Figure 7. Normal mode analysis output for thehs CENP-HIKM complex model, showing the (A) main-chain
deformability, (B) Bfactor, (C) Eigenvalues, (D) Variance, (E)
Covariance map and the (F) Elastic network map.
The quality and stability of the hypothetical hs CENP-HIKM model
were evaluated through the iMod-estimated elastic network map,
deformability, covariance map, eigenvalue and the B-factor (Figure 7).
The deformability of the main chain is an estimation of the deformation
capability of a molecule at each of its residues. The Bfactor (a
crystallographic atomic displacement parameter) is reported for most
X-ray crystal structure of proteins and it is directly related to the
fluctuations due to static disorder or motion in structures. The Bfactor
also provides a measure of an averaged root mean square (RMS). Motion
stiffness is represented by the eigenvalue that is associated to each
normal mode. Its value is related directly to the required energy for
structural deformation. The green and red colored bars show the
cummulative and individual variances respectively, while the covariance
matrix denotes residue pair coupling, i.e. whether the paired residues
experience anti-correlated, uncorrelated or correlated motions (colored
in blue, white and green respectively). Atom pairs that are connected by
springs are defined by the elastic network model. Each graphical dot
represent a spring between the corresponding atom pairs. The dots are
colored based on their stiffness, which means the darker gray colors
denote stiffer springs and vice versa. Figure 7 shows an average root
mean square in the Bfactor and an insignificant hinge. The high
eigenvalue (1.375238e-06) is an indication of a low deformation chance,
while the elasticity and correlation also demonstrated the high quality
of the hypothetical protein complex model (Figure 7).