Soft motions encoded by the fold and mediated by conserved hinge sites drive V‐ ATPase allosteric machinery and autoinhibition

Eukaryotic vacuolar H ⁺ ‐ATPase (V‐ATPase) is a multisubunit rotary proton pump that acidifies intracellular compartments, energized by ATP hydrolysis. Despite extensive structural data, our understanding of the molecular basis of its conformational changes and functionally critical sites remains incomplete. Using elastic network models, we performed spectral decomposition of the intrinsic modes of motion of human V‐ATPase, identifying hinge residues governing its most cooperative structural rearrangements. Most of these hinges are evolutionarily conserved or co‐evolutionarily coupled, underscoring their mechanical role in the allosteric machinery. Experimentally observed structural transitions, including rotary state changes, V ₁ V ₀ dissociation, and autoinhibition, are encoded in the softest intrinsically accessible modes. These structure‐encoded soft modes provide conformational paths to alternate functional states and highlight new sites for pharmacological interventions.