Fig. 2

Structural and molecular dynamics (MD) simulation analyses of lin2189-YTM. a The molecular details of the lin2189 E157A/E185L-YTM crystal structure. Green ball-and-stick cartoon, the substrate (YTM); cyan spheres, polar residues; yellow spheres, aromatic residues; and blue spheres, hydrophobic residues. b Interactions between native lin2189 and YTM from MD simulations. Black dash, H-bond interactions. c The normalized interaction frequency of native lin2189-YTM calculated from unbiased MD simulations. d The intrinsic mobility of lin2189 calculated from the principal component analysis (PCA). The cyan vector length correlates with the domain-motion scale. Yellow sphere, the substrate molecule (YTM) from docking; red region, the catalytic pocket. PCA analysis showed that loops A, B and C next to the catalytic pocket are very flexible. e The substrate entrance pathway sampled by metaMD simulations. Yellow stick, final pose of the substrate YTM. Green stick, the catalytic trait in the binding pocket. Blue spheres, the mass center of the substrate molecule along the simulation trajectory. f The product leaving pathway sampled by metaMD simulations. g The catalytic residues and aromatic cage of CCHs are highly conserved. YtkR7, and the 1695 similar proteins were used to create the sequence logo. The residue numbers correspond to those of lin2189