Morpheus-3D: Structural Diversity-Guided Detection and Localization of Protein Fold Switching

Abstract

Proteins that reversibly adopt multiple stable folds challenge the classical sequence–structure paradigm, yet their discovery remains limited because fold switching is difficult to detect experimentally and current computational methods fail to resolve the underlying conformationally plastic regions. Here we present Morpheus-3D, a sequence-based framework that quantifies residue-level tertiary structural diversity using entropy profiles derived from the Foldseek 3Di structural alphabet. By capturing variation in tertiary interaction environments rather than secondary structure alone, Morpheus-3D identifies fold-switching proteins while simultaneously localizing the sequence regions responsible for structural transitions. The framework outperforms existing predictors, accurately recovers experimentally characterized switching regions, generalizes to recently discovered natural and engineered fold-switching proteins absent from training, and detects conformational plasticity inaccessible to secondary-structure-based approaches. Application to 57 representative proteomes reveals that fold-switching potential is widespread but enriched in regulatory, pathogenic, and environmentally adaptive lineages. Integration with ancestral sequence reconstruction further un-covers evolutionary trajectories through which conformational plasticity emerges. To make these predictions directly accessible, we implemented Morpheus-3D as an interactive web platform (https://morpheus.slicearrow.com/), in which per-residue entropy profiles, sequence and three-dimensional structure are displayed together and respond as one, allowing predicted fold-switching regions to be mapped onto the structure and exported for downstream analysis. Morpheus-3D provides a scalable framework for discovering metamorphic proteins and investigating the origins, mechanisms, and evolution of structural plasticity directly from sequence.