Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii

Structure

Volumn 24, Issue 2, 2016, Pages 221-231

  Zahn, Michael ^a   Bhamidimarri, Satya Prathyusha ^b   Baslé, Arnaud ^a   Winterhalter, Mathias ^b   Van Den Berg, Bert ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

^b JACOBS UNIVERSITY BREMEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMPICILLIN; ARGININE; BENZOIC ACID; FOSFOMYCIN; GLUCOSE; GLUTAMIC ACID; GLUTAMINE; GLYCINE; IMIPENEM; LIPOSOME; MALTOSE; MEROPENEM; PHENYLALANINE; PUTRESCINE; TRYPTOPHAN; OUTER MEMBRANE PROTEIN;

ACINETOBACTER BAUMANNII; ARTICLE; BACTERIAL OUTER MEMBRANE; BACTERIAL STRAIN; CRYSTAL STRUCTURE; HISTOGRAM; MEMBRANE PERMEABILITY; NONHUMAN; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; X RAY CRYSTALLOGRAPHY; CHEMISTRY; ENZYME SPECIFICITY; METABOLISM; MOLECULAR MODEL; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE;

ACINETOBACTER BAUMANNII; BACTERIAL OUTER MEMBRANE PROTEINS; CRYSTALLOGRAPHY, X-RAY; LIPOSOMES; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SUBSTRATE SPECIFICITY;

EID: 84955517726     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2015.12.009     Document Type: Article

References (49)

