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. 2001 Aug;81(2):1037–1046. doi: 10.1016/S0006-3495(01)75761-X

Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa.

R D Lins 1, T P Straatsma 1
PMCID: PMC1301573  PMID: 11463645

Abstract

Lipopolysaccharides (LPSs) form the major constituent of the outer membrane of Gram-negative bacteria, and are believed to play a key role in processes that govern microbial metal binding, microbial adsorption to mineral surfaces, and microbe-mediated oxidation/reduction reactions at the bacterial exterior surface. A computational modeling capability is being developed for the study of geochemical reactions at the outer bacterial envelope of Gram-negative bacteria. A molecular model for the rough LPS of Pseudomonas aeruginosa has been designed based on experimentally determined structural information. An electrostatic model was developed based on Hartree-Fock SCF calculations of the complete LPS molecule to obtain partial atomic charges. The exterior of the bacterial membrane was assembled by replication of a single LPS molecule and a single phospholipid molecule. Molecular dynamics simulations of the rough LPS membrane of P. aeruginosa were carried out and trajectories were analyzed for the energetic and structural factors that determine the role of LPS in processes at the cell surface.

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Selected References

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  1. Amadei A., Linssen A. B., Berendsen H. J. Essential dynamics of proteins. Proteins. 1993 Dec;17(4):412–425. doi: 10.1002/prot.340170408. [DOI] [PubMed] [Google Scholar]
  2. Burrows L. L., Charter D. F., Lam J. S. Molecular characterization of the Pseudomonas aeruginosa serotype O5 (PAO1) B-band lipopolysaccharide gene cluster. Mol Microbiol. 1996 Nov;22(3):481–495. doi: 10.1046/j.1365-2958.1996.1351503.x. [DOI] [PubMed] [Google Scholar]
  3. Burrows L. L., Lam J. S. Effect of wzx (rfbX) mutations on A-band and B-band lipopolysaccharide biosynthesis in Pseudomonas aeruginosa O5. J Bacteriol. 1999 Feb;181(3):973–980. doi: 10.1128/jb.181.3.973-980.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. DeFlaun M. F., Oppenheimer S. R., Streger S., Condee C. W., Fletcher M. Alterations in adhesion, transport, and membrane characteristics in an adhesion-deficient pseudomonad. Appl Environ Microbiol. 1999 Feb;65(2):759–765. doi: 10.1128/aem.65.2.759-765.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Kastowsky M., Gutberlet T., Bradaczek H. Molecular modelling of the three-dimensional structure and conformational flexibility of bacterial lipopolysaccharide. J Bacteriol. 1992 Jul;174(14):4798–4806. doi: 10.1128/jb.174.14.4798-4806.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Knirel YuA, Vinogradov E. V., Kocharova N. A., Paramonov N. A., Kochetkov N. K., Dmitriev B. A., Stanislavsky E. S., Lányi B. The structure of O-specific polysaccharides and serological classification of Pseudomonas aeruginosa (a review). Acta Microbiol Hung. 1988;35(1):3–24. [PubMed] [Google Scholar]
  7. Lam J. S., Graham L. L., Lightfoot J., Dasgupta T., Beveridge T. J. Ultrastructural examination of the lipopolysaccharides of Pseudomonas aeruginosa strains and their isogenic rough mutants by freeze-substitution. J Bacteriol. 1992 Nov;174(22):7159–7167. doi: 10.1128/jb.174.22.7159-7167.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Langley S., Beveridge T. J. Effect of O-side-chain-lipopolysaccharide chemistry on metal binding. Appl Environ Microbiol. 1999 Feb;65(2):489–498. doi: 10.1128/aem.65.2.489-498.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lins R. D., Briggs J. M., Straatsma T. P., Carlson H. A., Greenwald J., Choe S., McCammon J. A. Molecular dynamics studies on the HIV-1 integrase catalytic domain. Biophys J. 1999 Jun;76(6):2999–3011. doi: 10.1016/s0006-3495(99)77453-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Lins R. D., Straatsma T. P., Briggs J. M. Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding. Biopolymers. 2000 Apr 5;53(4):308–315. doi: 10.1002/(SICI)1097-0282(20000405)53:4<308::AID-BIP3>3.0.CO;2-H. [DOI] [PubMed] [Google Scholar]
