2.1 System construction
Based on the crystal structure of NocTE bound to the mimic structure of
the hydrolytic tetrahedral intermediate of nocardicin G (PDB ID:
6OJD)6, two catalytic systems of NocTE covalently
bound to epi -nocardicin G (NocTE-LSub) and nocardicin G
(NocTE-DSub) were modeled respectively. The protonation state for each
residue was determined via pKa calculations on PDB2PQR
web serve14. For parameter preparations, the
substrates covalently bound to NocTE were capped with -CO-CH3 group in
the N-terminal and -NH-CH3 group in the C-terminal. Then the capped
geometric structure was optimized at
M062X15/6-31G*16 level and
electrostatic surface potential (ESP) charge calculations were carried
out at HF17/6-31G* level using Gaussian 09
program18. The charge distribution information used
for system construction was calculated by a two-step restrained
electrostatic potential (RESP)19 method through
Multiwfn20 program and the
antechamber21 package implemented in AMBER
1822. These systems were set up within an octahedral
box of TIP3P water molecules. Besides, 15 sodium ions were added to
maintain the electroneutrality in each system.