The new mega dataset combined with a deep neural network makes progress in predicting the impact of single mutations on protein stability

Abstract

Prediction of proteins stability change ({Delta}{Delta}G) due to single mutation is important for biotechnology, medicine, and our understanding of physics underlying protein folding. Despite the recent tremendous success in 3D protein structure prediction, the apparently simpler problem of predicting the effect of mutations on protein stability has been hampered by the low amount of experimental data. With the recent high-throughput measurements of mutational effects in mega experiment for ~850,000 mutations [Tsuboyama et al., bioRxiv, 2022] it becomes possible to apply the state-of-the-art deep learning methods. Here we explore the ability of ESM2 deep neural network architecture with added Light Attention mechanism to predict the change of protein stability due to single mutations. The resulting method ABYSSAL predicts well the data from the mega experiment (Pearson correlation 0.85) while the prediction of {Delta}{Delta}G values from previous experiments is more modest (Pearson correlation 0.50). ABYSSAL also shows a perfect satisfaction of the antisymmetry property. The ABYSSAL training demonstrated that the dataset should contain around ~100,000 data points for taking advantage of the state-of-the-art deep learning methods. Overall, our study shows great perspectives for developing the deep learning {Delta}{Delta}G predictors.