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Vornholt T, Mutný M, Schmidt GW, Schellhaas C, Tachibana R, Panke S, Ward TR, Krause A, Jeschek M. Enhanced Sequence-Activity Mapping and Evolution of Artificial Metalloenzymes by Active Learning. ACS CENTRAL SCIENCE 2024; 10:1357-1370. [PMID: 39071060 PMCID: PMC11273458 DOI: 10.1021/acscentsci.4c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/22/2024] [Accepted: 05/02/2024] [Indexed: 07/30/2024]
Abstract
Tailored enzymes are crucial for the transition to a sustainable bioeconomy. However, enzyme engineering is laborious and failure-prone due to its reliance on serendipity. The efficiency and success rates of engineering campaigns may be improved by applying machine learning to map the sequence-activity landscape based on small experimental data sets. Yet, it often proves challenging to reliably model large sequence spaces while keeping the experimental effort tractable. To address this challenge, we present an integrated pipeline combining large-scale screening with active machine learning, which we applied to engineer an artificial metalloenzyme (ArM) catalyzing a new-to-nature hydroamination reaction. Combining lab automation and next-generation sequencing, we acquired sequence-activity data for several thousand ArM variants. We then used Gaussian process regression to model the activity landscape and guide further screening rounds. Critical characteristics of our pipeline include the cost-effective generation of information-rich data sets, the integration of an explorative round to improve the model's performance, and the inclusion of experimental noise. Our approach led to an order-of-magnitude boost in the hit rate while making efficient use of experimental resources. Search strategies like this should find broad utility in enzyme engineering and accelerate the development of novel biocatalysts.
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Affiliation(s)
- Tobias Vornholt
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- National
Centre of Competence in Research (NCCR) Molecular Systems Engineering, 4056 Basel,Switzerland
| | - Mojmír Mutný
- Department
of Computer Science, ETH Zurich, Andreasstrasse 5, 8092 Zurich, Switzerland
| | - Gregor W. Schmidt
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Christian Schellhaas
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Ryo Tachibana
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Sven Panke
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- National
Centre of Competence in Research (NCCR) Molecular Systems Engineering, 4056 Basel,Switzerland
| | - Thomas R. Ward
- National
Centre of Competence in Research (NCCR) Molecular Systems Engineering, 4056 Basel,Switzerland
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, 4058 Basel, Switzerland
| | - Andreas Krause
- Department
of Computer Science, ETH Zurich, Andreasstrasse 5, 8092 Zurich, Switzerland
| | - Markus Jeschek
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
- Institute
of Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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Chen L, Yu K, Ma A, Zhu W, Wang H, Tang X, Tang Y, Li Y, Li J. Enhanced Thermostability of Nattokinase by Computation-Based Rational Redesign of Flexible Regions. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14241-14254. [PMID: 38864682 DOI: 10.1021/acs.jafc.4c02335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Nattokinase is a nutrient in healthy food natto that has the function of preventing and treating blood thrombus. However, its low thermostability and fibrinolytic activity limit its application in food and pharmaceuticals. In this study, we used bioinformatics analysis to identify two loops (loop10 and loop12) in the flexible region of nattokinase rAprY. Using this basis, we screened the G131S-S161T variant, which showed a 2.38-fold increase in half-life at 55 °C, and the M3 variant, which showed a 2.01-fold increase in activity, by using a thermostability prediction algorithm. Bioinformatics analysis revealed that the enhanced thermostability of the G131S-S161T variant was due to the increased rigidity and structural shrinkage of the overall structure. Additionally, the increased rigidity of the local region surrounding the active center and its mutated sites helps maintain its normal conformation in high-temperature environments. The increased catalytic activity of the M3 variant may be due to its more efficient substrate binding mechanism. We investigated strategies to improve the thermostability and fibrinolytic activity of nattokinase, and the resulting variants show promise for industrial production and application.
