DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes.

Autor: Deng R; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China.; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China., Wu K; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China., Lin J; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China., Wang D; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China., Huang Y; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China., Li Y; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.; University of Chinese Academy of Sciences, Beijing 100049, China., Shi Z; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China., Zhang Z; School of Computer Science and Technology, Beijing Institute of Technology, Beijing 100081, China., Wang Z; Key Laboratory of Systems Bioengineering (Ministry of Education), Frontier Science Center for Synthetic Biology (Ministry of Education), Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China., Mao Z; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China., Liao X; Haihe Laboratory of Synthetic Biology, Tianjin 300308, China.; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China., Ma H; Biodesign Center, Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
Jazyk: angličtina
Zdroj: International journal of molecular sciences [Int J Mol Sci] 2024 Apr 28; Vol. 25 (9). Date of Electronic Publication: 2024 Apr 28.
DOI: 10.3390/ijms25094803
Abstrakt: The molecular weight (MW) of an enzyme is a critical parameter in enzyme-constrained models (ecModels). It is determined by two factors: the presence of subunits and the abundance of each subunit. Although the number of subunits (NS) can potentially be obtained from UniProt, this information is not readily available for most proteins. In this study, we addressed this gap by extracting and curating subunit information from the UniProt database to establish a robust benchmark dataset. Subsequently, we propose a novel model named DeepSub, which leverages the protein language model and Bi-directional Gated Recurrent Unit (GRU), to predict NS in homo-oligomers solely based on protein sequences. DeepSub demonstrates remarkable accuracy, achieving an accuracy rate as high as 0.967, surpassing the performance of QUEEN. To validate the effectiveness of DeepSub, we performed predictions for protein homo-oligomers that have been reported in the literature but are not documented in the UniProt database. Examples include homoserine dehydrogenase from Corynebacterium glutamicum , Matrilin-4 from Mus musculus and Homo sapiens , and the Multimerins protein family from M. musculus and H. sapiens . The predicted results align closely with the reported findings in the literature, underscoring the reliability and utility of DeepSub.
Databáze: MEDLINE
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