1. I. Abbott, G.M. Cerqueira, S. Bhuiyan, and A.Y. Peleg Carbapenem resistance in Acinetobacter baumannii: laboratory challenges, mechanistic insights and therapeutic strategies Expert Rev. Anti Infect. Ther. 11 2013 395 409
2. S. Acosta-Gutierrez, M.A. Scorciapino, I. Bodrenko, and M. Ceccarelli Filtering with electric field: the case of E. coli porins J. Phys. Chem. Lett. 6 2015 1807 1812
3. R. Benz, G. Francis, T. Nakae, and T. Ferenci Investigation of the selectivity of maltoporin channels using mutant LamB proteins: mutations changing the maltodextrin binding site Biochim. Biophys. Acta 1104 1992 299 307
4. S. Biswas, M.M. Mohammad, D.R. Patel, L. Movileanu, and B. van den Berg Structural insight into OprD substrate specificity Nat. Struct. Mol. Biol. 14 2007 1108 1109
5. M.P. Cabral, N.C. Soares, J. Aranda, J.R. Parreira, C. Rumbo, M. Poza, J. Valle, V. Calamia, I. Lasa, and G. Bou Proteomic and functional analyses reveal a unique lifestyle for Acinetobacter baumannii biofilms and a key role for histidine metabolism J. Proteome Res. 10 2011 3399 3417
6. M. Catel-Ferreira, R. Nehme, V. Molle, J. Aranda, E. Bouffartigues, S. Chevalier, G. Bou, T. Jouenne, and E. De Deciphering the function of the outer membrane protein OprD homologue of Acinetobacter baumannii Antimicrob. Agents Chemother. 56 2012 3826 3832
7. V.B. Chen, W.B. Arendall 3rd, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. D Biol. Crystallogr. 66 2010 12 21
8. T.J. Clark, C. Momany, and E.L. Neidle The benPK operon, proposed to play a role in transport, is part of a regulon for benzoate catabolism in Acinetobacter sp. strain ADP1 Microbiology 148 2002 1213 1223
9. C. Danelon, A. Suenaga, M. Winterhalter, and I. Yamato Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation Biophys. Chem. 104 2003 591 603
10. M. Dupont, J.M. Pages, D. Lafitte, A. Siroy, and C. Bollet Identification of an OprD homologue in Acinetobacter baumannii J. Proteome Res. 4 2005 2386 2390
11. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132
12. E. Eren, J. Vijayaraghavan, J. Liu, B.R. Cheneke, D.S. Touw, B.W. Lepore, M. Indic, L. Movileanu, and B. van den Berg Substrate specificity within a family of outer membrane carboxylate channels PLoS Biol. 10 2012 e1001242
13. J.S. Esterly, C.L. Richardson, N.S. Eltoukhy, C. Qi, and M.H. Scheetz Genetic mechanisms of antimicrobial resistance of Acinetobacter baumannii Ann. Pharmacother. 45 2011 218 228
14. F. Fernandez-Cuenca, Y. Smani, M.C. Gomez-Sanchez, F. Docobo-Perez, F.J. Caballero-Moyano, J. Dominguez-Herrera, A. Pascual, and J. Pachon Attenuated virulence of a slow-growing pandrug-resistant Acinetobacter baumannii is associated with decreased expression of genes encoding the porins CarO and OprD-like Int. J. Antimicrob. Agents 38 2011 548 549
15. L.M. Guzman, D. Belin, M.J. Carson, and J. Beckwith Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter J. Bacteriol. 177 1995 4121 4130
16. R.E. Hancock Resistance mechanisms in Pseudomonas aeruginosa and other nonfermentative gram-negative bacteria Clin. Infect. Dis. 27 Suppl 1 1998 S93 S99
17. R.E.W. Hancock, and A.M. Carey Protein-D1 - a glucose-inducible, pore-forming protein from the outer-membrane of Pseudomonas aeruginosa FEMS Microbiol. Lett. 8 1980 105 109
18. R.E. Hancock, C. Egli, R. Benz, and R.J. Siehnel Overexpression in Escherichia coli and functional analysis of a novel PPi-selective porin, oprO, from Pseudomonas aeruginosa J. Bacteriol. 174 1992 471 476
19. L. Holm, and P. Rosenström Dali server: conservation mapping in 3D Nucleic Acids Res. 38 2010 W545 W549
20. V.M. Isabella, A.J. Campbell, J. Manchester, M. Sylvester, A.S. Nayar, K.E. Ferguson, R. Tommasi, and A.A. Miller Toward the rational design of carbapenem uptake in Pseudomonas aeruginosa Chem. Biol. 22 2015 535 547
21. S. Jo, M. Vargyas, J. Vasko-Szedlar, B. Roux, and W. Im PBEQ-Solver for online visualization of electrostatic potential of biomolecules Nucleic Acids Res. 36 2008 W270 W275
22. W. Kabsch XDS Acta Crystallogr. D Biol. Crystallogr. 66 2010 125 132
23. A. Kumar, E. Hajjar, P. Ruggerone, and M. Ceccarelli Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations J. Phys. Condens. Matter 22 2010 454125
24. R. Laskowski, M. MacArthur, D. Moss, and J. Thornton PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26 1993 283 291
25. P.D. Lister, D.J. Wolter, and N.D. Hanson Antibacterial-resistant Pseudomonas aeruginosa: clinical impact and complex regulation of chromosomally encoded resistance mechanisms Clin. Microbiol. Rev. 22 2009 582 610
