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).