Two-dimensional PCA projections of trajectories obtained from MD simulations for various CycT1 proteins.

<p>Initially, PCA calculations were carried out with all the CycT1 models including WT, and CycT1 mutants, Q46A, Q50A, Q46AQ50A and F176A, in order to obtain the coordinate for each component. Then, using the rmsd distance data for Cα atoms of TRR obtained from this coordinate, each trajectory data set was plotted in accordance with principal components 1 and 2 for abscissa and ordinate, respectively. 2-D (primary component 1 (PC1)-PC2) plots of trajectories obtained with WT (a) and various CycT1 molecules (b). The position of 3MI9 CycT1 is indicated as “*”. Probability distribution (right) of MD trajectories based on PCA was estimated using kernel density estimation method in R version 3.1.1.