Essential dynamics
Principal component analysis (PCA) or Essential dynamics (ED) was performed to understand the impact of the NPDKV and DGGGR motifs on the global motion of the atomic coordinates of RpoE10 and RpoE10(Mut1, Mut2, and Del1) forms during 200ns MD simulation. The backbone atoms of the protein molecules were considered for this analysis. The principal components analysis is done by building a covariance matrix of the atomic fluctuations. Diagonalisation of this matrix yields a set of eigenvectors and eigenvalues that describe collective modes of fluctuations of the protein. The largest-amplitude collective motions are represented by the eigenvectors corresponding to the largest eigenvalues and are called ”principal components”32-34{Campagne, 2014 #80;Lane, 2006 #81;Campbell, 2002 #89}. The covariance matrix was constructed and diagonalized using g_covar and g_anaeig programs of Gromacs 2019.2, respectively, to generate the eigenvectors and eigenvalues. The prominent mobile regions of RpoE10 were carefully inspected and interpreted from the PCA and covariance matrix data.