Rognan D, Mukhija S, Folkers G, Zerbe O
Department of Applied Biosciences, Swiss Federal Institute of Technology, Zürich.
J Comput Aided Mol Des. 2001 Feb;15(2):103-15. doi: 10.1023/a:1008145813315.
Starting from the NMR structure of the binary complex between the N-terminal 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-bound conformation itself was determined by NMR using transferred nuclear Overhauser effects. Two phosphorylation models of the peptide inhibitor were investigated and shown to be both functional. Interestingly, one model is very similar to that of the complex between EIN and its natural substrate HPr. The present study demonstrates that NMR-guided flexible docking constitutes an interesting tool for docking highly flexible peptide ligands and facilitates the upcoming protein-based design of nonpeptide EIN inhibitors for discovering new antibiotics.
糖磷酸转移酶（PTS）未磷酸化的酶I（EIN）的N端结构域与含组氨酸的磷酸载体蛋白（HPr）之间的二元复合物的NMR结构出发，使用受限模拟退火建立了相关复合物磷酸化过渡态的分子模型。然后，在第二步中，将磷酸化EIN酶的坐标用于EIN十肽抑制剂的柔性对接，该抑制剂与酶结合的构象本身是通过使用转移核Overhauser效应的NMR确定的。研究了肽抑制剂的两种磷酸化模型，并证明它们都具有功能。有趣的是，一种模型与EIN及其天然底物HPr之间的复合物非常相似。本研究表明，NMR引导的柔性对接是对接高度柔性肽配体的一种有趣工具，并有助于即将开展的基于蛋白质的非肽EIN抑制剂设计，以发现新的抗生素。
