Figure 4.

Projection of MD simulation trajectories to the first two PCA modes. The scatter plots of simulation frame projections are colored by their simulation times, and the clusters are indicated with green, red, and magenta for clusters 1, 2, and 3, respectively. (a) Bent integrin presented two clusters, centered at (0, 0) and (−4600, 2400), respectively. Structures representative of these two clusters were extracted at time step 456.9 ns and 353.1 ns. (b) Int1 presented four clusters, centered at (450, 450), (300, −2000), (−5200, 850), and (−5500, −1500). Representative structures of each cluster were extracted at time step 359.1 ns, 471.7 ns, 134.4 ns, and 485.9 ns. (c) Int2 presented two clusters, centered at (3000, 0) and (−4000, 0). Representative structures were extracted at 295.1 ns and 101.1 ns. (d) Open α_IIbβ₃ presented three clusters, centered at (6500, 400), (−1000, 200), and (400, −2500), respectively. Representative structures were extracted at 28.2 ns, 445.9 ns and 45.8 ns. To see this figure in color, go online.