Non-Refoldability is Pervasive Across the E. coli Proteome

Abstract

The foundational paradigm of protein folding is that the primary sequence of a protein contains all the information needed for it to adopt a specific native structure1,2. This remarkable property is explained by Anfinsens thermodynamic hypothesis3,4, which asserts that because native states minimize the Gibbs free energy of a protein molecule under physiological conditions, proteins can reliably navigate to their native structures and remain in those states by ergodically sampling their free energy landscapes5. Most experiments of protein folding - conducted on purified, small, single-domain soluble proteins - follow the proportion of protein molecules that are folded as a function of time, temperature, denaturant concentration, or sequence6-8, and have yielded immense insight into the molecular determinants that underpin stable globular folds9,10. However, our reliance on the thermodynamic hypothesis as a ground truth to interpret these experiments has limited our ability to study the folding of complex proteins or to consider alternative non-thermodynamic scenarios11,12. Here, we introduce an experimental approach to probe protein refolding for whole proteomes. We accomplish this by first unfolding and refolding E. coli lysates, and then interrogating the resulting protein structures using a permissive protease that preferentially cleaves at flexible regions. Using mass spectrometry, we analyze the digestion patterns to globally assess structural differences between native and refolded proteins. These studies reveal that following denaturation, many proteins are incapable of navigating back to their native structures. Our results signal a pervasive role for co-translational folding in shaping protein biogenesis, and suggest that the apparent stability of many native states derive from kinetic persistence rather than thermodynamic stability.