Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model

Shiwei Liu, Tian Zhu, Milong Ren, Yu Chungong, Dongbo Bu, Haicang Zhang

Keywords: Riemannian Diffusion Probabilistic Model, Mutation, Protein-protein binding

TL;DR: We predict mutational effects on protein-protein binding using a side-chain diffusion probabilistic model.

Abstract: Many crucial biological processes rely on networks of protein-protein interactions. Predicting the effect of amino acid mutations on protein-protein binding is important in protein engineering, including therapeutic discovery. However, the scarcity of annotated experimental data on binding energy poses a significant challenge for developing computational approaches, particularly deep learning-based methods. In this work, we propose SidechainDiff, a novel representation learning-based approach that leverages unlabelled experimental protein structures. SidechainDiff utilizes a Riemannian diffusion model to learn the generative process of side-chain conformations and can also give the structural context representations of mutations on the protein-protein interface. Leveraging the learned representations, we achieve state-of-the-art performance in predicting the mutational effects on protein-protein binding. Furthermore, SidechainDiff is the first diffusion-based generative model for side-chains, distinguishing it from prior efforts that have predominantly focused on the generation of protein backbone structures.

Submission Number: 7105