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Deep learning-based...
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Li, Feiran,1993Chalmers tekniska högskola,Chalmers University of Technology
(author)
Deep learning-based k(cat) prediction enables improved enzyme-constrained model reconstruction
- Article/chapterEnglish2022
Publisher, publication year, extent ...
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2022-06-16
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Springer Science and Business Media LLC,2022
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electronicrdacarrier
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LIBRIS-ID:oai:research.chalmers.se:064df9d5-9fb9-42b1-8e7e-29895be24007
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https://doi.org/10.1038/s41929-022-00798-zDOI
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https://research.chalmers.se/publication/530988URI
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Language:English
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Summary in:English
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Subject category:art swepub-publicationtype
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Subject category:ref swepub-contenttype
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Enzyme turnover numbers (k(cat)) are key to understanding cellular metabolism, proteome allocation and physiological diversity, but experimentally measured k(cat) data are sparse and noisy. Here we provide a deep learning approach (DLKcat) for high-throughput k(cat) prediction for metabolic enzymes from any organism merely from substrate structures and protein sequences. DLKcat can capture k(cat) changes for mutated enzymes and identify amino acid residues with a strong impact on k(cat) values. We applied this approach to predict genome-scale k(cat) values for more than 300 yeast species. Additionally, we designed a Bayesian pipeline to parameterize enzyme-constrained genome-scale metabolic models from predicted k(cat) values. The resulting models outperformed the corresponding original enzyme-constrained genome-scale metabolic models from previous pipelines in predicting phenotypes and proteomes, and enabled us to explain phenotypic differences. DLKcat and the enzyme-constrained genome-scale metabolic model construction pipeline are valuable tools to uncover global trends of enzyme kinetics and physiological diversity, and to further elucidate cellular metabolism on a large scale.
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Yuan, Le,1994Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)leyu
(author)
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Lu, Hongzhong,1987Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)luho
(author)
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Li, Gang,1991Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)gangl
(author)
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Chen, Yu,1990Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)cheyu
(author)
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Engqvist, Martin,1983Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)marengq
(author)
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Kerkhoven, Eduard,1985Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)eduardk
(author)
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Nielsen, Jens B,1962Chalmers tekniska högskola,Chalmers University of Technology,BioInnovation Institute (BII)(Swepub:cth)nielsenj
(author)
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Chalmers tekniska högskolaBioInnovation Institute (BII)
(creator_code:org_t)
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In:Nature Catalysis: Springer Science and Business Media LLC5:8, s. 662-6722520-1158
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Li, Feiran, 1993
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