Enzymatic Hydrolysis of Tertiary Amide Bonds by anti Nucleophilic Attack and Protonation

The molecular mechanisms conferring high resistance of planar tertiary amide bonds to hydrolysis by most enzymes have remained elusive. To provide a chemical explanation to this unresolved puzzle, UB3LYP calculations were performed on an active site model of Xaa-Pro peptidases. The calculated reaction mechanism demonstrates that biocatalysts capable of tertiary amide bond hydrolysis capitalize on anti nucleophilic attack and protonation of the amide nitrogen, in contrast to the traditional syn displayed by amidases and proteases acting on secondary amide bonds.

平面型叔酰胺键对多数酶水解具有高抗性的分子机制，迄今仍未得到清晰阐明。为破解这一悬而未决的科学难题，研究人员针对Xaa-脯氨酸肽酶（Xaa-Pro peptidases）的活性位点模型开展了UB3LYP量化计算。计算揭示的反应机制显示：相较于作用于仲酰胺键的酰胺酶与蛋白酶所采用的经典顺式（syn）亲核进攻路径，具备叔酰胺键水解能力的生物催化剂，其催化过程依托于反式（anti）亲核进攻与酰胺氮的质子化作用。