Computational Study on the Inhibitor Binding Mode and Allosteric Regulation Mechanism in Hepatitis C Virus NS3/4A Protein
Figure 2
Global properties for molecular dynamics simulations.
(A) The backbone atom root mean square deviation (RMSD) for apo, inhibitor bound, apo (truncated) and inhibitor bound (truncated) HCV NS3/4A protein, calculated with respect to the initial structure during the 100 ns molecular dynamics simulation. (B) Root mean square fluctuations (RMSF) of CĪ± for apo, inhibitor bound, apo (truncated) and inhibitor bound (truncated) HCV NS3/4A protein averaged over the simulation. (C) RMSD of the backbone atoms of residues 101ā172 and 331ā420 with respect to the first snapshot as a function of time.