TY - JOUR TI - QM guided computational enzyme design DO - https://doi.org/doi:10.7282/T3445K5W PY - 2014 AB - PT3 is a redesigned adenosine deaminase that could catalyze the hydrolysis of organophosphate. In this present work, we evaluate the impact of previous designed mutations by investigating the mechanism of PT3. We started from the high-resolution crystal structure and truncated the active site residues as the QM model. Then the potential surface of the reaction was discovered by locating the transition states and intermediates along the reaction path with QM method B3LYP. The results showed a similar energy profile compared to natural phosphotriesterase and the nucleophilic attack turned out to be the rate-limiting step. The impact of a single mutation V218F that leaded to 20-fold increase in the catalytic rate kcat was rationalized by including this residue in QM model and a 5.0 kcal/mol difference of the reaction barrier was discovered. Then with the rationalized model, we performed a low-level QM calculation with key bond lengths fixed at a value from high-level QM results. The barrier difference of V218F changed to 3.6kcal/mol, which was still consistent with experimental results while the computation time was cut half. With this fast computational setting, we are able to analyze more mutations of their impact on the reaction barrier quantum mechanically. KW - Chemistry and Chemical Biology KW - Enzymes--Design KW - Quantum theory LA - eng ER -