Membrane protein dynamics in different environments: simulation study of the outer membrane protein X in a lipid bilayer and in a micelle |
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Authors: | Alexandra?Choutko Alice?Gl?ttli César?Fernández Christian?Hilty Kurt?Wüthrich Email author" target="_blank">Wilfred?F?van?GunsterenEmail author |
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Institution: | (1) Institute for Physical Chemistry, Swiss Federal Institute of Technology, ETH Zurich, 8093 Zurich, Switzerland;(2) Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, ETH Zurich, 8093 Zurich, Switzerland;(3) Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA; |
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Abstract: | The bacterial outer membrane protein OmpX from Escherichia coli has been investigated by molecular dynamics simulations when embedded in a phospholipid bilayer and as a protein-micelle
aggregate. The resulting simulation trajectories were analysed in terms of structural and dynamic properties of the membrane
protein. In agreement with experimental observations, highest relative stability was found for the β-barrel region that is
embedded in the lipophilic phase, whereas an extracellular protruding β-sheet, which is a unique structural feature of OmpX
that supposedly plays an important role in cell adhesion and invasion, shows larger structure fluctuations. Additionally,
we investigated water permeation into the core of the β-barrel protein, which contains a tight salt-bridge and hydrogen-bond
network, so that extensive water flux is unlikely. Differences between the bilayer and the micellar system were observed in
the length of the barrel and its position inside the lipid environment, and in the protein interactions with the hydrophilic
part of the lipids near the lipid/water interface. Those variations suggest that micelles and other detergent environments
might not offer a wholly membrane-like milieu to promote adoption of the physiological conformational state by OmpX. |
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