Enzymes catalyze complicated chemical reactions in a highly specific, efficient, and selective manner. Many enzymes require cofactors, that usually participate in biocatalytic cycles that involve the formation of organometallic, ionic or radical reactive intermediate species. These reactive intermediates can then evolve through divergent reaction pathways, being a source for enzymatic promiscuity and thus serving as starting points for the design of new enzyme-catalyzed reactions. The accurate characterization of enzymatic “fleeting” reactive intermediates has been proved to be experimentally very challenging due to limitations of structural and spectroscopic techniques, while computational methods have been shown to be an important alternative in describing those intermediate species at the atomic level precision.^[1],[2] Our research program aims to develop and apply new multiscale computational protocols to study, characterize and rationally improve the formation and stabilization of reactive intermediates generated in enzyme active sites that are involved in key catalytic cycle steps.^[1]

Herein, we will present recent successful cases where the combination of different multiscale computational techniques,^[²^]including small truncated models, molecular dynamics (MD) simulations and QM/MM calculations, allowed us to unveil the molecular basis for enzymatic catalysis of natural and laboratory evolved enzymes that involve the formation of key reactive intermediates using iron-based cofactors.^[3],[4],[5] Our computational studies provide atomistic descriptions and basic knowledge about how natural and laboratory engineered enzymes can catalyze such reactions. This information is finally used for computationally-guide rational protein engineering toward new reactivities and selectivities not observed in Nature.

Marc Garcia-Borras

Appearances