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Universality of fold-encoded localized vibrations in enzymes

Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to sho...

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Autores principales: Chalopin, Yann, Piazza, Francesco, Mayboroda, Svitlana, Weisbuch, Claude, Filoche, Marcel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731342/
https://www.ncbi.nlm.nih.gov/pubmed/31492876
http://dx.doi.org/10.1038/s41598-019-48905-8
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author Chalopin, Yann
Piazza, Francesco
Mayboroda, Svitlana
Weisbuch, Claude
Filoche, Marcel
author_facet Chalopin, Yann
Piazza, Francesco
Mayboroda, Svitlana
Weisbuch, Claude
Filoche, Marcel
author_sort Chalopin, Yann
collection PubMed
description Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.
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spelling pubmed-67313422019-09-18 Universality of fold-encoded localized vibrations in enzymes Chalopin, Yann Piazza, Francesco Mayboroda, Svitlana Weisbuch, Claude Filoche, Marcel Sci Rep Article Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins. Nature Publishing Group UK 2019-09-06 /pmc/articles/PMC6731342/ /pubmed/31492876 http://dx.doi.org/10.1038/s41598-019-48905-8 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Chalopin, Yann
Piazza, Francesco
Mayboroda, Svitlana
Weisbuch, Claude
Filoche, Marcel
Universality of fold-encoded localized vibrations in enzymes
title Universality of fold-encoded localized vibrations in enzymes
title_full Universality of fold-encoded localized vibrations in enzymes
title_fullStr Universality of fold-encoded localized vibrations in enzymes
title_full_unstemmed Universality of fold-encoded localized vibrations in enzymes
title_short Universality of fold-encoded localized vibrations in enzymes
title_sort universality of fold-encoded localized vibrations in enzymes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731342/
https://www.ncbi.nlm.nih.gov/pubmed/31492876
http://dx.doi.org/10.1038/s41598-019-48905-8
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