Figure 2. AA accumulates around ASICs.... | Rockefeller University Press

Figure 2.

$AA accumulates around ASICs. AA headgroup occupancy maps colored by occupancy as a fraction of frames. (A) Occupancy of AA headgroups, as defined by the charged COO bead, around hASIC3 channel. (B) Occupancy of AA headgroups around hASIC1 channel. (C) Occupancy of a subsample of 60 randomly selected POPC headgroups, as defined by the PO4 bead, around hASIC3 channel. Maps show an average of occupancy across three repeats of 30 μs simulations for each system. The systems were aligned on the TMD of the protein prior to calculating the occupancy. Top-down view of hASIC3 homology model TMD is displayed as surface and colored as in Fig. 1. (D) Left: Example of calculated AA density from 500 ns atomistic simulation of hASIC3 open state. Middle: Example of calculated POPC density from 100 ns atomistic simulation. Right: Electron density attributed to lipids in recently solved chicken ASIC1 desensitized state structure (PDB: 6VTK; Yoder et al., 2020).$

AA accumulates around ASICs. AA headgroup occupancy maps colored by occupancy as a fraction of frames. (A) Occupancy of AA headgroups, as defined by the charged COO bead, around hASIC3 channel. (B) Occupancy of AA headgroups around hASIC1 channel. (C) Occupancy of a subsample of 60 randomly selected POPC headgroups, as defined by the PO4 bead, around hASIC3 channel. Maps show an average of occupancy across three repeats of 30 μs simulations for each system. The systems were aligned on the TMD of the protein prior to calculating the occupancy. Top-down view of hASIC3 homology model TMD is displayed as surface and colored as in Fig. 1. (D) Left: Example of calculated AA density from 500 ns atomistic simulation of hASIC3 open state. Middle: Example of calculated POPC density from 100 ns atomistic simulation. Right: Electron density attributed to lipids in recently solved chicken ASIC1 desensitized state structure (PDB: 6VTK; Yoder et al., 2020).