Effect of ligand binding on the conformation of the MIDAS/ADMIDAS region studied by MD simulations. (A) Illustration of the simulating system with GSBP. The region inside the sphere with a radius of 20 Å centered on Ser132 (red dotted circle) was allowed to undergo explicit dynamics, whereas atoms in the rest of the system are taken into account implicitly. (B) Occurrence of the ADMIDAS dissociation in 10 independent 40-nanosecond simulations with and without RGD. The ADMIDAS Ca²⁺ was considered to have escaped when the three interactions holding ADMIDAS (Ca²⁺…Ser134, Ca²⁺…Ala342, and Asp138…Ser344) were all broken and when the distance between MIDAS Mg²⁺ and ADMIDAS Ca²⁺ became >11 Å. Each trajectory is divided into 10 bins (4 nanoseconds for each), and the dissociation state for each bin is indicated on the vertical axis (state = 1 means that the event occurrence exceeded 50%). (C) Example of the ADMIDAS escape. Structural snapshots before (0 nanoseconds; top) and after (40 nanoseconds; bottom) the MD simulation in trajectory no. 10 of +RGD simulation reveals loss of two coordination bonds (black dotted lines) and an increase in the distance between MIDAS and ADMIDAS (red dotted lines). See also Video 5. (D) Stabilization of the water-mediated coordination of S134 to Mg²⁺ by RGD binding. Distances between the Oγ of S134 and the MIDAS Mg²⁺ (inset) were traced over time. Representative tracings for simulations in the presence (+RGD, trajectory no. 8; see also Video 6) or the absence (ligand-free, trajectory no. 9; see also Video 7) are shown. See Fig. S4 for tracings of all trajectories.