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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 ...

  • 2022-06-16
  • Springer Science and Business Media LLC,2022
  • electronicrdacarrier

Numbers

  • LIBRIS-ID:oai:research.chalmers.se:064df9d5-9fb9-42b1-8e7e-29895be24007
  • https://doi.org/10.1038/s41929-022-00798-zDOI
  • https://research.chalmers.se/publication/530988URI

Supplementary language notes

  • Language:English
  • Summary in:English

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  • Subject category:art swepub-publicationtype
  • Subject category:ref swepub-contenttype

Notes

  • 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.

Subject headings and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Yuan, Le,1994Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)leyu (author)
  • Lu, Hongzhong,1987Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)luho (author)
  • Li, Gang,1991Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)gangl (author)
  • Chen, Yu,1990Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)cheyu (author)
  • Engqvist, Martin,1983Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)marengq (author)
  • Kerkhoven, Eduard,1985Chalmers tekniska högskola,Chalmers University of Technology(Swepub:cth)eduardk (author)
  • Nielsen, Jens B,1962Chalmers tekniska högskola,Chalmers University of Technology,BioInnovation Institute (BII)(Swepub:cth)nielsenj (author)
  • Chalmers tekniska högskolaBioInnovation Institute (BII) (creator_code:org_t)

Related titles

  • In:Nature Catalysis: Springer Science and Business Media LLC5:8, s. 662-6722520-1158

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