NEXT-FRET maps nonequilibrium rerouting of <i>Escherichia coli</i> maltose-binding protein folding by its signal peptide and chaperones

Maltose-Binding Protein (MBP) and pre-MBP to reveal a long-sought closed on-pathway intermediate that exchanges with both native and unfolded states. The signal peptide raises the barrier selectively for the intermediate-to-native transition. Profiling interactions with chaperones shows that each stabilizes nonnative conformations distinctively, generating kinetic traps. These findings demonstrate that sequence features and proteostasis factors actively reshape the folding landscape. By following molecules out of equilibrium, NEXT-FRET reveals intermediates invisible at equilibrium. This reflects the inherent nonequilibrium character of cells, which maintain order through ongoing energy exchange and dissipation, with fluctuations governing the kinetics and connectivity of biomolecular states. By exposing transient intermediates and quantifying kinetic flows, NEXT-FRET offers a scalable strategy to interrogate nonequilibrium dynamics, providing mechanistic insights into protein (mis)folding, enzyme catalysis, ligand binding and broader biomolecular reactions with implications for biotechnology and therapeutics.