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. 2022 Dec 23;122(3):533–543. doi: 10.1016/j.bpj.2022.12.032

Figure 3.

Figure 3

PCA analysis and evaluation of atomistic MD fluctuations. (a) Cumulative variance of Cα fluctuations for the four integrin conformations as a function of the principal components from 1 to 10. Data were extracted from the Cα trajectories during 500 ns of equilibrium MD simulations. (b) Fluctuations between the headpiece and lower legs of the four αIIbβ3 integrin conformations for the first 10 modes, calculated between 200 and 400 ns of equilibrium MD simulations. The values were obtained from evaluation of the fluctuations in distance between headpiece and lower legs from the principal modes. (c) Extensional stiffness of the four αIIbβ3 integrins from PCA of the equilibrium atomistic MD between 200 and 400 ns. The stiffness corresponding to the number of components having a cumulative variance of more than 95% was chosen for each integrin conformation. (d) Average distance of the headpiece from the legs, computed between the pulling group (residues: E220, S121, S123, D119, D251 in the MIDAS domain, D217, N215, D158, P219 in the LIMBS domain, and D126, D127, M335 in the ADMIDAS domain) and the reference group (residues: W967–W988 in the α chain and V696–W715 in the β chain). To see this figure in color, go online.