channels. J. Mol. Biol. 294: 1159-1167.
37. Schirmer, T., Keller, T.A., Wang, Y.F., and Rosenbusch, J.P. 1995. Structural basis for sugar translocation through maltoporin channels at 3.1 Å resolution. Science (Washington, D.C.), 267: 512-514.
38. Schulz, G.E. 1996. Porins: general to specific, native to engineered passive pores. Curr. Opin. Struct. Biol. 6: 485-490.
39. Soares, C.M., Bjorksten, J., and Tapia, O. 1995. L3 loop-mediated mechanisms of pore closing in porin: a molecular dynamics perturbation approach. Protein Eng. 8: 5-12.
40. Tieleman, D.P., and Berendsen, H.J. 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.
41. Tieleman, D.P., Biggin, P.C., Smith, G.R., and Sansom, M.S. 2001. Simulation approaches to ion channel structure-function relationships. Q. Rev. Biophys. 34: 473-561.
42. Todt, J.C., Rocque, W.J., and McGroarty, E.J. 1992. Effects of pH on bacterial porin function. Biochemistry, 31: 10 471 - 10 478.
43. Van Gelder, P., Saint, N., Phale, P., Eppens, E.F., Prilipov, A., van Boxtel, R., Rosenbusch, J.P., and Tommassen, J. 1997. Voltage sensing in the PhoE and OmpF outer membrane porins of Escherichia coli: role of charged residues. J. Mol. Biol. 269: 468-472.
44. Watanabe, M., Rosenbusch, J., Schirmer, T., and Karplus, M. 1997. Computer simulations of the OmpF porin from the outer membrane of Escherichia coli. Biophys. J. 72: 2094-2102.
45. Weiss, M.S., and Schulz, G.E. 1992. Structure of porin refined at 1.8 Å resolution. J. Mol. Biol. 227: 493-509.