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. Author manuscript; available in PMC: 2021 Aug 1.
Published in final edited form as: FEBS J. 2020 Jan 23;287(15):3235–3254. doi: 10.1111/febs.15207

Figure 9: Molecular dynamics simulations of inhibitor-bound PR and PRS5B and calculated non-bonded interaction energies of inhibitors.

Figure 9:

A. Trajectories of the 10 ns simulations of APV and DRV complexes of PR and PRS5B. RMSD of Cα atoms after superposition with the starting crystal structure plotted for the 10 ns time course. Simulations are colored as follows: PR/DRV (blue), PR/APV (green), PRS5B/DRV (red), and PRS5B/APV (purple).

B. Frequency plot of total non-bonded interaction energies of inhibitors in PR (left) and PRS5B (right) simulations. Simulations are colored as in A.

C. Comparison of PR with PRS5B for DRV (left) and APV (right) simulations. Snapshots of PR (grey shades, grey inhibitor as sticks) and PRS5B (cyan and blue, orange inhibitor as sticks) models for every 2 ns of the simulation are shown as superimposed ribbons. The starting crystal structures PR (black) and PRS5B (green) are shown. Red arrows indicate large conformational differences between wild-type and mutant protease. Structure figures were generated using PyMOL.