26. J. Liu, A.J. Wolfe, E. Eren, J. Vijayaraghavan, M. Indic, B. van den Berg, and L. Movileanu Cation selectivity is a conserved feature in the OccD subfamily of Pseudomonas aeruginosa Biochim. Biophys. Acta 1818 2012 2908 2916
27. B. Lugtenberg, and L. Vanalphen Molecular architecture and functioning of the outer membrane of Escherichia coli and other gram-negative bacteria Biochim. Biophys. Acta 737 1983 51 115
28. K.R. Mahendran, P.R. Singh, J. Arning, S. Stolte, U. Kleinekathofer, and M. Winterhalter Permeation through nanochannels: revealing fast kinetics J. Phys. Condens. Matter 22 2010 454131
29. N. Modi, S. Ganguly, I. Barcena-Uribarri, R. Benz, B. van den Berg, and U. Kleinekathofer Structure, dynamics, and substrate specificity of the OprO porin from Pseudomonas aeruginosa Biophys. J. 109 2015 1429 1438
30. M. Montal, and P. Mueller Formation of bimolecular membranes from lipid monolayers and a study of their electrical properties Proc. Natl. Acad. Sci. USA 69 1972 3561 3566
31. T.F. Moraes, M. Bains, R.E. Hancock, and N.C. Strynadka An arginine ladder in OprP mediates phosphate-specific transfer across the outer membrane Nat. Struct. Mol. Biol. 14 2007 85 87
32. R. Mosca, and T.R. Schneider RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes Nucleic Acids Res. 36 2008 W42 W46
33. G.N. Murshudov, P. Skubak, A.A. Lebedev, N.S. Pannu, R.A. Steiner, R.A. Nicholls, M.D. Winn, F. Long, and A.A. Vagin REFMAC5 for the refinement of macromolecular crystal structures Acta Crystallogr. D Biol. Crystallogr. 67 2011 355 367
34. M.A. Mussi, A.S. Limansky, and A.M. Viale Acquisition of resistance to carbapenems in multidrug-resistant clinical strains of Acinetobacter baumannii: natural insertional inactivation of a gene encoding a member of a novel family of beta-barrel outer membrane proteins Antimicrob. Agents Chemother. 49 2005 1432 1440
35. E.M. Nestorovich, C. Danelon, M. Winterhalter, and S.M. Bezrukov Designed to penetrate: time-resolved interaction of single antibiotic molecules with bacterial pores Proc. Natl. Acad. Sci. USA 99 2002 9789 9794
36. H. Nikaido, and E.Y. Rosenberg Porin channels in Escherichia coli: studies with liposomes reconstituted from purified proteins J. Bacteriol. 153 1983 241 252
37. J.M. Pages, C.E. James, and M. Winterhalter The porin and the permeating antibiotic: a selective diffusion barrier in Gram-negative bacteria Nat. Rev. Microbiol. 6 2008 893 903
38. X. Robert, and P. Gouet Deciphering key features in protein structures with the new ENDscript server Nucleic Acids Res. 42 2014 W320 W324
39. G.E. Schulz The structure of bacterial outer membrane proteins Biochim. Biophys. Acta 1565 2002 308 317
40. A. Segura, P.V. Bunz, D.A. D'Argenio, and L.N. Ornston Genetic analysis of a chromosomal region containing vanA and vanB, genes required for conversion of either ferulate or vanillate to protocatechuate in Acinetobacter J. Bacteriol. 181 1999 3494 3504
41. Y. Smani, and J. Pachon Loss of the OprD homologue protein in Acinetobacter baumannii: impact on carbapenem susceptibility Antimicrob. Agents Chemother. 57 2013 677
42. O.S. Smart, J.G. Neduvelil, X. Wang, B.A. Wallace, and M.S. Sansom HOLE: a program for the analysis of the pore dimensions of ion channel structural models J. Mol. Graph. 14 1996 354 360 376
43. M.A. Smith, V.B. Weaver, D.M. Young, and L.N. Ornston Genes for chlorogenate and hydroxycinnamate catabolism (hca) are linked to functionally related genes in the dca-pca-qui-pob-hca chromosomal cluster of Acinetobacter sp. strain ADP1 Appl. Environ. Microbiol. 69 2003 524 532
44. E. Sugawara, and H. Nikaido OmpA is the principal nonspecific slow porin of Acinetobacter baumannii J. Bacteriol. 194 2012 4089 4096
45. S. Tamber, M.M. Ochs, and R.E. Hancock Role of the novel OprD family of porins in nutrient uptake in Pseudomonas aeruginosa J. Bacteriol. 188 2006 45 54
46. A. Vagin, and A. Teplyakov Molecular replacement with MOLREP Acta Crystallogr. D Biol. Crystallogr. 66 2010 22 25
47. B. Van den Berg, W.M. Clemons Jr., I. Collinson, Y. Modis, E. Hartmann, S.C. Harrison, and T.A. Rapoport X-ray structure of a protein-conducting channel Nature 427 2004 36 44
48. J. Vila, S. Marti, and J. Sanchez-Cespedes Porins, efflux pumps and multidrug resistance in Acinetobacter baumannii J. Antimicrob. Chemother. 59 2007 1210 1215
49. M. Zahn, T. D'Agostino, E. Eren, A. Basle, M. Ceccarelli, and B. van den Berg Small-molecule transport by CarO, an abundant eight-stranded beta-barrel outer membrane protein from Acinetobacter baumannii J. Mol. Biol. 427 2015 2329 2339