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Temperature-sensitive contacts in disordered loops tune enzyme I activity

Homologous enzymes with identical folds often exhibit different thermal and kinetic behaviors. Understanding how an enzyme sequence encodes catalytic activity at functionally optimal temperatures is a fundamental problem in biophysics. Recently it was shown that the residues that tune catalytic acti...

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Autores principales: Burns, Daniel, Singh, Aayushi, Venditti, Vincenzo, Potoyan, Davit A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704738/
https://www.ncbi.nlm.nih.gov/pubmed/36375052
http://dx.doi.org/10.1073/pnas.2210537119
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author Burns, Daniel
Singh, Aayushi
Venditti, Vincenzo
Potoyan, Davit A.
author_facet Burns, Daniel
Singh, Aayushi
Venditti, Vincenzo
Potoyan, Davit A.
author_sort Burns, Daniel
collection PubMed
description Homologous enzymes with identical folds often exhibit different thermal and kinetic behaviors. Understanding how an enzyme sequence encodes catalytic activity at functionally optimal temperatures is a fundamental problem in biophysics. Recently it was shown that the residues that tune catalytic activities of thermophilic/mesophilic variants of the C-terminal domain of bacterial enzyme I (EIC) are largely localized within disordered loops, offering a model system with which to investigate this phenomenon. In this work, we use molecular dynamics simulations and mutagenesis experiments to reveal a mechanism of sequence-dependent activity tuning of EIC homologs. We find that a network of contacts in the catalytic loops is particularly sensitive to changes in temperature, with some contacts exhibiting distinct linear or nonlinear temperature-dependent trends. Moreover, these trends define structurally clustered dynamical modes and can distinguish regions that tend toward order or disorder at higher temperatures. Assaying several thermophilic EIC mutants, we show that complementary mesophilic mutations to the most temperature-sensitive positions exhibit the most enhanced activity, while mutations to relatively temperature insensitive positions exhibit the least enhanced activities. These results provide a mechanistic explanation of sequence-dependent temperature tuning and offer a computational method for rational enzyme modification.
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spelling pubmed-97047382022-11-29 Temperature-sensitive contacts in disordered loops tune enzyme I activity Burns, Daniel Singh, Aayushi Venditti, Vincenzo Potoyan, Davit A. Proc Natl Acad Sci U S A Biological Sciences Homologous enzymes with identical folds often exhibit different thermal and kinetic behaviors. Understanding how an enzyme sequence encodes catalytic activity at functionally optimal temperatures is a fundamental problem in biophysics. Recently it was shown that the residues that tune catalytic activities of thermophilic/mesophilic variants of the C-terminal domain of bacterial enzyme I (EIC) are largely localized within disordered loops, offering a model system with which to investigate this phenomenon. In this work, we use molecular dynamics simulations and mutagenesis experiments to reveal a mechanism of sequence-dependent activity tuning of EIC homologs. We find that a network of contacts in the catalytic loops is particularly sensitive to changes in temperature, with some contacts exhibiting distinct linear or nonlinear temperature-dependent trends. Moreover, these trends define structurally clustered dynamical modes and can distinguish regions that tend toward order or disorder at higher temperatures. Assaying several thermophilic EIC mutants, we show that complementary mesophilic mutations to the most temperature-sensitive positions exhibit the most enhanced activity, while mutations to relatively temperature insensitive positions exhibit the least enhanced activities. These results provide a mechanistic explanation of sequence-dependent temperature tuning and offer a computational method for rational enzyme modification. National Academy of Sciences 2022-11-14 2022-11-22 /pmc/articles/PMC9704738/ /pubmed/36375052 http://dx.doi.org/10.1073/pnas.2210537119 Text en Copyright © 2022 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Burns, Daniel
Singh, Aayushi
Venditti, Vincenzo
Potoyan, Davit A.
Temperature-sensitive contacts in disordered loops tune enzyme I activity
title Temperature-sensitive contacts in disordered loops tune enzyme I activity
title_full Temperature-sensitive contacts in disordered loops tune enzyme I activity
title_fullStr Temperature-sensitive contacts in disordered loops tune enzyme I activity
title_full_unstemmed Temperature-sensitive contacts in disordered loops tune enzyme I activity
title_short Temperature-sensitive contacts in disordered loops tune enzyme I activity
title_sort temperature-sensitive contacts in disordered loops tune enzyme i activity
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9704738/
https://www.ncbi.nlm.nih.gov/pubmed/36375052
http://dx.doi.org/10.1073/pnas.2210537119
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