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Design and optimization of enzymatic activity in a de novo β‐barrel scaffold

While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated scaffolds an exciting alternative. Here we explore the customization of the backbone and sequence of a de no...

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Autores principales: Kipnis, Yakov, Chaib, Anissa Ouald, Vorobieva, Anastassia A., Cai, Guangyang, Reggiano, Gabriella, Basanta, Benjamin, Kumar, Eshan, Mittl, Peer R.E., Hilvert, Donald, Baker, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601869/
https://www.ncbi.nlm.nih.gov/pubmed/36305767
http://dx.doi.org/10.1002/pro.4405
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author Kipnis, Yakov
Chaib, Anissa Ouald
Vorobieva, Anastassia A.
Cai, Guangyang
Reggiano, Gabriella
Basanta, Benjamin
Kumar, Eshan
Mittl, Peer R.E.
Hilvert, Donald
Baker, David
author_facet Kipnis, Yakov
Chaib, Anissa Ouald
Vorobieva, Anastassia A.
Cai, Guangyang
Reggiano, Gabriella
Basanta, Benjamin
Kumar, Eshan
Mittl, Peer R.E.
Hilvert, Donald
Baker, David
author_sort Kipnis, Yakov
collection PubMed
description While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated scaffolds an exciting alternative. Here we explore the customization of the backbone and sequence of a de novo designed eight stranded β‐barrel protein to create catalysts for a retro‐aldolase model reaction. We show that active and specific catalysts can be designed in this fold and use directed evolution to further optimize activity and stereoselectivity. Our results support previous suggestions that different folds have different inherent amenability to evolution and this property could account, in part, for the distribution of natural enzymes among different folds.
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spelling pubmed-96018692022-10-27 Design and optimization of enzymatic activity in a de novo β‐barrel scaffold Kipnis, Yakov Chaib, Anissa Ouald Vorobieva, Anastassia A. Cai, Guangyang Reggiano, Gabriella Basanta, Benjamin Kumar, Eshan Mittl, Peer R.E. Hilvert, Donald Baker, David Protein Sci Full‐length Papers While native scaffolds offer a large diversity of shapes and topologies for enzyme engineering, their often unpredictable behavior in response to sequence modification makes de novo generated scaffolds an exciting alternative. Here we explore the customization of the backbone and sequence of a de novo designed eight stranded β‐barrel protein to create catalysts for a retro‐aldolase model reaction. We show that active and specific catalysts can be designed in this fold and use directed evolution to further optimize activity and stereoselectivity. Our results support previous suggestions that different folds have different inherent amenability to evolution and this property could account, in part, for the distribution of natural enzymes among different folds. John Wiley & Sons, Inc. 2022-10-26 2022-11 /pmc/articles/PMC9601869/ /pubmed/36305767 http://dx.doi.org/10.1002/pro.4405 Text en © 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society. https://creativecommons.org/licenses/by-nc/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Full‐length Papers
Kipnis, Yakov
Chaib, Anissa Ouald
Vorobieva, Anastassia A.
Cai, Guangyang
Reggiano, Gabriella
Basanta, Benjamin
Kumar, Eshan
Mittl, Peer R.E.
Hilvert, Donald
Baker, David
Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
title Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
title_full Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
title_fullStr Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
title_full_unstemmed Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
title_short Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
title_sort design and optimization of enzymatic activity in a de novo β‐barrel scaffold
topic Full‐length Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9601869/
https://www.ncbi.nlm.nih.gov/pubmed/36305767
http://dx.doi.org/10.1002/pro.4405
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