Figure 7.

Molecular dynamics simulations of Pocket three mutants.A, the root mean square deviation (RMSD) of the protein backbone was determined for WT PLpro and the Pocket three mutants Y251A and Y305A. MD simulations of Pocket one and two mutants did not reveal major structural variations between the mutants and WT PLpro. B, time-dependent analyses of the distance between the side chains of Y213 of the finger domain and E307 of the palm domain throughout the 200 ns of MD simulations. The distance between the side chains of Y213 and E307 is 2.5 Å in the crystal structure of WT PLpro.