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.