From Brewing to Plastic Degradation: Uncovering the Polyurethanase Potential of R. chinensis Lipase through Atomistic Simulations

Reduced molecular dynamics (MD) trajectories for the open-lid Rhizopus chinensis lipase (RCL) with 4-nitrophenyl butyrate (pNPB) (3,000 snapshots each, representing 300 ns of GBIS simulation). Reduced MD trajectories for the system containing the apo protein and 40 pNPB molecules placed in the vicinity of the lid and pro-peptide domains (5,000 snapshots each, representing 500 ns of simulation). Reduced molecular dynamics (MD) trajectories for the quasi-open model chosen for the MD simulations using explicit solvation for RCL with pNPB and 4-nitrophenyl benzylcarbamate (pNC) in both poses Pose A and Pose B (5,000 snapshots each, representing 500 ns of simulation for 3 replicas for each system). The corresponding starting geometries for all systems mentioned are provided in PDB format. The simulations were performed using the MM level of theory, the AMBER force field, and the NAMD software package.