Mechanistic analysis of peptide macrocyclization by PsnB using computational and experimental approaches
Cyclic peptides have been recognized as an important class of drug leads because they have pharmacokinetic qualities of small molecules and target binding affinity of biologics at the same time. However, one of the major challenges for developing cyclic peptide drugs is the large-scale synthesis of cyclic peptides with structural and chemical diversity. Enzymatic synthesis of macrocyclic peptides could be a solution for this issue. In this work, we explored the biosynthesis of plesiocin, a member of ribosomally synthesized and post-translationally modified peptides (RiPPs). The Galaxy protein modeling package and molecular dynamics simulation were performed to predict the interactions between the enzyme PsnB, the substrate PsnA, and cofactors ATP and Mg2+. Then the predictions were tested with biochemical experiments. Through this modeling-experiment collaboration, we proposed the reaction mechanism of PsnB where phosphorylation of glutamate in PsnA, enzyme-guided bending of substrate backbone, and intramolecular cross-linking reaction occur in a highly coupled manner.