3 RESULTS AND DISCUSSION
3.1 Deprotonation
conformation distribution
Both pentapeptides and tripeptides containing the β-lactam ring can be
catalyzed efficiently by NocTE, and more importantly, tripeptides have
simpler structure and more detailed experimental
observations.5 Therefore, epi -nocardicin G
covalently bound to NocTE (NocTE-LSub) system was constructed to explore
the catalytic mechanism of NocTE. According to the hypothesis from
Andrew M. Gulick’s studies6, the proton acceptor H1901
may be involved in not only hydrolysis but also epimerization.
Considering the conformation difference of surrounding residues between
the epimerization reaction and hydrolysis reaction, the deprotonation
distance d(H1901Nε-LSubHα) was
restrained between 3.00 Å and 3.50 Å to gain an appropriate initial
structure, and then six replicas of 100 ns MD simulations without this
restraint were performed to capture deprotonation conformations for
epimerization (Figure S2).