Figure 8. Visual analysis of the hypotheticalhs CENP-HIKM complex (A) deformation energy and (B) atomic fluctuation. The deformation and fluctuation magnitude is represented by the differential coloration of the 3D structure. Low, moderate and high deformation and fluctuation magnitudes are represented by the blue, white and red colors respectively. (C) NMA-based representation of the trajectory for the first non-trivial mode of the hypotheticalhs CENP-HIKM complex. The figure shows the superimposition of each mode in the trajectory.
A similar analysis was conducted using DynaMut. The DynaMut normal mode analysis protocol is based on a bio3D package that utilizes a default C-alpha force field. The DynaMut-calculated deformation energy gives an estimation of protein complex local flexibility while the atomic fluctuation shows the amplitude for the absolute atomic motion. The predominant blue coloration of the 3D protein complex structure as depicted in Figure 8A and B, denotes a high level of structural stability. All calculations were performed over the first ten non-trivial modes of the protein complex. Included in the DynaMut output also is the flexibility trajectory of the protein complex based on normal mode analysis (Figure 8C), and the correlation map which reveals the anti-correlated and correlated regions in the protein complex. Both regions (anti-correlated and correlated) on the map are colored in blue and red respectively (Supplementary Figure S4). A 3D animation was also generated to simulate the motion of the protein complex (Supplementary Figure S5).