Figure 4.

Quantification of size and dynamics of the Ca²⁺-binding site in different RyR1 functional states. To estimate the size of Ca²⁺-binding site, SASA of Ca²⁺-binding site residues Glu-3893, Glu-3967, and Thr-5001 was measured in different RyR1 systems. Evaluation of SASA with respect to the simulation time suggests that the Ca²⁺-binding site exhibits wide and expanded conformation of SASA in the absence of Ca²⁺ (plot A). The binding of Ca²⁺ along with ATP, caffeine, or both displayed stable and closed conformation of Ca²⁺-binding site of SASA (plot B). C, structural superposition of average Ca²⁺-binding sites extracted from last 20 ns of respective simulation trajectories to the average conformation of Ca²⁺-binding site of open RyR1 + ATP/Caf/Ca²⁺ (orange color). The Ca²⁺-binding site residues are shown in stick representation, and bound ions (Ca²⁺/Na⁺) are shown as spheres. The color code for Ca²⁺-binding site is as follows: apo-RyR1 (purple), RyR1 + Ca²⁺ (black), RyR1 + ATP (blue), RyR1 + Caf (red), RyR1 + ATP/Caf (green), RyR1 + ATP/Caf/Na⁺ (yellow), closed RyR1 + ATP/Caf/Ca²⁺ (brown), open RyR1 + ATP/Caf/Ca²⁺ (orange), RyR1 + ATP/Ca²⁺ (magenta), and RyR1 + Caf/Ca²⁺ (cyan). To avoid complexity, we maintained same color for Ca²⁺-binding site and corresponding bound Ca²⁺/Na⁺ ions. RyR1, ryanodine receptor type 1; SASA, solvent-accessible surface area.