Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde:Ab initio and free energy quantum mechanical/molecular mechanicalcalculations

摘要

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase aredetermined for three reaction pathways using quantum mechanicallmolecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained atthe stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employlocal correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- andquadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections forbasis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theoryis used to generate free energy profiles at the DFT(B3LYP)/MM level for the most importantreaction steps by sampling along the corresponding reaction paths using molecular dynamics. Theab initio and FEP QM/MM results are combined to derive improved estimates of the free energybarriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about3 kcal mol~(-1).The present results confirm the qualitative mechanistic conclusions from a previousDFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with aninitial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack thatyields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competingmetal center activated pathway has the same final step but needs to overcome a higher barrier in theinitial step on the route to IM2. The concerted mechanism has the highest free energy barrier andcan be ruled out. While confirming the qualitative mechanistic scenario proposed previously on thebasis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculationsprovide corrections to the barriers that are important when aiming at high accuracy.