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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 LU orcid and Bruix, Marta , et al. (2017) In Nature Communications 8.
Abstract

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... (More)

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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publishing date
type
Contribution to journal
publication status
published
keywords
Catalytic Domain, Escherichia coli, Evolution, Molecular, Molecular Dynamics Simulation, Protein Engineering, beta-Lactamases/metabolism
in
Nature Communications
volume
8
article number
16113
publisher
Nature Publishing Group
external identifiers
  • pmid:28719578
  • scopus:85024906997
ISSN
2041-1723
DOI
10.1038/ncomms16113
language
English
LU publication?
no
id
6be74366-06f2-4f20-8d4b-381e071d354a
date added to LUP
2025-01-11 21:23:54
date last changed
2025-04-20 11:50:17
@article{6be74366-06f2-4f20-8d4b-381e071d354a,
  abstract     = {{<p>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.</p>}},
  author       = {{Risso, Valeria A and Martinez-Rodriguez, Sergio and Candel, Adela M and Krüger, Dennis M and Pantoja-Uceda, David and Ortega-Muñoz, Mariano and Santoyo-Gonzalez, Francisco and Gaucher, Eric A and Kamerlin, Shina C L and Bruix, Marta and Gavira, Jose A and Sanchez-Ruiz, Jose M}},
  issn         = {{2041-1723}},
  keywords     = {{Catalytic Domain; Escherichia coli; Evolution, Molecular; Molecular Dynamics Simulation; Protein Engineering; beta-Lactamases/metabolism}},
  language     = {{eng}},
  month        = {{07}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Nature Communications}},
  title        = {{<i>De novo</i> active sites for resurrected Precambrian enzymes}},
  url          = {{http://dx.doi.org/10.1038/ncomms16113}},
  doi          = {{10.1038/ncomms16113}},
  volume       = {{8}},
  year         = {{2017}},
}