LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries
Enzymes are potent catalysts with high specificity and selectivity. To leverage nature’s synthetic potential for industrial applications, various protein engineering techniques have emerged which allow to tailor the catalytic, biophysical, and molecular recognition properties of enzymes. However, th...
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ftpubmed:oai:pubmedcentral.nih.gov:10510078 2023-10-09T21:50:41+02:00 LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries Patsch, David Eichenberger, Michael Voss, Moritz Bornscheuer, Uwe T. Buller, Rebecca M. 2023-09-14 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510078/ https://doi.org/10.1016/j.csbj.2023.09.013 en eng Research Network of Computational and Structural Biotechnology http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510078/ http://dx.doi.org/10.1016/j.csbj.2023.09.013 © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Comput Struct Biotechnol J Software/Web Server Article Text 2023 ftpubmed https://doi.org/10.1016/j.csbj.2023.09.013 2023-09-24T00:56:50Z Enzymes are potent catalysts with high specificity and selectivity. To leverage nature’s synthetic potential for industrial applications, various protein engineering techniques have emerged which allow to tailor the catalytic, biophysical, and molecular recognition properties of enzymes. However, the many possible ways a protein can be altered forces researchers to carefully balance between the exhaustiveness of an enzyme screening campaign and the required resources. Consequently, the optimal engineering strategy is often defined on a case-by-case basis. Strikingly, while predicting mutations that lead to an improved target function is challenging, here we show that the prediction and exclusion of deleterious mutations is a much more straightforward task as analyzed for an engineered carbonic acid anhydrase, a transaminase, a squalene-hopene cyclase and a Kemp eliminase. Combining such a pre-selection of allowed residues with advanced gene synthesis methods opens a path toward an efficient and generalizable library construction approach for protein engineering. To give researchers easy access to this methodology, we provide the website LibGENiE containing the bioinformatic tools for the library design workflow. Text Carbonic acid PubMed Central (PMC) Computational and Structural Biotechnology Journal 21 4488 4496 |
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Software/Web Server Article Patsch, David Eichenberger, Michael Voss, Moritz Bornscheuer, Uwe T. Buller, Rebecca M. LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries |
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Software/Web Server Article |
description |
Enzymes are potent catalysts with high specificity and selectivity. To leverage nature’s synthetic potential for industrial applications, various protein engineering techniques have emerged which allow to tailor the catalytic, biophysical, and molecular recognition properties of enzymes. However, the many possible ways a protein can be altered forces researchers to carefully balance between the exhaustiveness of an enzyme screening campaign and the required resources. Consequently, the optimal engineering strategy is often defined on a case-by-case basis. Strikingly, while predicting mutations that lead to an improved target function is challenging, here we show that the prediction and exclusion of deleterious mutations is a much more straightforward task as analyzed for an engineered carbonic acid anhydrase, a transaminase, a squalene-hopene cyclase and a Kemp eliminase. Combining such a pre-selection of allowed residues with advanced gene synthesis methods opens a path toward an efficient and generalizable library construction approach for protein engineering. To give researchers easy access to this methodology, we provide the website LibGENiE containing the bioinformatic tools for the library design workflow. |
format |
Text |
author |
Patsch, David Eichenberger, Michael Voss, Moritz Bornscheuer, Uwe T. Buller, Rebecca M. |
author_facet |
Patsch, David Eichenberger, Michael Voss, Moritz Bornscheuer, Uwe T. Buller, Rebecca M. |
author_sort |
Patsch, David |
title |
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries |
title_short |
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries |
title_full |
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries |
title_fullStr |
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries |
title_full_unstemmed |
LibGENiE – A bioinformatic pipeline for the design of information-enriched enzyme libraries |
title_sort |
libgenie – a bioinformatic pipeline for the design of information-enriched enzyme libraries |
publisher |
Research Network of Computational and Structural Biotechnology |
publishDate |
2023 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510078/ https://doi.org/10.1016/j.csbj.2023.09.013 |
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Carbonic acid |
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Carbonic acid |
op_source |
Comput Struct Biotechnol J |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10510078/ http://dx.doi.org/10.1016/j.csbj.2023.09.013 |
op_rights |
© 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
op_doi |
https://doi.org/10.1016/j.csbj.2023.09.013 |
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Computational and Structural Biotechnology Journal |
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21 |
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4488 |
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4496 |
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1779313749105049600 |