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Significance In the cell, proteins are continuously synthesized and degraded. Degradation as well as unraveling of aggregated proteins depends on the activity of a family of ATP-driven ring-shaped unfoldases that catalyze unfolding of protein substrates by threading them through central ring channels. Here we follow the unfolding, translocation, and refolding of a substrate as it passes through the central pore of VAT, an archetypal unfoldase, using a method based on chemical cross-linking and methyl transverse relaxation-optimized NMR spectroscopy. The approach yields insights about how molecular machines are able to unfold protein targets, showing that for multidomain proteins unfolding can proceed in a series of steps that vary depending on whether the substrate is unfolded from its N or C terminus.

Cotranslocational processing of the protein substrate calmodulin by an AAA+ unfoldase occurs via unfolding and refolding intermediates