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Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics

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BABKOVÁ Petra DUNAJOVÁ Zuzana CHALOUPKOVÁ Radka DAMBORSKÝ Jiří BEDNÁŘ David MAREK Martin

Rok publikování 2020
Druh Článek v odborném periodiku
Časopis / Zdroj Computational and Structural Biotechnology Journal
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
www https://doi.org/10.1016/j.csbj.2020.06.021
Doi http://dx.doi.org/10.1016/j.csbj.2020.06.021
Klíčová slova Enzyme; Haloalkane dehalogenase; Ancestral sequence reconstruction; Thermostability; X-ray crystallography; Protein simulations; Conformational flexibility; Protein design
Přiložené soubory
Popis Ancestral sequence reconstruction is a powerful method for inferring ancestors of modern enzymes and for studying structure-function relationships of enzymes. We have previously applied this approach to haloalkane dehalogenases (HLDs) from the subfamily HLD-II and obtained thermodynamically highly stabilized enzymes (Delta T-m up to 24 degrees C), showing improved catalytic properties. Here we combined crystallographic structural analysis and computational molecular dynamics simulations to gain insight into the mechanisms by which ancestral HLDs became more robust enzymes with novel catalytic properties. Reconstructed ancestors exhibited similar structure topology as their descendants with the exception of a few loop deviations. Strikingly, molecular dynamics simulations revealed restricted conformational dynamics of ancestral enzymes, which prefer a single state, in contrast to modern enzymes adopting two different conformational states. The restricted dynamics can potentially be linked to their exceptional stabilization. The study provides molecular insights into protein stabilization due to ancestral sequence reconstruction, which is becoming a widely used approach for obtaining robust protein catalysts.
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