The deformation in the direction of fluctuations and the additional asymmetry of the protease monomers is recovered considerably by this coevolution.
The directions of fluctuations in the most cooperative functional modes differ mainly around the dynamically key regions, i.e., the hinge axes, which appear to be more flexible in substrate complexes.
First, note that the alignment along preferential directions of fluctuations in the atoms indicates that QAA can identify and characterize conformational sub-states with low populations in the landscape.
The severity of changes revealed by clinical inspection was not supported by similar directions of fluctuations in the instrumental assessments.
The severity of the changes revealed by clinical inspection was not supported by similar directions of fluctuations in the instrumental assessments.
The residues with maximum orientational differences between their directions of fluctuations can also be observed on the structures in Fig. 5, as color coded according to the change in the correlation of the NC-p1WT (Fig. 5B, E) and AP2VNC-p1V82A (Fig. 5C, F) compared to the average of the wild-type protease structures bound to the other six natural substrates.
The structures in Fig. 4 display the residues that exhibit the maximum variations between the directions of fluctuations, as color coded according to the change in the correlation values of NC-p1V82A (Fig. 4B, E) and AP2VNC-p1V82A (Fig. 4C, F) compared to NC-p1WT.
The residues that display the maximum variations between the directions of fluctuations can also be visualized on the structures in Fig. 3, as color coded according to the change in the correlation values of p1-p6D30N/N88D (Fig. 3B, E) and LP1′Fp1-p6D30N/N88D (Fig. 3C, F) compared to p1-p6WT.
The analysis generates an estimation of the direction of conformational fluctuation that in many cases agrees with experimentally observed changes in structure (Tama and Sanejouand, 2001).
Furthermore, the transfer direction of pressure fluctuations can be identified according to the similarity of pressure profiles, as shown in Fig. 7.
p53-miRs could therefore tune the production rate of the downstream p53 target gene opposite to the direction of p53's fluctuation.
