THICKNESS & CURVATURE

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Analysis of membrane deformations as a result of embedded proteins in terms of lipid-protein interactions usually come secondary to the analysis of individual interactions of proteins with lipids, and they are even less frequently visualized in detail. The importance of the bulk lipid environment has been noted in the literature, in particular for GPCRs.

Using this application, we can visualize membrane thickness and curvature in great detail. The calculation method for the thickness and curvature profiles uses g_surf, a tool developed by our group and described here. As described in the paper g_surf uses three interpolated grid-surfaces (upper, middle, and lower) from which thickness and curvature are calculated. Surface averages are calculated for the last 5 μs of simulation trajectories.

The application visualizes these results in an interactive format. You can visualize the results as either a point or surface mesh presentation. Each has its own options and parameters which can be tweaked to allow the user to select a part of the figure and control the detail of whatever aspect of it. We also show the position of embedded proteins as a point presentation with a coloring scheme that runs from black to red to pink to white as the GPCR sequence goes from TM1 to TM7/8. This makes it possible to clearly see which part of the protein is causing what deformation in the membrane. Considering that there are four protein copies in our simulation setups, this also allows for the comparison of the deformation caused by one protein to the others, as considering the size of the systems, each proteins' activity should be independent to that of the others'.