A computational essential dynamics approach to investigate structural influences of ligand binding on Papain like protease from SARS-CoV-2.

Finally, the control molecule, i.e., PLpro-VIR251 complex, displays stabilisation at 20 ns which is followed by an increasing trend in the RMSD of the complex and a dip around 60 ns timepoint and an eventual convergence at 80 ns.

also in 63,971 other papers

Since the protein is present in a solvent for the simulation, we have studied the SASA for the protein and its complexes which showed a trend of PLpro-VIR251 > PLpro-ZINC000064033452 > PLpro-ZINC000000596945 > PLpro, which shows that upon ligand binding significant changes occur in the tertiary structure of the protein.

also in 53,322 other papers

The trajectory of Rg for the native protein shows an expected trend of decrease until the first 7 ns, followed by a stable trajectory until an absorbing perturbation from 34 to 35 ns, where it reaches a maximum peak of 2.48 nm at 35.06 ns.

also in 319 other papers