Fig. 4: Allosteric site engagement alters the dynamic profile of the MKP5-CD.

a Changes in ¹H¹⁵N HSQC resonance (peak) intensity when MKP5 is bound to Cmpd 1 at the allosteric site, calculated relative to apo MKP5 for WT (gray) and Y435W (blue). Light gray vertical lines indicate residues that are unassigned. b Δ peak intensity is plotted onto the MKP5 structure (PDB: 6MC1), with blue and red spheres representing decreases and increases in resonance intensity, respectively, and the color gradient denoting the magnitude of the change in resonance intensity. Residue 435 is represented by a cyan sphere, and the catalytic side-chains are highlighted in yellow. Cmpd 1 is modeled into the allosteric pocket for reference. c RMSF distributions of WT (apo), WT (holo), and Y435W (holo), computed on the active site and α4-α5 loop. d Dynamics of WT, WT-Cmpd 1, and Y435W-Cmpd 1 shown through Kernel density estimates of the Kullback-Leibler (KLD) divergence distributions of WT (apo; gray), WT (holo; dark-gray), and Y435W (holo; light-blue) MD-sampled configurations with respect to the crystal structure (PDB: 6MC1). The KLD was computed using the heavy atoms belonging to the active site and α4-α5 loop. e Kernel density estimates of RMSD distributions of WT (apo), WT (holo), and Y435W (holo), computed on the active site and allosteric site heavy atoms. f In red, distribution of distances between the active site center-of-mass and heavy atoms in the β5-α3 loop. In light green, distribution of distances between the allosteric site center-of-mass and heavy atoms in the α4-α5 loop. In dark green, distribution of distances between the active site center-of-mass and heavy atoms in the α4-α5 loop. Centers-of-mass are computed using heavy atoms in the active site (residues 408–414) and in the allosteric site (residues 442–452). g MKP5-CD structure showing the allosteric site (green), active site (red), and the centers-of-mass of each site (light-green and red spheres, respectively). Allosteric site center-of-mass to α4-α5 loop Cα-atom distances are shown in light-green lines. Active site center-of-mass to α4-α5 loop Cα-atom distances are shown in dark-green lines. Active site center-of-mass to β5-α3 loop Cα-atom distances are shown in red lines.