  11. Makin S. A., Beveridge T. J. The influence of A-band and B-band lipopolysaccharide on the surface characteristics and adhesion of Pseudomonas aeruginosa to surfaces. Microbiology. 1996 Feb;142(Pt 2):299–307. doi: 10.1099/13500872-142-2-299. [DOI] [PubMed] [Google Scholar]
  12. Manca M. C., Weintraub A., Widmalm G. Structural studies of the Escherichia coli O26 O-antigen polysaccharide. Carbohydr Res. 1996 Feb 7;281(1):155–160. doi: 10.1016/0008-6215(95)00333-9. [DOI] [PubMed] [Google Scholar]
  13. McIntosh T. J., Simon S. A. Area per molecule and distribution of water in fully hydrated dilauroylphosphatidylethanolamine bilayers. Biochemistry. 1986 Aug 26;25(17):4948–4952. doi: 10.1021/bi00365a034. [DOI] [PubMed] [Google Scholar]
  14. Pristovsek P., Kidric J. Solution structure of polymyxins B and E and effect of binding to lipopolysaccharide: an NMR and molecular modeling study. J Med Chem. 1999 Nov 4;42(22):4604–4613. doi: 10.1021/jm991031b. [DOI] [PubMed] [Google Scholar]
  15. Rivera M., McGroarty E. J. Analysis of a common-antigen lipopolysaccharide from Pseudomonas aeruginosa. J Bacteriol. 1989 Apr;171(4):2244–2248. doi: 10.1128/jb.171.4.2244-2248.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Sadovskaya I., Brisson J. R., Lam J. S., Richards J. C., Altman E. Structural elucidation of the lipopolysaccharide core regions of the wild-type strain PAO1 and O-chain-deficient mutant strains AK1401 and AK1012 from Pseudomonas aeruginosa serotype O5. Eur J Biochem. 1998 Aug 1;255(3):673–684. doi: 10.1046/j.1432-1327.1998.2550673.x. [DOI] [PubMed] [Google Scholar]
  17. Sadovskaya I., Brisson J. R., Thibault P., Richards J. C., Lam J. S., Altman E. Structural characterization of the outer core and the O-chain linkage region of lipopolysaccharide from Pseudomonas aeruginosa serotype O5. Eur J Biochem. 2000 Mar;267(6):1640–1650. doi: 10.1046/j.1432-1327.2000.01156.x. [DOI] [PubMed] [Google Scholar]
  18. Sengupta P., Bhattacharyya T., Shashkov A. S., Kochanowski H., Basu S. Structure of the O-specific side chain of the Escherichia coli O128 lipopolysaccharide. Carbohydr Res. 1995 Nov 22;277(2):283–290. doi: 10.1016/0008-6215(95)00215-f. [DOI] [PubMed] [Google Scholar]
  19. Seydel U., Eberstein W., Schröder G., Brandenburg K. Electrostatic potential barrier in asymmetric planar lipopolysaccharide/phospholipid bilayers probed with the valinomycin-K+ complex. Z Naturforsch C. 1992 Sep-Oct;47(9-10):757–761. doi: 10.1515/znc-1992-9-1020. [DOI] [PubMed] [Google Scholar]
  20. Snyder S., Kim D., McIntosh T. J. Lipopolysaccharide bilayer structure: effect of chemotype, core mutations, divalent cations, and temperature. Biochemistry. 1999 Aug 17;38(33):10758–10767. doi: 10.1021/bi990867d. [DOI] [PubMed] [Google Scholar]
  21. Wang Y., Hollingsworth R. I. An NMR spectroscopy and molecular mechanics study of the molecular basis for the supramolecular structure of lipopolysaccharides. Biochemistry. 1996 May 7;35(18):5647–5654. doi: 10.1021/bi950645p. [DOI] [PubMed] [Google Scholar]
  22. Weber W., Demirdjian H., Lins R. D., Briggs J. M., Ferreira R., McCammon J. A. Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain. J Biomol Struct Dyn. 1998 Dec;16(3):733–745. doi: 10.1080/07391102.1998.10508285. [DOI] [PubMed] [Google Scholar]
  23. Wiese A., Schröder G., Brandenburg K., Hirsch A., Welte W., Seydel U. Influence of the lipid matrix on incorporation and function of LPS-free porin from Paracoccus denitrificans. Biochim Biophys Acta. 1994 Mar 23;1190(2):231–242. doi: 10.1016/0005-2736(94)90079-5. [DOI] [PubMed] [Google Scholar]

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