From single-sequence structure prediction to protein fitness landscape through a composable, epistasis-aware mutation atlas

Abstract

Mapping the multi-mutant fitness landscape is vital to protein engineering, but is challenging due to the vast combinatorial sequence space awaiting exploration. A central difficulty lies in the accurate and efficient modeling of non-additive epistatic effects among individual mutations, which partially arise from the physical inter-residue interactions prescribed by the protein structure. Existing fitness predictors usually perform well on single mutants but become less powerful for higher-order mutants, due to the lack of explicitly considering the relationship between sequence, structure and function of the target protein. Here, we present an end-to-end framework named Cerebra-Epistasis, which couples a single-sequence structure predictor that explicitly endows the structure awareness beyond the conventional sequence-fitness mapping with a downstream fitness prediction network that deliberately models the non-linear epistatic effects beyond the traditional additive terms. When evaluated across diverse assays, Cerebra-Epistasis outperforms the other state-of-the-art baselines in multi-mutant fitness prediction, with enhanced advantage over increasing mutation orders. Moreover, our special design on the epistasis modeling allows reliable extrapolation from low-order mutant data to unseen higher-order combinations, enabling one-shot inference of the overall mutation atlas from the starting sequence, a benefit that supposedly introduces three orders of magnitude acceleration in the landscape-scale prediction.