NMR-restrained docking of a peptidic inhibitor to the N-terminal domain ofthe phosphoenolpyruvate : sugar phosphotransferase enzyme I

Starting from the NMR structure of the binary complex between the N-termina l domain of the unphosphorylated enzyme I (EIN) of the phosphoenolpyruvate: sugar phosphotransferase (PTS) and the histidine-containing phosphocarrier protein (HPr), a molecular model of the phosphorylated transition state of the related complex was established using constrained simulated annealing. The coordinates of the phosphorylated EIN enzyme were then used in a second step for flexible docking of a decapeptide inhibitor of EIN whose enzyme-b ound conformation itself was determined by NMR using transferred nuclear Ov erhauser effects. Two phosphorylation models of the peptide inhibitor were investigated and shown to be both functional. Interestingly, one model is v ery similar to that of the complex between EIN and its natural substrate HP r. The present study demonstrates that NMR-guided flexible docking constitu tes an interesting tool for docking highly flexible peptide ligands and fac ilitates the upcoming protein-based design of nonpeptide EIN inhibitors for discovering new antibiotics.