Characterization of the Outer Membrane Protein OprF of Pseudomonas aeruginosa in a Lipopolysaccharide Membrane by Computer Simulation

Straatsma, TP; Soares, Thereza A

doi:10.1002/prot.22165

Title: Characterization of the Outer Membrane Protein OprF of Pseudomonas aeruginosa in a Lipopolysaccharide Membrane by Computer Simulation

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Abstract

The N-terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight-stranded anti-parallel β-barrel domain that folds into a membrane channel with low conductance. The structure of this protein has been modeled after the crystal structure of the homologous protein OmpA of Escherichia coli. A number of molecular dynamics simulations have been carried out for the homology modeled structure of OprF in an explicit molecular model for the rough lipopolysaccharide (LPS) outer membrane of P. aeruginosa. The structural stability of the outer membrane model as a result of the strong electrostatic interactions compared to simple lipid bilayers is restricting both the conformational flexibility and the lateral diffusion of the porin in the membrane. Constricting side-chain interactions within the pore are similar to those found in reported simulations of the protein in a solvated lipid bilayer membrane. Because of the strong interactions between the loop regions of OprF and functional groups in the saccharide core of the LPS, the entrance to the channel from the extracellular space is widened compared to the lipid bilayer simulations in which the loops are extruding in the solvent. The specific electrostatic signature of the LPS membrane, which results in a netmore »« less

Authors:: Straatsma, TP; Soares, Thereza A

Publication Date:: Sun Feb 01 00:00:00 EST 2009

Research Org.:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 947442

Report Number(s):: PNNL-SA-59443
400412000; TRN: US200909%%209

DOE Contract Number:: AC05-76RL01830

Resource Type:: Journal Article

Journal Name:: Proteins. Structure, Function, and Genetics, 74(2):475-488

Additional Journal Information:: Journal Volume: 74; Journal Issue: 2

Country of Publication:: United States

Language:: English

Subject:: 36 MATERIALS SCIENCE; COMPUTERIZED SIMULATION; CRYSTAL STRUCTURE; ESCHERICHIA COLI; EXTRACELLULAR SPACE; LIPOPOLYSACCHARIDES; MEMBRANE PROTEINS; MEMBRANES; MOLECULAR MODELS; PROTEINS; PSEUDOMONAS; STRONG INTERACTIONS

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                    Straatsma, TP, and Soares, Thereza A. Characterization of the Outer Membrane Protein OprF of Pseudomonas aeruginosa in a Lipopolysaccharide Membrane by Computer Simulation.  United States: N. p., 2009. 
        Web.  doi:10.1002/prot.22165.

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                    Straatsma, TP, & Soares, Thereza A. Characterization of the Outer Membrane Protein OprF of Pseudomonas aeruginosa in a Lipopolysaccharide Membrane by Computer Simulation.  United States.  https://doi.org/10.1002/prot.22165

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                    Straatsma, TP, and Soares, Thereza A. 2009.  
        "Characterization of the Outer Membrane Protein OprF of Pseudomonas aeruginosa in a Lipopolysaccharide Membrane by Computer Simulation".  United States.  https://doi.org/10.1002/prot.22165.

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@article{osti_947442,

  title        = {Characterization of the Outer Membrane Protein OprF of Pseudomonas aeruginosa in a Lipopolysaccharide Membrane by Computer Simulation},

  author       = {Straatsma, TP and Soares, Thereza A},

  abstractNote = {The N-terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight-stranded anti-parallel β-barrel domain that folds into a membrane channel with low conductance. The structure of this protein has been modeled after the crystal structure of the homologous protein OmpA of Escherichia coli. A number of molecular dynamics simulations have been carried out for the homology modeled structure of OprF in an explicit molecular model for the rough lipopolysaccharide (LPS) outer membrane of P. aeruginosa. The structural stability of the outer membrane model as a result of the strong electrostatic interactions compared to simple lipid bilayers is restricting both the conformational flexibility and the lateral diffusion of the porin in the membrane. Constricting side-chain interactions within the pore are similar to those found in reported simulations of the protein in a solvated lipid bilayer membrane. Because of the strong interactions between the loop regions of OprF and functional groups in the saccharide core of the LPS, the entrance to the channel from the extracellular space is widened compared to the lipid bilayer simulations in which the loops are extruding in the solvent. The specific electrostatic signature of the LPS membrane, which results in a net intrinsic dipole across the membrane, is found to be altered by the presence of OprF, resulting in a small electrically positive patch at the position of the channel.},

  doi          = {10.1002/prot.22165},

  url          = {https://www.osti.gov/biblio/947442},
  journal      = {Proteins. Structure, Function, and Genetics, 74(2):475-488},
number       = 2,

  volume       = 74,

  place        = {United States},

  year         = {Sun Feb 01 00:00:00 EST 2009},

  month        = {Sun Feb 01 00:00:00 EST 2009}

}

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