Facilitating NMR Resonance Assignment with Metabolic Tampering

The ability to assign amino acid resonances in multidimensional NMR spectra of biomolecules is necessary for detailed studies of protein structure and dynamics. Despite creative advances in isotopic labeling, unlabeling and multidimensional NMR experiments, resonance assignment remains a bottleneck in studies of large proteins. In this work, we show that the metabolic flux through biosynthetic pathways of amino acid production during protein expression can be modulated to aid in the identification of resonances in two-dimensional NMR spectra. This straightforward method involves doping ¹⁵ N-enriched minimal media with small amounts of rich natural abundance media to generate unique peak intensity attenuation patterns, producing type-specific signatures of amino acids in two-dimensional ¹⁵ N HSQC experiments. Using three model proteins, IGPS (51 kDa heterodimer), PTP1B (35 kDa), PHPT1 (14 kDa), we show that this method can disentangle several amino acid types, is robust to different expression conditions, and is a useful supplement for triple resonance experiments in protein backbone resonance assignments.