Research Article | Open Access

Volume 2024 |Article ID 0031 | https://doi.org/10.34133/bdr.0031

High-Temperature Tolerance Protein Engineering through Deep Evolution

Huanyu Chu,^1,2,5 Zhenyang Tian,^1,2,3,5 Lingling Hu,^1,2,4 Hejian Zhang,^1,2,4 Hong Chang,^1,2,4 Jie Bai,^1,2,4 Dingyu Liu,^1,2 Lina Lu,^1,2 Jian Cheng,^1,2 Huifeng Jiang ^1,2

¹Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
²National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, P. R. China
³Tianjin Zhonghe Gene Technology Co., LTD, Tianjin 300308, P. R. China
⁴College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
⁵These authors contributed equally to this work

Abstract

Protein engineering aimed at increasing temperature tolerance through iterative mutagenesis and high-throughput screening is often labor-intensive. Here, we developed a deep evolution (DeepEvo) strategy to engineer protein high-temperature tolerance by generating and selecting functional sequences using deep learning models. Drawing inspiration from the concept of evolution, we constructed a high-temperature tolerance selector based on a protein language model, acting as selective pressure in the high-dimensional latent spaces of protein sequences to enrich those with high-temperature tolerance. Simultaneously, we developed a variant generator using a generative adversarial network to produce protein sequence variants containing the desired function. Afterward, the iterative process involving the generator and selector was executed to accumulate high-temperature tolerance traits. We experimentally tested this approach on the model protein glyceraldehyde 3-phosphate dehydrogenase, obtaining 8 variants with high-temperature tolerance from just 30 generated sequences, achieving a success rate of over 26%, demonstrating the high efficiency of DeepEvo in engineering protein high-temperature tolerance.