Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations

Raw simulations of the acylation step by PETase on a PET dimer model substrate, ran with CP2K 6.1 software at the PBE:AMBER level. Details can be found in the original manuscript (https://doi.org/10.1021/acscatal.1c03700): Molecular topology in AMBER Parameter Topology format and Trajectories in CHARMM binary coordinate format DCD.

RESIDUE LIST:
GLY57
TYR58
SER131
MET132
TRP156
ASP177
SER178
ILE179
ALA180
HID208
MOL262

VMD selection:
(name CA C O HA2 HA3 and resname GLY and resid 57) or (name N CA CB H HA HB2 HB3 and resname TYR and resid 58) or (name CA C O OG CB HA HB2 HB3 HG and resname SER and resid 131) or (name N CA SD CE CB CG H HA HB2 HB3 HG2 HG3 HE1 HE2 HE3 and resname MET and resid 132) or (name CB CG CD1 CD2 CE2 CE3 NE1 CZ2 CZ3 CH2 HB2 HB3 HD1 HE1 HE3 HZ2 HZ3 HH2 and resname TRP and resid 156) or (name CG OD1 OD2 CB HB2 HB3 and resname ASP and resid 177) or (name C O and resname SER and resid 178) or (name N CA C O CG2 CD1 CB CG1 H HA HB HG12 HG13 HG21 HG22 HG23 HD11 HD12 HD13 and resname ILE and resid 179) or (name N CA H HA and resname ALA and resid 180) or (name CB CG CD2 ND1 CE1 NE2 HB2 HB3 HD1 HD2 HE1 and resname HID and resid 208) or (name C1 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C2 C20 C3 C4 C5 C6 C7 C8 C9 H1 H10 H11 H12 H13 H14 H15 H16 H17 H2 H3 H4 H5 H6 H7 H8 H9 O1 O2 O3 O4 O5 O6 O7 O8 O9 and resname MOL and resid 262)

PYMOL selection:
(name CA+C+O+HA2+HA3 & resn GLY & resi 57) | (name N+CA+CB+H+HA+HB2+HB3 & resn TYR & resi 58) | (name CA+C+O+OG+CB+HA+HB2+HB3+HG & resn SER & resi 131) | (name N+CA+SD+CE+CB+CG+H+HA+HB2+HB3+HG2+HG3+HE1+HE2+HE3 & resn MET & resi 132) | (name CB+CG+CD1+CD2+CE2+CE3+NE1+CZ2+CZ3+CH2+HB2+HB3+HD1+HE1+HE3+HZ2+HZ3+HH2 & resn TRP & resi 156) | (name CG+OD1+OD2+CB+HB2+HB3 & resn ASP & resi 177) | (name C+O & resn SER & resi 178) | (name N+CA+C+O+CG2+CD1+CB+CG1+H+HA+HB+HG12+HG13+HG21+HG22+HG23+HD11+HD12+HD13 & resn ILE & resi 179) | (name N+CA+H+HA & resn ALA & resi 180) | (name CB+CG+CD2+ND1+CE1+NE2+HB2+HB3+HD1+HD2+HE1 & resn HID & resi 208) | (name C1+C10+C11+C12+C13+C14+C15+C16+C17+C18+C19+C2+C20+C3+C4+C5+C6+C7+C8+C9+H1+H10+H11+H12+H13+H14+H15+H16+H17+H2+H3+H4+H5+H6+H7+H8+H9+O1+O2+O3+O4+O5+O6+O7+O8+O9 & resn MOL & resi 262)