Spatiotemporal graph neural networks reveal conformational binding signature in protein dynamics

Abstract

Biomolecular function is often controlled by structural and dynamical adaptations to binding events. Although molecular dynamics (MD) simulations can capture these events at atomic resolution, separating functional signatures from stochastic noise remains challenging. Traditional methods often struggle to isolate mechanistically relevant differences across independent replicas. Here, we introduce an explainable deep learning approach that learns state-specific dynamic signatures directly from MD trajectories. By coupling a dynamic protein graph representation with group-aware contrastive learning across independent replicas, the model detects the signatures, filtering out trajectory-specific correlations. An explainable AI framework then maps the identified differences on individual residues. We demonstrate this approach by identifying “binding-ready” conformations in a T4-Lysozyme mutant, recovering the allosteric determinants of peptide recognition in the PDZ3 domain, and isolating a ligand-independent activation signature for the A2A receptor. Our GISTnet-MD method generalizes across unseen data during comparative MD analysis, translating raw trajectory differences into residue-level determinants of protein function.