Multistep mechanism of chloride translocation in a strongly anion-selective porin channel

Biophysical Journal

Volumn 85, Issue 2, 2003, Pages 954-962

  Zachariae, Ulrich ^a   Helms, Volkhard ^b   Engelhardt, Harald ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b MAX PLANCK INSTITUTE OF BIOPHYSICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANION; ARGININE; CHLORIDE ION; PORIN; PROTEIN OMP32; UNCLASSIFIED DRUG;

ARTICLE; ATOM; BINDING AFFINITY; BINDING SITE; CHANNEL GATING; CHLORIDE TRANSPORT; CONDUCTANCE; DELFTIA ACIDOVORANS; ENERGY; GRAM NEGATIVE BACTERIUM; IMMOBILIZATION; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN INTERACTION; SIMULATION;

BACTERIA (MICROORGANISMS); DELFTIA; DELFTIA ACIDOVORANS; NEGIBACTERIA;

EID: 0041343084     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)74534-2     Document Type: Article

References (35)

1. Benz, R., K. Janko, W. Boos, and P. Läuger. 1978. Formation of large, ion-permeable membrane channels by the matrix protein (porin) of Escherichia coli. Biochim. Biophys. Acta. 511:305-319.
2. Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
3. + channel. Nature. 414:73-77.
4. Bofill, L., M. Wessolossky, E. Vicent, M. Salas, J. Besso, A. Merentes, R. Istúriz, M. Guzmán, and J. Murillo. 1996. Septic shock due to Comamonas acidovorans: a most unusual association. Infect. Dis. Clin. Pract. 5:73-74.
5. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem. 4:187-217.
6. Cowan, S. W., T. Schirmer, G. Rummel, M. Steiert, R. Ghosh, R. A. Pauptit, J. N. Jansonius, and J. P. Rosenbusch. 1992. Crystal structures explain functional properties of two E. coli porins. Nature. 358:727-733.
7. Dieckmann, G. R., J. D. Lear, Q. Zhong, M. L. Klein, W. F. DeGrado, and K. A. Sharp. 1999. Exploration of the structural features defining the conduction properties of a synthetic ion channel. Biophys. J. 76:618-630.
8. Dutzler, R., E. B. Campbell, M. Cadene, B. T. Chait, and R. MacKinnon. 2002. X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity. Nature. 415:287-294.
9. Grubmüller, H., B. Heymann, and P. Tavan. 1996. Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science. 271:997-999.
10. 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.
11. Im, W., and B. Roux. 2002a. 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.
12. Im, W., and B. Roux. 2002b. Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. J. Mol. Biol. 319:1177-1197.
13. Jap, B. K., and P. J. Walian. 1996. Structure and functional mechanism of porins. Physiol. Rev. 76:1073-1088.
14. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
15. Karplus, M., and J. A. McCammon. 2002. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:646-652.
16. Koebnik, R., K. P. Locher, and P. van Gelder. 2000. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol. Microbiol. 37:239-253.
17. MacKerell, Jr., A. D., D. Bashford, M. Bellott, R. L. Dunbrack Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
18. Mathes, A., and H. Engelhardt. 1998. Nonlinear and asymmetric open channel characteristics of an ion-selective porin in planar membranes. Biophys. J. 75:1255-1262.
19. + selectivity filter. Nature. 414:37-42.
20. Ohtaki, H., and T. Radnai. 1993. Structure and dynamics of hydrated ions. Chem. Rev. 93:1157-1204.
21. Phale, P. S., A. Phillipsen, C. Widmer, V. P. Phale, J. P. Rosenbusch, and T. Schirmer. 2001. Role of charged residues at the OmpF porin channel constriction probed by mutagenesis and simulation. Biochemistry. 40:6319-6325.
22. Przybylski, M., M. O. Glocker, U. Nestel, V. Schnaible, M. Bluggel, K. Diederichs, J. Weckesser, M. Schad, A. Schmid, W. Welte, and R. Benz. 1996. X-ray crystallographic and mass spectrometric structure determination and functional characterization of succinylated porin from Rhodobacter capsulatus: implications for ion selectivity and single-channel conductance. Protein Sci. 5:1477-1489.
23. Robertson, K. M., and D. P. Tieleman. 2002. Orientation and interactions of dipolar molecules during transport through OmpF porin. FEBS Lett. 528:53-57.
24. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of Cartesian equations of motion of a system with constraints - molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341.
25. Schirmer, T. 1998. General and specific porins from bacterial outer membranes. J. Struct. Biol. 121:101-109.
26. Schirmer, T., and P. S. Phale. 1999. Brownian dynamics simulation of ion flow through porin channels. J. Mol. Biol. 294:1159-1167.
27. Schulz, G. E. 1996. Porins: general to specific, native to engineered passive pores. Curr. Opin. Struct. Biol. 6:485-490.
28. Sen, K., J. Hellman, and H. Nikaido. 1988. Porin channels in intact cells of Escherichia coli are not affected by Donnan potentials across the outer membrane. J. Biol. Chem. 263:1182-1187.
29. Suenaga, A., Y. Komeiji, M. Uebayasi, T. Meguro, M. Saito, and L. Yamato. 1998. Computational observation of an ion permeation through a channel protein. Biosci. Rep. 18:39-48.
30. 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 palmitoyloleoyl-phosphatidylcholine bilayer. Biophys. J. 74:2786-2801.
31. 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.
32. Torrie, G. M., and J. P. Valleau. 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comp. Phys. 23:187-199.
33. Willems, A., P. de Vos, and J. de Ley. 1992. The genus Comamonas. In The Prokaryotes, Vol. III. A. Balows, H. G. Trüper, M. Dworkin, W. Harder, and K. H. Schleifer, editors. Springer-Verlag, New York, NY. pp.2583-2590.
34. Zachariae, U., A. Koumanov, H. Engelhardt, and A. Karshikoff. 2002. Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins. Protein Sci. 11:1309-1319.
35. Zeth, K., K. Diederichs, W. Welte, and H. Engelhardt. 2000. Crystal structure of Omp32, the anion-selective porin from Comamonas acidovorans, in complex with a periplasmic peptide at 2.1 Å resolution. Structure. 8:981-992.