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A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase

Fig 2

Molecular dynamics simulations for TYMV PRO/DUB and structure-based flap mutants.

25-ns simulations were performed in identical conditions for wild type PRO/DUB (A) and mutants D843A (B), G865A (C) and P866G/P867G (D). Top, evolution along the simulations of the distance between Cα carbons of P867 and L820. Middle, snapshot taken from the end of each simulation (t = 25 ns), that shows a representative view of the GPP flap for all systems. Mutated residues' side chains are displayed as sticks, as well as L820. For L820 and for residues that are glycines or were mutated to glycines, Cα carbons are also shown as spheres. For clarity, hydrogens added for the simulations are omitted. Bottom, evolution along the simulations of the distance between the Sγ of C783 and the Nδ1 of H869. The dotted-and-broken line signals a 3.2 Å value below which the activating hydrogen bond between H869 and C783 is formed. (A) The three P867-L820 distances found in the crystal structures are labeled "Open" (dotted line, for a molecule taken from the PRO:PRO complex, the conformation from which the simulations were started), "Interm." (solid line, value found in the ΔC5 'A' conformation) and "Closed" (broken line, value found in the ΔC5 'B' conformation).

Fig 2

doi: https://doi.org/10.1371/journal.ppat.1006714.g002