Membrane protein dynamics and detergent interactions within a crystal: A simulation study of OmpA

Bond et al. 10.1073/pnas.0600398103.

Supporting Information

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Supporting Figure 5
Supporting Figure 6
Supporting Movie 1

Fig. 5. Ca rmsd vs. time for all atoms (black) and for the b-barrel region only (red) for the trajectory obtained by averaging over the four OmpA chains. All structures were fitted to the respective b-barrel region in the simulation starting structure.

Supporting Figure 6

Fig. 6. Sampling of conformational space over different simulation time windows. (A) Ca B factors of OmpA chains A-D (black, red, green, and blue lines) from the final 45 ns of the simulation, for time windows of different sizes averaged over all equivalent windows. These were calculated for all atoms and the fraction of those constituting the maximum and minimum 10% (thin lines) and also for the b-barrel atoms only (thick lines). Error bars represent the standard deviations about the average over windows of the same length. (B) Mean fractional covariance matrix overlap between consecutive time windows for all Ca atoms of OmpA chains A to D (black, red, green, and blue lines) for the final 45 ns of the simulation. For each time length, overlaps were calculated between the covariance matrices from consecutive time windows and then averaged over all equivalent windows. Error bars represent the standard deviations about the average over windows of the same length.

Supporting Movie 1

Movie 1. A movie from the simulations of OmpA in a crystal. One OmpA molecule is shown in cartoon format in blue; adjacent monomers are shown in Ca trace format in red, yellow, and purple. Selected detergent molecules are shown as van der Waals spheres, with their C atoms in cyan, orange, yellow, or purple and their O atoms in red; other detergent molecules are shown as dotted surfaces. The movie was made by using VMD.