Fig. 2.

Coarse-grained MD simulations of Brag2 on a membrane showing multiple PIP₂ lipid-binding sites. (A) Coarse-grained MD simulation of Brag2 on a membrane bilayer containing PIP₂ lipids at the end of the simulation, for one run. Multiple PIP₂s bind to the protein at various interaction sites at the end of the simulation. The PC lipids and the tails of the PS and PIP₂ lipids are not shown for clarity. (B) Close-up of Brag2 at the end of the simulation run, for one run. The protein binds primarily to PIP₂ molecules in the membrane at multiple binding sites. The view is rotated by 90° with respect to A. (C) Time-averaged number of interactions between Sec7 domain residues and PIP₂ lipids. The Inset shows a close-up of the interactions of the residues in the α8-α9 loop. Additional interactions are also seen in the loop between the Sec7 domain and the linker (residues 580–599). (D) Time-averaged number of interactions between residues of the linker and the PH domain, and PIP₂ lipids. See Fig. 1A and Fig. S1C for the localization of the structural elements bearing these residues. Positively charged residues (lysines and arginines) are in dark blue. PIP₂ lipids are in red; PS lipids are in orange; PC lipids are in gray.