Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences
White-rot fungi secrete a repertoire of high-redox potential oxidoreductases to efficiently decompose lignin. Of these enzymes, versatile peroxidases (VPs) are the most promiscuous biocatalysts. VPs are attractive enzymes for research and industrial use but their recombinant production is extremely challenging. To date, only a single VP has been structurally characterized and optimized for recombinant functional expression, stability, and activity. Computational enzyme optimization methods can be applied to many enzymes in parallel but they require accurate structures. Here, we demonstrate that model structures computed by deep-learning-based ab initio structure prediction methods are reliable starting points for one-shot PROSS stability-design calculations. Four designed VPs encoding as many as 43 mutations relative to the wildtype enzymes are functionally expressed in yeast, whereas their wildtype parents are not. Three of these designs exhibit substantial and useful diversity in their reactivity profiles and tolerance to environmental conditions. The reliability of the new generation of structure predictors and design methods increases the scale and scope of computational enzyme optimization, enabling efficient discovery and exploitation of the functional diversity in natural enzyme families directly from genomic databases.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2022 |
|---|---|
| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:144 |
|---|---|
| Enthalten in: |
Journal of the American Chemical Society - 144(2022), 8 vom: 02. März, Seite 3564-3571 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Barber-Zucker, Shiran [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
9005-53-2 |
|---|
| Anmerkungen: |
Date Completed 18.04.2022 Date Revised 31.05.2022 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1021/jacs.1c12433 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM33711739X |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM33711739X | ||
| 003 | DE-627 | ||
| 005 | 20231225233700.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231225s2022 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1021/jacs.1c12433 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1123.xml |
| 035 | |a (DE-627)NLM33711739X | ||
| 035 | |a (NLM)35179866 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Barber-Zucker, Shiran |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences |
| 264 | 1 | |c 2022 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 18.04.2022 | ||
| 500 | |a Date Revised 31.05.2022 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a White-rot fungi secrete a repertoire of high-redox potential oxidoreductases to efficiently decompose lignin. Of these enzymes, versatile peroxidases (VPs) are the most promiscuous biocatalysts. VPs are attractive enzymes for research and industrial use but their recombinant production is extremely challenging. To date, only a single VP has been structurally characterized and optimized for recombinant functional expression, stability, and activity. Computational enzyme optimization methods can be applied to many enzymes in parallel but they require accurate structures. Here, we demonstrate that model structures computed by deep-learning-based ab initio structure prediction methods are reliable starting points for one-shot PROSS stability-design calculations. Four designed VPs encoding as many as 43 mutations relative to the wildtype enzymes are functionally expressed in yeast, whereas their wildtype parents are not. Three of these designs exhibit substantial and useful diversity in their reactivity profiles and tolerance to environmental conditions. The reliability of the new generation of structure predictors and design methods increases the scale and scope of computational enzyme optimization, enabling efficient discovery and exploitation of the functional diversity in natural enzyme families directly from genomic databases | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 7 | |a Lignin |2 NLM | |
| 650 | 7 | |a 9005-53-2 |2 NLM | |
| 650 | 7 | |a Peroxidases |2 NLM | |
| 650 | 7 | |a EC 1.11.1.- |2 NLM | |
| 700 | 1 | |a Mindel, Vladimir |e verfasserin |4 aut | |
| 700 | 1 | |a Garcia-Ruiz, Eva |e verfasserin |4 aut | |
| 700 | 1 | |a Weinstein, Jonathan J |e verfasserin |4 aut | |
| 700 | 1 | |a Alcalde, Miguel |e verfasserin |4 aut | |
| 700 | 1 | |a Fleishman, Sarel J |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of the American Chemical Society |d 1945 |g 144(2022), 8 vom: 02. März, Seite 3564-3571 |w (DE-627)NLM00000569X |x 1520-5126 |7 nnns |
| 773 | 1 | 8 | |g volume:144 |g year:2022 |g number:8 |g day:02 |g month:03 |g pages:3564-3571 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1021/jacs.1c12433 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 144 |j 2022 |e 8 |b 02 |c 03 |h 3564-3571 | ||