Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa

R. D. Lins; T. P. Straatsma

doi:10.1016/S0006-3495(01)75761-X

Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa

R. D. Lins, T. P. Straatsma

Research output: Contribution to journal › Article › peer-review

108 Scopus citations

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.

Original language	English
Pages (from-to)	1037-1046
Number of pages	10
Journal	Biophysical Journal
Volume	81
Issue number	2
DOIs	https://doi.org/10.1016/S0006-3495(01)75761-X
State	Published - 2001
Externally published	Yes

Funding

We thank Drs. Andy R. Felmy, David A. Dixon, and Lukas Schuler for many useful discussions. The Geosciences Research Program of the U.S. Department of Energy, Office of Basic Energy Sciences supported this project. Computing resources were available through a Computational Grand Challenge Application grant from the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory. The NWChem 4.0 computational chemistry package for massively parallel computers used in this study was developed by the High Performance Computational Chemistry group, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory. Battelle Memorial Institute operates Pacific Northwest National Laboratory for the U.S. Department of Energy.

Funders	Funder number
U.S. Department of Energy
Basic Energy Sciences

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10.1016/S0006-3495(01)75761-X

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Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa

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