Figure 3.
Molecular dynamics simulations of RapR-Shp2 reveal potential allosteric mechanism of regulation by iFKBP insert. (A) Root-mean-square fluctuation (RMSF) of individual amino acid residues of RapR-Shp2 in the absence of Rapamycin and FRB (red), RapR-Shp2 bound to Rapamycin and FRB (green), and wild-type Shp2 (black). Average RMSF values were determined from three 50 ns simulations for each model. (B–D) Tube representation of average RMSF (B) RapR-Shp2 without Rapamycin or FRB (PDB accession no. 4GDP for Shp2 and 4FAP for FKBP-Rapamycin-FRB), (C) RapR-Shp2 bound to FRB/Rapamycin, and (D) Wild-type Shp2.Tube thickness and color correspond to increased RMSF. Blue indicates low RMSF, while red colors indicate high RMSF. A zoomed-in representation of the substrate loop is shown in callout.

Molecular dynamics simulations of RapR-Shp2 reveal potential allosteric mechanism of regulation by iFKBP insert. (A) Root-mean-square fluctuation (RMSF) of individual amino acid residues of RapR-Shp2 in the absence of Rapamycin and FRB (red), RapR-Shp2 bound to Rapamycin and FRB (green), and wild-type Shp2 (black). Average RMSF values were determined from three 50 ns simulations for each model. (B–D) Tube representation of average RMSF (B) RapR-Shp2 without Rapamycin or FRB (PDB accession no. 4GDP for Shp2 and 4FAP for FKBP-Rapamycin-FRB), (C) RapR-Shp2 bound to FRB/Rapamycin, and (D) Wild-type Shp2.Tube thickness and color correspond to increased RMSF. Blue indicates low RMSF, while red colors indicate high RMSF. A zoomed-in representation of the substrate loop is shown in callout.

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