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Molecular dynamics or: How I learned to stop worrying and love the membrane

Molecular dynamics or: How I learned to stop worrying and love the membrane
Molecular dynamics or: How I learned to stop worrying and love the membrane
The rise of antibiotic resistant bacterial species is an international problem. The structure, function and dynamic behaviour of the bacterial cell envelope must be thoroughly understood in order to design novel antimicrobial molecules. This thesis presents the use of molecular dynamics techniques to investigate the function of the Gram-negative outer membrane enzyme LpxR, as well as the subsequent effect of the protein on the dynamics of the outer membrane. LpxR covalently modifies a constituent of the outer membrane, lipopolysaccharide, which can modulate the immune response of the host. Simulations enabled the identification of a putative closed conformation for the protein, as well as a secondary ion binding site. These observations led to the proposition of an evaluated catalytic mechanism for the membrane enzyme.

The effect of lipopolysaccharide deacylation on wider membrane properties and dynamics was also investigated. Deacylated lipopolysaccharide induced positive curvature on the membrane when in distinct patches; cardiolipin phospholipids also clustered in areas of the inner leaflet corresponding with the patches of deacylated lipopolysaccharide in the outer leaflet. The application of an electric field to these modified membranes identified structural weaknesses at the interface between deacylated and wildtype lipopolysaccharide. Electroporation of the outer membrane model with OmpA embedded was also performed, and these simulations indicated that the presence of integral proteins may cause localised weakness in the membrane. Finally, the interactions between polymyxin B1, an antimicrobial peptide, and the outer membrane were examined, to gain a further understanding of how the molecule infiltrates the Gram-negative cell envelope. The peptides were observed to permeate through both the outer and inner membrane models, resulting in phospholipid flipflopping, thereby degrading the lipid asymmetry of the outer membrane. Data presented here provide the basis for an updated self-promoted uptake mechanism of cellular infiltration for polymyxin B1.
University of Southampton
Saunders, Graham Michael
0dc09f56-5dfd-457d-bb89-236e10a20ded
Saunders, Graham Michael
0dc09f56-5dfd-457d-bb89-236e10a20ded
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394

Saunders, Graham Michael (2019) Molecular dynamics or: How I learned to stop worrying and love the membrane. University of Southampton, Doctoral Thesis, 270pp.

Record type: Thesis (Doctoral)

Abstract

The rise of antibiotic resistant bacterial species is an international problem. The structure, function and dynamic behaviour of the bacterial cell envelope must be thoroughly understood in order to design novel antimicrobial molecules. This thesis presents the use of molecular dynamics techniques to investigate the function of the Gram-negative outer membrane enzyme LpxR, as well as the subsequent effect of the protein on the dynamics of the outer membrane. LpxR covalently modifies a constituent of the outer membrane, lipopolysaccharide, which can modulate the immune response of the host. Simulations enabled the identification of a putative closed conformation for the protein, as well as a secondary ion binding site. These observations led to the proposition of an evaluated catalytic mechanism for the membrane enzyme.

The effect of lipopolysaccharide deacylation on wider membrane properties and dynamics was also investigated. Deacylated lipopolysaccharide induced positive curvature on the membrane when in distinct patches; cardiolipin phospholipids also clustered in areas of the inner leaflet corresponding with the patches of deacylated lipopolysaccharide in the outer leaflet. The application of an electric field to these modified membranes identified structural weaknesses at the interface between deacylated and wildtype lipopolysaccharide. Electroporation of the outer membrane model with OmpA embedded was also performed, and these simulations indicated that the presence of integral proteins may cause localised weakness in the membrane. Finally, the interactions between polymyxin B1, an antimicrobial peptide, and the outer membrane were examined, to gain a further understanding of how the molecule infiltrates the Gram-negative cell envelope. The peptides were observed to permeate through both the outer and inner membrane models, resulting in phospholipid flipflopping, thereby degrading the lipid asymmetry of the outer membrane. Data presented here provide the basis for an updated self-promoted uptake mechanism of cellular infiltration for polymyxin B1.

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Molecular Dynamics or: How I Learned to Stop Worrying and Love the Membrane - Version of Record
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Published date: September 2019

Identifiers

Local EPrints ID: 438683
URI: http://eprints.soton.ac.uk/id/eprint/438683
PURE UUID: 8b7ee06f-a482-4616-8913-eea40b776a5e
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

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Date deposited: 20 Mar 2020 17:33
Last modified: 21 Mar 2020 01:29

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Contributors

Author: Graham Michael Saunders
Thesis advisor: Syma Khalid ORCID iD

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