Deconvolving mutation effects on protein stability and function with disentangled protein language models

Abstract

Understanding how evolutionary constraints shape protein sequences is fundamental to deciphering the molecular mechanisms underlying protein stability and function, which has broad implications in protein engineering and therapeutics development. Recent advances in protein language models (pLMs) have enabled accurate prediction of mutation effects through evolutionary information, effectively capturing the selective pressure that governs protein sequence variation. A critical challenge, however, remains in disentangling the intertwined mutation effects on protein stability and function, as evolutionary signals conflate both stability-driven and function-driven pressures, obscuring the mechanistic basis of mutation effects and limiting their utility for rational protein engineering. In this work, we introduce DETANGO, a novel deep learning framework that explicitly deconvolves the mutation effects on protein functions by removing components attributable to stability perturbations from the pLM-predicted mutation effects. Guided by computational or experimental stability measurements, DETANGO estimates a functional plausibility score for each single-point mutation that is the component of the mutation effect not accounted for by changes in stability. Single-point mutations with low functional plausibility are predicted to be stable-but-inactive (SBI) variants, whose compromised activities are caused by direct perturbations on functional mechanisms rather than structural stability. Residues enriched for such variants are inferred to be functionally critical, as indicated by the strong evolutionary pressures to maintain protein function. Through extensive benchmarking experiments, we show that DETANGO accurately identifies SBI variants and pinpoints functionally important residues across contexts, including ligand binding, catalysis, and allostery. Moreover, extending DETANGO from individual proteins to homologous protein families reveals shared and distinctive functional patterns across protein families. Collectively, these results establish DETANGO as a biologically grounded framework for disentangling evolutionary constraints on protein stability and function, advancing mechanistic understanding of protein function, and informing rational protein engineering.