Microscopic mechanism of antibiotics translocation through a porin

Biophysical Journal

Volumn 87, Issue 1, 2004, Pages 58-64

  Ceccarelli, Matteo ^a,d   Danelon, Christophe ^b,c   Laio, Alessandro ^a   Parrinello, Michele ^a  

^a ETH ZURICH   (Switzerland)

^b INSTITUT DE PHARMACOLOGIE ET DE BIOLOGIE STRUCTURALE   (France)

^c EPFL   (Switzerland)

^d UNIVERSITY OF CAGLIARI   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMPICILLIN; ANTIBIOTIC AGENT; ARGININE; ASPARTIC ACID; BETA LACTAM ANTIBIOTIC; GLUTAMIC ACID; LYSINE; OUTER MEMBRANE PROTEIN F; PORIN; TYROSINE;

ALGORITHM; ARTICLE; BACTERIAL OUTER MEMBRANE; COMPUTER SIMULATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG TRANSPORT; ESCHERICHIA COLI; MOLECULAR DYNAMICS; NONHUMAN; STEREOCHEMISTRY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 3042772813     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.103.037283     Document Type: Article

References (27)

1. Ceccarelli, M., and M. Marchi. 2003. Simulation and modeling of the rhodobacter sphaeroides bacterial reaction center: structure and interactions. J. Phys. Chem. B. 107:1423-1431.
2. Ceccarelli, M., P. Procacci, and M. Marchi. 2003. An ab initio force field for the cofactors of bacterial photosynthesis. J. Comput. Chem. 24:129-142.
3. Cornell, W. D., P. Cieplak, C. I. Bavly, I. R. Gould, K. M. Merz, Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. Kollmann. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-5197.
4. 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.
5. de Groot, B. L., and H. Grubmüller. 2001. Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and glpf. Science. 294:2353-2357.
6. Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103:8577-8593,
7. Grubmüller, H. 1995. Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys, Rev. E. 52:2893-2906,
8. Iannuzzi, M., A. Laio, and M. Parrinello. 2003. Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Phys. Rev. Lett, 90:238302.
9. Im, W., and B. Roux. 2002. Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KC1 aqueous salt solution. J. Mol. Biol. 319:1177-1197.
10. Isralewitz, B., M. Gao, and K. Schulten. 2001. Steered molecular dynamics and mechanical functions of proteins. Curr. Opin. Struct. Biol. 11:224-230.
11. Jeanteur, D., T. Schirmer, D. Fourel, V. Simonet, G. Rummel, C. Widmer, J. P. Rosenbusch, F. Pattus, and J. M. Pages. 1994. Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli. Proc. Natl. Acad. Sci. USA. 91:10675-10679.
12. Jensen, M. O., E. Tajkhorshid, S. Park, and K. Schulten. 2002. Energetics of glycerol conduction through aquaglyceroporin glpf. Proc. Natl. Acad. Sci. USA. 99:6731-6736.
13. Laio, A., and M. Parrinello. 2002. Escaping free-energy minima. Proc. Natl. Acad. Sci. USA. 20:12562-12566.
14. Marchi, M., and P. Procacci. 1999. Coordinates scaling and multiple time step algorithms for simulation of solvated proteins in the NPT ensemble. J. Chem. Phys. 109:5194-5202.
15. Micheletti, C., A. Laio, and M. Parrinello. 2003. Reconstructing the density of states by history-dependent metadynamics. Phys. Rev. Lett. 92:170601.
16. Nestorovich, E. M., C. Danelon, M. Winterhalter, and S. M. Bezrukov. 2002. Designed to penetrate: time-resolved interaction of single antibiotic molecules with bacterial pores. Proc. Natl. Acad. Sci. USA. 99:9789-9794.
17. Nikaido, H. 1989. Outer membrane barrier as a mechanism of antimicrobial resistance. Antimicrob. Agents Chemoter. 33:1831-1836.
18. Phale, P. S., A. Philippsen, 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.
19. Procacci, P., E. Paci, T. Darden, and M. Marchi. 1997. Orac: a molecular dynamics program to simulate complex molecular systems with realistic electrostatic interactions. J. Comput. Chem. 18:1848-1862.
20. Robertson, K. M., and D. P. Tieleman. 2002. Orientation and interactions of dipolar molecules during transport through OmpF porin. FEBS Lett. 528:53-57.
21. Roth, M., A. Lewit-Bentley, H. Michel, J. Deisenhofer, R. Huber, and D. Oesterhelt. 1989. Detergent structure in crystals of a bacterial photosynthetic reaction centre. Science. 340:659-662.
22. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
23. Simonet, V., M. Mallea, and J. M. Pages. 2000. Substitutions in the eyelet region disrupt cefepime diffusion through the Escherichia coli OmpF channel. Antimicrob. Agents Chemother. 44:311-315.
24. 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. 18:39-47.
25. Tajkhorshid, E., P. Nollert, M. O. Jensen, L. J. W. Miercke, J. O'Connell, R. M. Stroud, and K. Schulten. 2002. Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science. 296:525-530.
26. Tuckerman, M. E., B. Berne, and G. Martyna. 1992. Reversible multiple time scale molecular dynamics. J. Chem. Phys, 97:1990-2001.
27. 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.