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Affiliation(s)
- Liangqi Chen
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Kongfang Yu
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
| | - Aixia Ma
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Wenhui Zhu
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
| | - Hong Wang
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
| | - Xiyu Tang
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Yaolei Tang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
- The Third People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830000, China
| | - Yuan Li
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Jinyao Li
- Institute of Materia Medica, College of Pharmacy, Xinjiang University, Urumqi 830017, China
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
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Tripp A, Braun M, Wieser F, Oberdorfer G, Lechner H. Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering. Chembiochem 2024:e202400092. [PMID: 38634409 DOI: 10.1002/cbic.202400092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Enzyme engineering, though pivotal across various biotechnological domains, is often plagued by its time-consuming and labor-intensive nature. This review aims to offer an overview of supportive in silico methodologies for this demanding endeavor. Starting from methods to predict protein structures, to classification of their activity and even the discovery of new enzymes we continue with describing tools used to increase thermostability and production yields of selected targets. Subsequently, we discuss computational methods to modulate both, the activity as well as selectivity of enzymes. Last, we present recent approaches based on cutting-edge machine learning methods to redesign enzymes. With exception of the last chapter, there is a strong focus on methods easily accessible via web-interfaces or simple Python-scripts, therefore readily useable for a diverse and broad community.
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Affiliation(s)
- Adrian Tripp
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Markus Braun
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Florian Wieser
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Gustav Oberdorfer
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
| | - Horst Lechner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
- BioTechMed, Graz, Austria
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Markus B, C GC, Andreas K, Arkadij K, Stefan L, Gustav O, Elina S, Radka S. Accelerating Biocatalysis Discovery with Machine Learning: A Paradigm Shift in Enzyme Engineering, Discovery, and Design. ACS Catal 2023; 13:14454-14469. [PMID: 37942268 PMCID: PMC10629211 DOI: 10.1021/acscatal.3c03417] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023]
Abstract
Emerging computational tools promise to revolutionize protein engineering for biocatalytic applications and accelerate the development timelines previously needed to optimize an enzyme to its more efficient variant. For over a decade, the benefits of predictive algorithms have helped scientists and engineers navigate the complexity of functional protein sequence space. More recently, spurred by dramatic advances in underlying computational tools, the promise of faster, cheaper, and more accurate enzyme identification, characterization, and engineering has catapulted terms such as artificial intelligence and machine learning to the must-have vocabulary in the field. This Perspective aims to showcase the current status of applications in pharmaceutical industry and also to discuss and celebrate the innovative approaches in protein science by highlighting their potential in selected recent developments and offering thoughts on future opportunities for biocatalysis. It also critically assesses the technology's limitations, unanswered questions, and unmet challenges.
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Affiliation(s)
- Braun Markus
- Department
of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Gruber Christian C
- Enzyme
and Drug Discovery, Innophore. 1700 Montgomery Street, San Francisco, California 94111, United States
| | - Krassnigg Andreas
- Enzyme
and Drug Discovery, Innophore. 1700 Montgomery Street, San Francisco, California 94111, United States
| | - Kummer Arkadij
- Moderna,
Inc., 200 Technology
Square, Cambridge, Massachusetts 02139, United States
| | - Lutz Stefan
- Codexis
Inc., 200 Penobscot Drive, Redwood City, California 94063, United States
| | - Oberdorfer Gustav
- Department
of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Siirola Elina
- Novartis
Institute for Biomedical Research, Global Discovery Chemistry, Basel CH-4108, Switzerland
| | - Snajdrova Radka
- Novartis
Institute for Biomedical Research, Global Discovery Chemistry, Basel CH-4108, Switzerland
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Cadet F, Saavedra E, Syren PO, Gontero B. Editorial: Machine learning, epistasis, and protein engineering: From sequence-structure-function relationships to regulation of metabolic pathways. Front Mol Biosci 2022; 9:1098289. [DOI: 10.3389/fmolb.2022.1098289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
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6
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Wittmund M, Cadet F, Davari MD. Learning Epistasis and Residue Coevolution Patterns: Current Trends and Future Perspectives for Advancing Enzyme Engineering. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marcel Wittmund
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Frederic Cadet
- Laboratory of Excellence LABEX GR, DSIMB, Inserm UMR S1134, University of Paris city & University of Reunion, Paris 75014, France
| | - Mehdi D. Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
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