DFT studies on the β-glycosidase catalytic mechanism: The deglycosylation step

Abstract

We have used computational methods to study the second step of the mechanism of reaction of retainingglycosidases in atomic detail. The model system included a simplified reaction center and a small substratemolecule to capture the intrinsic reactivity of the active-site motif. Using DFT calculations we wereable to confirm and provide molecular-level detail to the general mechanism proposed in the literaturefor this family of enzymes. Of particular interest are the substrate distortion observed at the transitionstate and the dissociative character of the reaction mechanism. Different electrostatic environments weremimicked using a solvent continuum model and it was verified that a less specific surrounding gives asmall, but measurable contribution for the reaction pathway.The performance of a wide variety of DFT functionals was also investigated. Density functionals of thedifferent classes, namely, meta-generalized gradient approximation (meta-GGA), hybrid-GGA andhybrid-meta-GGA density functionals were tested. The DFT results were compared with high-levelab initio calculations carried out at the MP2, MP3, MP4 and QCISD(T) levels of theory.