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).