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. 2016 Jun 7;110(11):2463–2474. doi: 10.1016/j.bpj.2016.05.003

Figure 6.

Figure 6

CD81-GM contacts over time and interaction sites. (a) Snapshot of the simulation system after a 7.5 μs MD simulation. Gangliosides are colored in blue and proteins are in yellow/gray (side-chain/backbone particles) or, in the case of the two example states in (b), in orange/gray. (b) Left: configuration in which gangliosides form glycolipid bridges among three nondirectly interacting CD81 molecules. Right: direct CD81-CD81 interaction. Protein surfaces are shown as semitransparent. A gray-to-red color gradient indicates protein interactions per residue within 0.6 nm. (c) Protein-lipid RDF. The red area indicates the range of CD81-lipid distances used for contact definition (distance threshold = 0.6 nm). (d) Number of protein-lipid interactions as a function of time (black, CD81-PC interactions; blue, CD81-GM interactions). (e) CD81-GM contacts per residue scaled to the residue distance to the hydrophobic belt center of the protein (see Fig. S6 for original data and residue distances). To see this figure in color, go online.