Figure 4
T4 lysozyme. (A) Cartoon representation of the cluster centroids (orange and green), 150L-MD snapshot (dark-grey) and 256L-MD snapshot; (B). Root Mean Square Fluctuation (RMSF) analysis shows high flexibility in both the region for cluster-1 (orange) as observed for 150L-MD (dark-gray), while cluster-2 exhibited low flexibility in the correspondence of C-terminal as observed for 256L-MD (light-gray); (C). Principal Component Analysis for both clusters and MD simulations highlighted the protein internal movement showing a cluster-1 (orange) flexibility comparable to 150L-MD (dark-gray) and cluster-2 (green) flexibility comparable to 256L-MD (light gray); (D). First principal component density distribution plot for 150L-MD (dark-grey), 256L-MD (light-grey), cluster-1 (orange) and cluster-2 (green) unveiled that the clustered-1 and clustered-2 models resemble the closed and open conformation respectively; (E) distance/angle correlation analysis of cluster-1 (orange) and cluster-2 (green) overlap with the conformational space explored by the closed 150L-MD and open 256L-MD conformation respectively. AlphaFold2 prediction from EMBLDB was not public available. Google Colab model prediction (red spheres) explored closed conformation space. The closed and open X-ray T4 lysozyme conformations are specified with a black dot. The images were generated using 3D protein imaging webserver (https://3dproteinimaging.com/protein-imager/).
