Deep learning on protein language model embeddings unlocks accurate prediction of protein solubility

Protein misfolding is a major limitation in prokaryotic expression systems, which lack post-translational modifications and exhibit distinct intracellular environments. This severely hinders the functional expression of many heterologous proteins, especially in Escherichia coli. Accurate prediction of protein solubility is crucial for synthetic biology and protein engineering but remains a challenging task.

Here, we present DeepSolNet, a deep learning model that leverages advanced protein language models to enhance solubility prediction. DeepSolNet adopts a multi-module architecture, integrating contextual embeddings from ESM Cambrian with bidirectional long short-term memory networks, convolutional neural networks, and attention mechanisms.

On the validation set, DeepSolNet achieved an accuracy of 0.75 and a Matthews correlation coefficient of 0.50 for soluble/insoluble protein classification. On an independently constructed test set containing gammabody, transglutaminase, and aldehyde dehydrogenase sequences, the model maintained high performance with an accuracy of 0.53, achieving state-of-the-art performance. Visualization analyses further showed that DeepSolNet is sensitive to key residues influencing protein solubility.

These results demonstrate that DeepSolNet serves as a powerful and generalizable tool for large-scale protein design and expression optimization. The tool is freely available at https://github.com/wangxinglong1990/DeepSolNet.