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Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics

Yu, H; Dalby, PA; (2018) Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics. Proceedings of the National Academy of Sciences of the United States of America , 115 (47) E11043-E11052. 10.1073/pnas.1810324115. Green open access

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Abstract

Multiple mutations are typically required to significantly improve protein stability or aggregation kinetics. However, when several substitutions are made in a single protein, the mutations can potentially interact in a nonadditive manner, resulting in epistatic effects, which can hamper protein-engineering strategies to improve thermostability or aggregation kinetics. Here, we have examined the role of protein dynamics in mediating epistasis between pairs of mutations. With Escherichia coli transketolase (TK) as a model, we explored the epistatic interactions between two single variants H192P and A282P, and also between the double-mutant H192P/A282P and two single variants, I365L or G506A. Epistasis was determined for several measures of protein stability, including the following: the free-energy barrier to kinetic inactivation, ∆∆G‡; thermal transition midpoint temperatures, Tm; and aggregation onset temperatures, Tagg. Nonadditive epistasis was observed between neighboring mutations as expected, but also for distant mutations located in the surface and core regions of different domains. Surprisingly, the epistatic behaviors for each measure of stability were often different for any given pairwise recombination, highlighting that kinetic and thermodynamic stabilities do not always depend on the same structural features. Molecular-dynamics simulations and a pairwise cross-correlation analysis revealed that mutations influence the dynamics of their local environment, but also in some cases the dynamics of regions distant in the structure. This effect was found to mediate epistatic interactions between distant mutations and could therefore be exploited in future protein-engineering strategies.

Type: Article
Title: Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
Open access status: An open access version is available from UCL Discovery
DOI: 10.1073/pnas.1810324115
Publisher version: https://doi.org/10.1073/pnas.1810324115
Language: English
Additional information: Copyright © 2018 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY): http://creativecommons.org/licenses/by/4.0/
Keywords: dynamics,epistasis, stability, protein engineering, transketolase
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Engineering Science > Dept of Biochemical Engineering
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry
URI: https://discovery.ucl.ac.uk/id/eprint/10064091
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