High-pH NMR to Identify Macromolecular Hydrogen-Bonds and Foldons

Hydrogen bond (H-bond) restraints are critical for NMR structure determination, yet their experimental identification can be challenging for marginally stable structures that afford insufficient protection from (H/D) exchange in D ₂ O. As an alternative, we explored the use of NMR between pH 10 and 11 conditions that promote rapid exchange, for identifying backbone amide protons involved in H-bonds. We analyzed ∼750 amide sites distributed across ten proteins with known structures. Persistence of amide protons at high pH in standard 2D ¹ H- ¹⁵ N HSQC spectra for ¹⁵ N-labeled proteins in H2O, or TOCSY for unlabeled proteins, identifies H-bonds with ∼91% accuracy that exceeds the ∼80% accuracy of traditional H/D exchange experiments in D ₂ O. For two α-helical coiled coils and three globular proteins, we performed alkaline unfolding experiments taking advantage of amide NMR signal attenuation from unstructured polypeptides. Increasing the sample pH led to a progressive loss of native amide proton NMR signals, revealing an unfolding hierarchy where "foldons" remaining at the highest pH values had the most persistent H-bonds under EX1 exchange conditions. The foldons observed at high pH are consistent with partially folded structures previously characterized near neutral pH by native state hydrogen exchange, equilibrium unfolding, and protein fragment studies. For β-sheet proteins, foldons correspond to regions with high inter-residue contact density, whereas in coiled coils they demarcate regions with high α-helical propensity. High-pH NMR experiments provide a sensitive, fast, inexpensive, and broadly applicable approach to map H-bonding in marginally stable or partially folded proteins. Additionally, they offer the opportunity to explore uncharted protein dynamics and unfolding pathways under basic pH conditions.