Computational studies of the Retro-Aldol reaction catalyzed by different protein scaffolds. Towards the redesign of an improved enzyme

Abstract

The main objective of this dissertation was to investigate the structure-function relationship in different designed Retro-Aldolases, to understand not only their catalytic efficiency but to provide information to design a new more efficient enzyme. In particular, the first step of the project was to investigate and analyze the reaction mechanism of two previously published de novo Retro-Aldolases (RA95.5-5 and RA95.5-8F) and one catalytic antibody (33F12). The free-energy landscape of the whole chemical process was explored through statistical methods with multiscale quantum mechanics / molecular mechanics (QM/MM) potentials, in terms of the PMF. The agreement between the theoretical predictions and the experimental data allowed to carry out deeper analysis, exploring the structural function and the interaction with the residues. The comparative analysis of the data generated from the computational simulations on the three protein scaffolds allowed to suggest a new variant of de novo Retro-Aldolase with a predicted higher catalytic efficiency.