Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region
Fig 2
Association of the TCR-CD3 cytoplasmic region with the membrane.
(A) Side view of the entire TCR-CD3 (top) and intracellular view of its cytoplasmic region (bottom) taken from the end of the five CGMD simulations of membrane 1. The box highlights the most common CYR conformation calculated by the clustering analysis. (B) Distances between the center of mass (COM) of the TCR-CD3 CYR and the COM of membrane 1 calculated from the five CGMD simulations along the vertical (Z) axis versus time. (C) Radius of gyration (Rg) of the TCR-CD3 CYR versus time from all CGMD simulations. In (B) and (C), distance(Z) and Rg were also calculated from ATMD simulations performed for 100 ns. Comparison of the average distance(Z) and Rg between the ATMD (red) and CGMD (blue) simulations is shown in the inset graph. Standard deviation is shown in cyan for CGMD and in orange for ATMD.