Figure 7. PCA Analysis of (𝛔2-𝛔4) - SnoaL2 correlated motions.PCA scatter plots (PC1 vs. PC2) representing the projections of the Cα
displacements along the trajectory onto the first principal eigenvector,
PC1 (x-axis), vs. the projections onto the second principal eigenvector,
PC2 (y-axis), as derived from MD replicas of RpoE10 (A) wild-type, (B)
Mut1, (C) Mut2(D) Del1 models. A larger subspace of B) RpoE10(Mut1) and
D) RpoE10(Mut1) relative to the wild-type A) RpoE10 and B) RpoE10 (Mut2)
suggested an association with the enhanced flexible behavior upon
mutation in NPDKV or the deletion of the proximal SnoaL2 domain. E)
Eigenvalues (variance) plotted against eigenvector indices constructed
from PCA of the 200ns MD trajectories of backbone atoms for RpoE10 (a)
wild-type, (b) Mut1, (c) Mut2 (d) Del1. The line represents the
eigenvalues of the covariance matrix of the first 20 eigenvectors. The
index with value 1 indicates the largest eigenvalue. An altered
Eigenvalues shows the signals for critical transitions in the
conformational changes of the protein. F, G, H and I: Essential
dynamics analysis of Rpo10 and its mutant (Mut1 and Mut2. The
superimposition of structural coordinates associated with the principal
component 1 (PC1) of F) RpoE10 and mutant (RpoE10 (G) Mut1, H) Mut2 and
I) Del1)) conformers are displaying global motion. The initial
conformations are colored (σ2- red, σ4-blue, and SnoaL2- yellow), and
the final and the intermediate ones are shown in grey. A circle marks
the fluctuations in L3-loop connecting the α2 and α3. The orientations
of correlated and anti-correlated motions are indicated with a red and
blue double arrow at -10 promoter binding groove, respectively. The
differential movement of motif residues was recorded with divergent
displacements. The direction of displacement of the NPDKV (Cyan),
DGGGR(Magenta), and WLPEP(Green) motifs are labeled and shown below the
respective conformers (Magnitude is given in Supplemental Table S5). Red
and Blue color balls represent initial and final conformation,
respectively. The RpoE10 and its mutant forms are described in the tube
model.