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

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-eng...

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Autores principales: Yu, Haoran, Dalby, Paul A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255212/
https://www.ncbi.nlm.nih.gov/pubmed/30404916
http://dx.doi.org/10.1073/pnas.1810324115
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author Yu, Haoran
Dalby, Paul A.
author_facet Yu, Haoran
Dalby, Paul A.
author_sort Yu, Haoran
collection PubMed
description 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, T(m); and aggregation onset temperatures, T(agg). 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.
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spelling pubmed-62552122018-11-30 Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics Yu, Haoran Dalby, Paul A. Proc Natl Acad Sci U S A PNAS Plus 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, T(m); and aggregation onset temperatures, T(agg). 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. National Academy of Sciences 2018-11-20 2018-11-07 /pmc/articles/PMC6255212/ /pubmed/30404916 http://dx.doi.org/10.1073/pnas.1810324115 Text en Copyright © 2018 the Author(s). Published by PNAS. http://creativecommons.org/licenses/by/4.0/ This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (http://creativecommons.org/licenses/by/4.0/) .
spellingShingle PNAS Plus
Yu, Haoran
Dalby, Paul A.
Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
title Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
title_full Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
title_fullStr Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
title_full_unstemmed Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
title_short Coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
title_sort coupled molecular dynamics mediate long- and short-range epistasis between mutations that affect stability and aggregation kinetics
topic PNAS Plus
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255212/
https://www.ncbi.nlm.nih.gov/pubmed/30404916
http://dx.doi.org/10.1073/pnas.1810324115
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