After billions of years of evolution, Nature has evolved Enzymes conferring them unique capabilities fundamental for life. Enzymes (i.e. biocatalysts) are highly efficient, specific and selective. Indeed, they are the most proficient catalysts known. Biocatalysts can operate under physiological mild conditions, are biodegradable and non-toxic, offering exquisite control of biochemical transformations. All these characteristics make biocatalysts the best alternative to synthetic reagents for chemical manufacturing. Nevertheless, the existing enzymes in nature are specifically evolved to optimally operate on natural substrates catalyzing chemical transformations that may not be of industrial interest. Thus, because of this limit scope of substrates and synthetically useful chemical transformations, enzymes need to be modified to accomplish that purposes.<br/>In this talk, the use of different computational tools, including quantum mechanics (QM) and molecular dynamics (MD) simulations, to reveal how mutations alter the structure and organization of enzyme active sites is presented. As initially proposed by Pauling, and elaborated by many others since then, biocatalysis is efficient when the catalytic residues in the active site of an enzyme are in optimal positions for transition state stabilization. Using MD simulations, we explore the dynamical pre-organization of the active sites of designed and evolved enzymes, by analyzing the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state, and relates the populations of the catalytic conformational ensemble to enzyme activity. The understanding of how distal mutations to the active modify enzymatic activities is of utmost importance to further develop new protocols to computationally design new enzymes with new and useful capabilities.

Computational tools for the evaluation of laboratory-engineered biocatalysts

253rd National Meeting (2017)

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