Mechanistic Insight from Full Quantum Mechanical Modeling: Laccase as a Detoxifier of Aflatoxins

Zaccaria, M.; Dawson, W.; Kish, D. R.; Reverberi, M.; Bonaccorsi di Patti, M. C.; Domin, M.; Cristiglio, V.; Dellafiora, L.; Gabel, F.; Nakajima, T.; Genovese, L.; Momeni, B.

doi:10.1101/2020.12.31.424992

bioRxiv · 10.1101/2020.12.31.424992

Mechanistic Insight from Full Quantum Mechanical Modeling: Laccase as a Detoxifier of Aflatoxins

Zaccaria, M.·Dawson, W.·Kish, D. R.·Reverberi, M.·Bonaccorsi di Patti, M. C.·Domin, M.·Cristiglio, V.·Dellafiora, L.·Gabel, F.·Nakajima, T.·Genovese, L.·Momeni, B.

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Abstract

We demonstrate a path towards full Quantum Mechanics (QM) characterization of enzymatic activity. As a case-study, we investigate the detoxification of aflatoxin, a carcinogenic food contaminant, by laccase, a versatile oxidase capable of--but not efficient for--degrading aflatoxin. We use a combination of quantitative experimentation and QM modeling to show that low enzymatic steric affinity for aflatoxin is the main bottleneck, rather that the oxidative activity of laccase. To identify the structural elements responsible for low reaction rates, we perform a density functional theory (DFT) based modeling of both the substrate and the enzyme in a full QM simulation of more than 7,000 atoms. Thanks to our approach we point to amino acid residues that determine the affinity of laccase for aflatoxin. We show that these residues are substrate-dependent, making a full QM approach necessary for enzyme optimization. Altogether, we establish a roadmap for rational enzyme engineering applicable beyond our case study.

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Zaccaria, M., Dawson, W., Kish, D. R., Reverberi, M., Bonaccorsi di Patti, M. C., Domin, M., Cristiglio, V., Dellafiora, L., Gabel, F., Nakajima, T., Genovese, L., Momeni, B.. 2021-01-03. Mechanistic Insight from Full Quantum Mechanical Modeling: Laccase as a Detoxifier of Aflatoxins. https://doi.org/10.1101/2020.12.31.424992

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