Translocation and interactions of l-arabinose in OmpF porin: A molecular dynamics study

Biochemical and Biophysical Research Communications

Volumn 352, Issue 1, 2007, Pages 104-110

  Malek, Kourosh ^a,b   Maghari, Ali ^a  

^a UNIVERSITY OF TEHRAN   (Iran)

^b EINDHOVEN UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

Arabinose; Chiral translocation; Diffusion; Molecular dynamics; OmpF

Indexed keywords

ARABINOSE; OUTER MEMBRANE PROTEIN F;

ARTICLE; CHIRALITY; CHROMATOGRAPHY; ESCHERICHIA COLI; MOLECULAR DYNAMICS; MOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TRANSPORT;

ARABINOSE; COMPUTER SIMULATION; ESCHERICHIA COLI; MODELS, MOLECULAR; PORINS; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN TRANSPORT;

ESCHERICHIA COLI;

EID: 33751398214     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.10.183     Document Type: Article

References (25)

1. Schulz G.E. Porins: General to specific, native to engineered passive pores. Curr. Opin. Struct. Biol. 6 (1996) 485-490
2. Nikaido H. Porins and specific diffusion channels in bacterial outer membranes. J. Biol. Chem. 269 (1994) 3905-3908
3. Cowan S.W., Schirmer T., Rummel G., Steiert M., Ghosh R., Pauptit R.A., Jansonius J.N., and Rosenbusch J.P. Crystal-structures explain functional-properties of 2 Escherichia-coli porins. Nature 358 (1992) 727-733
4. Cowan S.W. Bacterial porins: Lessons from 3 high-resolution structures. Curr. Opin. Struct. Biol. 3 (1993) 501-507
5. Tieleman D.P., Biggin P.C., Smith G.R., and Sansom M.S. Simulation approaches to ion channel structure-function relationships. Q. Rev. Biophys. 34 (2001) 473-561
6. Im W., Seefeld S., and Roux B. A grand canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. Biophys. J. 79 (2000) 788-801
7. Schirmer T. General and specific porins from bacterial outer membranes. J. Struct. Biol. 121 (1998) 101-109
8. Varma S., and Jakobsson E. Ionization states of residues in OmpF and mutants: Effects of dielectric constant and interactions between residues. Biophys. J. 86 (2004) 690-704
9. Tieleman D.P., and Berendsen H.J.C. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. Biophys. J. 74 (1998) 2786-2801
10. Nestorovich E.M., Rostovtseva T.K., and Bezrukov S.M. Residue ionization and ion transport through OmpF channels. Biophys. J. 85 (2003) 3718-3729
11. Robertson K.M., and Tieleman D.P. Orientation and interactions of dipolar molecules during transport through OmpF porin. FEBS Lett. 528 (2002) 53-57
12. Ceccarelli M., Danelon C., Laio A., and Parrinello M. Microscopic mechanism of antibiotics translocation through a porin. Biophys. J. 87 (2004) 58-64
13. Dwyer D.S. Model of the 3-D structure of the GLUT3 glucose transporter and molecular dynamics simulation of glucose transport. Protein: Structure, Function and Genetics 42 (2001) 531-541
14. Sugawara E., and Nikaido H. OmpA protein of Escherichia-coli outer membrane occurs in open and closed channel forms. J. Biol. Chem. 269 (1994) 17981-17987
15. Tieleman D.P., MacCallum J.L., Ash W.L., Kandt C., Xu Z., and Monticelli L. Membrane protein simulations with a united-atom lipid and all-atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. J. Phys: Condens. Matter 18 (2006) S1221-S1234
16. Im W., and Roux B. 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 (2002) 1177-1197
17. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., and Hermans J. Intermolecular Forces (1981), Reidel, Dordrecht
18. van Gunsteren W.F., and Berendsen J.C. Computer-simulation of molecular dynamics methodology, applications and perspectives in chemistry. Angew. Chem. Int. Edn Engl. 29 (1990) 992-1023
19. Lindahl E., Hess B., and van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 (2001) 306-317
20. Berendsen H.J.C., van der Spoel D., and van Drunen R. GROMACS-A message-passing parallel molecular dynamics implementation. Comp. Phys. Comm. 91 (1995) 43-56
21. Humphrey W., Dalke A., and Schulten K. Visual molecular dynamics. J. Mol. Graph. 14 (1996) 33
22. Stewart J.J.P. Optimization of parameters for semiempirical methods 1: Method. J. Comp. Chem. 10 (1989) 209-220
23. J.R. Cheeseman, J.A. Montgomery Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G.A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Strat-mann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Cliord, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A. Pople, Gaussian 03, ReVision B01, Gaussian, Inc., Wallingford, CT, 2004.
24. Smart O.S., Neduvelil J.G., Wang X., Wallace B.A., and Sansom M.S.P. A program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14 (1996) 354
25. Sundaresan V., and Abrol R. Biological chiral recognition: The substrate's perspective. Chirality 17 (2005) S30-S39