The rational redesign of enzymes towards increased catalytic activity and stability is an ultimate test of our understanding of protein sequence-structure-function relationships. Although advances in computational tools have enabled construction of new enzymes catalyzing unnatural reactions,1 our ability to drastically improve enzyme activity towards a desired reaction in a rational manner has remained underdeveloped. In contrast, directed evolution (DE) experiments, in which fitness is elevated via random mutation and selection, is a highly successful method of improving enzyme function. Through joint academic (UCLA) and industrial (Codexis) efforts, a series of mutants in the biosynthetic enzyme LovD have been obtained whose activities towards an unnatural, pharmaceutically important, substrate (Simvastatin) are increased 1000-fold for the final mutant. In this communication, the structural basis of improved catalysis achieved by LovD mutants is studied using both Quantum Mechanics (QM) calculations and long scale Molecular Dynamics (MD) simulations. The QM ideal arrangement of the catalytic residues for catalysis has been compared to the three-dimensional disposition of the catalytic residues in the different rounds of DE mutants. MD simulations performed in the microsecond time scale on the apo and bound states for the mutants have been key to unveil the subtle DE strategies towards the goal of improved catalysis.1Rothlisberger, D. et al. Nature 2008 , 453, 190; Jiang, L. et al. Science 2008 , 319, 1387; Siegel, J. B. et al. Science 2010 , 329, 309.

Long scale dynamics unveil the structural basis of improved catalysis achieved by directed evolution on LovD mutants

245th National Meeting (2013)

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