Deep learning-based k(cat) prediction enables improved enzyme-constrained model reconstruction

• 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.

Ämnesord

NATURVETENSKAP  -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)

NATURVETENSKAP  -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)

NATURAL SCIENCES  -- Computer and Information Sciences -- Bioinformatics (hsv//eng)

NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)

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