title: Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations.
abstract: OmpA is a multidomain protein found in the outer membranes of most Gram-negative bacteria. Despite a wealth of reported structural and biophysical studies, the structure-function relationships of this protein remain unclear. For example, it is still debated whether it functions as a pore, and the precise molecular role it plays in attachment to the peptidoglycan of the periplasm is unknown. The absence of a consensus view is partly due to the lack of a complete structure of the full-length protein. To address this issue, we performed molecular-dynamics simulations of the full-length model of the OmpA dimer proposed by Robinson and co-workers. The N-terminal domains were embedded in an asymmetric model of the outer membrane, with lipopolysaccharide molecules in the outer leaflet and phospholipids in the inner leaflet. Our results reveal a large dimerization interface within the membrane environment, ensuring that the dimer is stable over the course of the simulations. The linker is flexible, expanding and contracting to pull the globular C-terminal domain up toward the membrane or push it down toward the periplasm, suggesting a possible mechanism for providing mechanical stability to the cell. The external loops were more stabilized than was observed in previous studies due to the extensive dimerization interface and presence of lipopolysaccharide molecules in our outer-membrane model, which may have functional consequences in terms of OmpA adhesion to host cells. In addition, the pore-gating behavior of the protein was modulated compared with previous observations, suggesting a possible role for dimerization in channel regulation.
authors.affiliation: School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom.
authors.forename: Maite L
authors.initials: ML
authors.lastname: Ortiz-Suarez
authors.affiliation: School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom.
authors.forename: Firdaus
authors.initials: F
authors.lastname: Samsudin
authors.affiliation: School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom.
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Piggot
authors.affiliation: Bioinformatics Institute (A(∗)STAR), Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore. Electronic address: peterjb@bii.a-star.edu.sg.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Bond
authors.affiliation: School of Chemistry, Highfield Campus, University of Southampton, Southampton, United Kingdom. Electronic address: s.khalid@soton.ac.uk.
authors.forename: Syma
authors.initials: S
authors.lastname: Khalid
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000378:metabolism*; D002462:Cell Membrane / Q000378:metabolism*; D007711:Klebsiella pneumoniae; D050356:Lipid Metabolism; D056004:Molecular Dynamics Simulation; D016062:Porosity; D011485:Protein Binding; D055503:Protein Multimerization; D055550:Protein Stability; D020836:Protein Structure, Quaternary; D021381:Protein Transport
chemical_list: D001425:Bacterial Outer Membrane Proteins; C078167:OMPA outer membrane proteins