Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase

Publikace nespadá pod Filozofickou fakultu, ale pod Přírodovědeckou fakultu. Oficiální stránka publikace je na webu muni.cz.

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JINDAL Garima SLÁNSKÁ Kateřina KOLEV Veselin DAMBORSKÝ Jiří PROKOP Zbyněk WARSHEL Arieh

Druh Článek v odborném periodiku
Časopis / Zdroj Proceedings of the National Academy of Sciences of the United States of America
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
www http://dx.doi.org/10.1073/pnas.1804979115
Doi http://dx.doi.org/10.1073/pnas.1804979115
Klíčová slova enzyme design; EVB; transient kinetics; dehalogenase; nucleophilic substitution
Popis Rational enzyme design presents a major challenge that has not been overcome by computational approaches. One of the key challenges is the difficulty in assessing the magnitude of the maximum possible catalytic activity. In an attempt to overcome this challenge, we introduce a strategy that takes an active enzyme (assuming that its activity is close to the maximum possible activity), design mutations that reduce the catalytic activity, and then try to restore that catalysis by mutating other residues. Here we take as a test case the enzyme haloalkane dehalogenase (DhlA), with a 1,2-dichloroethane substrate. We start by demonstrating our ability to reproduce the results of single mutations. Next, we design mutations that reduce the enzyme activity and finally design double mutations that are aimed at restoring the activity. Using the computational predictions as a guide, we conduct an experimental study that confirms our prediction in one case and leads to inconclusive results in another case with 1,2-dichloroethane as substrate. Interestingly, one of our predicted double mutants catalyzes dehalogenation of 1,2-dibromoethane more efficiently than the wild-type enzyme.
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