Mutation effect estimation on protein–protein interactions using deep contextualized representation learning

Abstract

The functional impact of protein mutations is reflected on the alteration of conformation and thermodynamics of protein–protein interactions (PPIs). Quantifying the changes of two interacting proteins upon mutations is commonly carried out by computational approaches. Hence, extensive research efforts have been put to the extraction of energetic or structural features on proteins, followed by statistical learning methods to estimate the effects of mutations on PPI properties. Nonetheless, such features require extensive human labors and expert knowledge to obtain, and have limited abilities to reflect point mutations. We present an end-to-end deep learning framework, MuPIPR (Mutation Effects in Protein–protein Interaction PRediction Using Contextualized Representations), to estimate the effects of mutations on PPIs. MuPIPR incorporates a contextualized representation mechanism of amino acids to propagate the effects of a point mutation to surrounding amino acid representations, therefore amplifying the subtle change in a long protein sequence. On top of that, MuPIPR leverages a Siamese residual recurrent convolutional neural encoder to encode a wild-type protein pair and its mutation pair. Multilayer perceptron regressors are applied to the protein pair representations to predict the quantifiable changes of PPI properties upon mutations. Experimental evaluations show that, with only sequence information, MuPIPR outperforms various state-of-the-art systems on estimating the changes of binding affinity for SKEMPI v1, and offers comparable performance on SKEMPI v2. Meanwhile, MuPIPR also demonstrates state-of-the-art performance on estimating the changes of buried surface areas. The software implementation is available at https://github. com/guangyu-zhou/MuPIPR.