DeepEnzyme: a robust deep learning model for improved enzyme turnover number prediction by utilizing features of protein 3D-structures
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Abstract
Turnover numbers (kcat), which indicate an enzyme's catalytic efficiency, have a wide range of applications in fields including protein engineering and synthetic biology. Experimentally measuring the enzymes' kcat is always time-consuming. Recently, the prediction of kcat using deep learning models has mitigated this problem. However, the accuracy and robustness in kcat prediction still needs to be improved significantly, particularly when dealing with enzymes with low sequence similarity compared to those within the training dataset. Herein, we present DeepEnzyme, a cutting-edge deep learning model that combines the most recent Transformer and Graph Convolutional Network (GCN) to capture the information of both the sequence and 3D-structure of a protein. To improve the prediction accuracy, DeepEnzyme was trained by leveraging the integrated features from both sequences and 3D-structures. Consequently, DeepEnzyme exhibits remarkable robustness when processing enzymes with low sequence similarity compared to those in the training dataset by utilizing additional features from high-quality protein 3D-structures. DeepEnzyme also makes it possible to evaluate how point mutations affect the catalytic activity of the enzyme, which helps identify residue sites that are crucial for the catalytic function. In summary, DeepEnzyme represents a pioneering effort in predicting enzymes' kcat values with improved accuracy and robustness compared to previous algorithms. This advancement will significantly contribute to our comprehension of enzyme function and its evolutionary patterns across species.
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Flagged first, then by citations
- Authors
- Wang, T., Xiang, G., He, S., Su, L., Wang, Y., Yan, X., & Lu, H.
- Affiliations
- Shanghai Jiao Tong University (CN)
- Chongqing University of Technology (CN)
- East China University of Science and Technology (CN)
- Corresponding author
- Lu, Hongzhong
- Venue
- Briefings in Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-07-25
- Volume
- 25
- Issue
- 5
- ISSN
- 1467-5463 (ISSN-L)
- 1477-4054
- PMC
- PMC11880767
- OpenAlex
- W4401715368
- Cited by
- 57
- References
- 18
- Citations by year
- 2026: 30 · 2025: 22 · 2024: 5
- FWCI
- 7.73
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Briefings in Bioinformatics (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Key R&D Program of China (2022YFA0913000)
- National Natural Science Foundation of China (22208211, 22378263)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- turnover number, catalytic efficiency, protein 3D structure, protein sequences, transformer models, graph convolutional networks, low sequence similarity, catalytic residues
- MeSH terms
- Deep Learning, Algorithms, Enzymes, Models, Molecular, Protein Conformation, Proteins, Computational Biology
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