Deep transfer learning for inter-chain contact predictions of transmembrane protein complexes

• Published in: Nature communications 2023-08, Vol.14 (1), p.4935-16, Article 4935
• Main Authors: Lin, Peicong, Yan, Yumeng, Tao, Huanyu, Huang, Sheng-You
• Format: Article
• Language: English
• Subjects: 631/114/1305; 631/114/2410; 631/114/2411; 631/535; 82/1; Algorithms; Coding; Coevolution; Computational Biology - methods; Deep learning; Genes; Humanities and Social Sciences; Humans; Machine Learning; Membrane Proteins - chemistry; Membrane Proteins - genetics; Membranes; Molecular modelling; multidisciplinary; Predictions; Protein structure; Proteins; Receptors, G-Protein-Coupled; Residues; Science; Science (multidisciplinary); Transfer learning; Transmembrane proteins; Triangles; Yeast
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-40426-3

Membrane proteins are encoded by approximately a quarter of human genes. Inter-chain residue-residue contact information is important for structure prediction of membrane protein complexes and valuable for understanding their molecular mechanism. Although many deep learning methods have been proposed to predict the intra-protein contacts or helix-helix interactions in membrane proteins, it is still challenging to accurately predict their inter-chain contacts due to the limited number of transmembrane proteins. Addressing the challenge, here we develop a deep transfer learning method for predicting inter-chain contacts of transmembrane protein complexes, named DeepTMP, by taking advantage of the knowledge pre-trained from a large data set of non-transmembrane proteins. DeepTMP utilizes a geometric triangle-aware module to capture the correct inter-chain interaction from the coevolution information generated by protein language models. DeepTMP is extensively evaluated on a test set of 52 self-associated transmembrane protein complexes, and compared with state-of-the-art methods including DeepHomo2.0, CDPred, GLINTER, DeepHomo, and DNCON2_Inter. It is shown that DeepTMP considerably improves the precision of inter-chain contact prediction and outperforms the existing approaches in both accuracy and robustness. Membrane proteins are encoded by approximately a quarter of human genes. Here, the authors propose a deep transfer learning method for predicting inter-chain residue-residue contacts of transmembrane protein complexes.