An Automatic Pathway Searching Strategy in Enzyme Catalysis: A Case Study of LmCpfC.

Abstract

To mitigate the artificial intervention on the exploration of the enzyme reaction mechanisms, an automatic pathway searching strategy based on discrete path sampling(DPS) is firstly employed to explore the reaction pathway of enzyme catalysis. For instance, in the case of Listeria monocytogenes coproporphyrin ferrochelatase (LmCpfC) catalyzing the insertion of Fe(II) into the substrate coproporphyrin III (cpIII), which is the first computational research about detailed mechanism of the CpfC. By searching the reaction pathways for Fe(II) insertion from both sides of cpIII, it is found that Fe(II) inserting from the Tyr12 side exhibited advantages in both thermodynamics and kinetics, which is consistent with experimental observations. The enthalpy change is determined to be -42.24 kcal mol^-1 and the barrier energy is 7.28 kcal mol^-1. In contrast, the insertion from the Glu263, His182 side has an enthalpy change of +21.88 kcal mol^-1 and a barrier energy of 34.64 kcal mol^-1. Compared with potential energy surface scanning and nudged elastic band methods, where the barrier energies are 9.78, 17.50 kcal mol^-1 from Tyr12 side and 85.09, 58.26 kcal mol^-1 from Glu263, His182 side, respectively, the DPS strategy yields obviously lower barriers reaction pathways with less intervention.