Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications
Figure 4
The Force Constant Stability Analysis of the apo-HtpG Chaperone.
(A) The residue-based force constant profile of apo-HtpG. The NTD residues are in green, MD residues are in blue, and CTD residues are in red. The residue-based dynamic profiles are annotated using the residue numbering in the original crystal structure [56]. The peaks of the force constant profiles corresponding to functionally important residues are indicated by arrows and annotated. Functional residues corresponding to the peaks in the force constant distribution are mapped onto the domain-colored crystal structure of apo-HtpG (B) and onto the functional dynamics profile of apo-HtpG (C). The functional dynamics profile is obtained using PCA of the MD-based conformational ensembles averaged over three lowest frequency modes. The color gradient in from blue to red indicates the decreasing structural stability (or increasing conformational mobility) of protein residues. Functional residues are annotated and shown in spheres, colored according to their domains in (B) and according to the level of rigidity (flexibility) in the functional dynamics profiles (C).