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bioRxiv · 10.1101/2020.03.02.973883

Full quantum mechanical modeling of the enzyme-substrate system: how laccase detoxifies aflatoxin

Zaccaria, M.·Dawson, W.·Kish, D. R.·Reverberi, M.·Domin, M.·Dellafiora, L.·Nakajima, T.·Genovese, L.·Momeni, B.
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Abstract

This work focuses on: 1) the development of a methodology to perform a full Quantum Mechanics (QM) characterization of enzymatic activity; 2) the development of a rational approach to laccase engineering as a food bioremediator. Aflatoxins are among the most dangerous natural carcinogens, and regularly contaminate reserves of staple crops worldwide. Decontamination of aflatoxin-polluted food is of great interest for ensuring food safety, and bioremediation is regarded as the most promising solution. The fungal isoforms of laccase display the rare potential to detoxify aflatoxin by tackling its aromatic moieties.. Yet, because of a generally low efficiency, large-scale application of naturally occurring isoforms has so far been unfeasible. We perform a combination of quantitative experimentation and quantum mechanical modeling on aflatoxin and reveal that: (1) detoxification efficiency is limited by the low enzymatic affinity for the substrate; and (2) aflatoxin is not detoxified by oxidative activity of laccase alone, but requires additional stimulation from the environment. QM modeling also allowed identification of the residues in the laccase tertiary structure that determine affinity of the enzymatic pocket for aflatoxin. We conclude that, for our case-study, a full QM approach is mandatory as a first step towards rational optimization. We detail a feasible approach towards this endeavor and argue that our full QM characterization can serve as a roadmap for enzyme development in other applications pertaining laccase as well as other enzymes.

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Zaccaria, M., Dawson, W., Kish, D. R., Reverberi, M., Domin, M., Dellafiora, L., Nakajima, T., Genovese, L., Momeni, B.. 2020-03-03. Full quantum mechanical modeling of the enzyme-substrate system: how laccase detoxifies aflatoxin. https://doi.org/10.1101/2020.03.02.973883

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