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De novo active sites for resurrected Precambrian enzymes

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefo...

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Autores principales: Risso, Valeria A., Martinez-Rodriguez, Sergio, Candel, Adela M., Krüger, Dennis M., Pantoja-Uceda, David, Ortega-Muñoz, Mariano, Santoyo-Gonzalez, Francisco, Gaucher, Eric A., Kamerlin, Shina C. L., Bruix, Marta, Gavira, Jose A., Sanchez-Ruiz, Jose M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520109/
https://www.ncbi.nlm.nih.gov/pubmed/28719578
http://dx.doi.org/10.1038/ncomms16113
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author Risso, Valeria A.
Martinez-Rodriguez, Sergio
Candel, Adela M.
Krüger, Dennis M.
Pantoja-Uceda, David
Ortega-Muñoz, Mariano
Santoyo-Gonzalez, Francisco
Gaucher, Eric A.
Kamerlin, Shina C. L.
Bruix, Marta
Gavira, Jose A.
Sanchez-Ruiz, Jose M.
author_facet Risso, Valeria A.
Martinez-Rodriguez, Sergio
Candel, Adela M.
Krüger, Dennis M.
Pantoja-Uceda, David
Ortega-Muñoz, Mariano
Santoyo-Gonzalez, Francisco
Gaucher, Eric A.
Kamerlin, Shina C. L.
Bruix, Marta
Gavira, Jose A.
Sanchez-Ruiz, Jose M.
author_sort Risso, Valeria A.
collection PubMed
description Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.
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spelling pubmed-55201092017-07-28 De novo active sites for resurrected Precambrian enzymes Risso, Valeria A. Martinez-Rodriguez, Sergio Candel, Adela M. Krüger, Dennis M. Pantoja-Uceda, David Ortega-Muñoz, Mariano Santoyo-Gonzalez, Francisco Gaucher, Eric A. Kamerlin, Shina C. L. Bruix, Marta Gavira, Jose A. Sanchez-Ruiz, Jose M. Nat Commun Article Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering. Nature Publishing Group 2017-07-18 /pmc/articles/PMC5520109/ /pubmed/28719578 http://dx.doi.org/10.1038/ncomms16113 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ 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
Risso, Valeria A.
Martinez-Rodriguez, Sergio
Candel, Adela M.
Krüger, Dennis M.
Pantoja-Uceda, David
Ortega-Muñoz, Mariano
Santoyo-Gonzalez, Francisco
Gaucher, Eric A.
Kamerlin, Shina C. L.
Bruix, Marta
Gavira, Jose A.
Sanchez-Ruiz, Jose M.
De novo active sites for resurrected Precambrian enzymes
title De novo active sites for resurrected Precambrian enzymes
title_full De novo active sites for resurrected Precambrian enzymes
title_fullStr De novo active sites for resurrected Precambrian enzymes
title_full_unstemmed De novo active sites for resurrected Precambrian enzymes
title_short De novo active sites for resurrected Precambrian enzymes
title_sort de novo active sites for resurrected precambrian enzymes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520109/
https://www.ncbi.nlm.nih.gov/pubmed/28719578
http://dx.doi.org/10.1038/ncomms16113
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