Atomic Structure of GNNQQNY Nanocrystals: A Validated Approach for Polymorphic Amyloids

Magic angle spinning (MAS) nuclear magnetic resonance (NMR) is a powerful tool for determining the structures of complex biological systems like amyloid fibrils, which are often challenging to study due to polymorphism. However, traditional MAS NMR techniques are often limited by low signal-to-noise ratios (SNR) for long-range distances and by spectral overlap in degenerate systems. Here we establish an approach to address these challenges using the amyloid heptapeptide GNNQQNY, an ideal model for studying polymorphism due to its ability to assemble into either crystals or fibrils depending on preparation conditions. By employing specific ¹³C,¹⁵N-labeling to resolve spectral degeneracy associated with three asparagine and two glutamine residues, we obtained numerous high-precision distance restraints using frequency-selective rotational echo double resonance (FSR) and z-filtered transfer echo double resonance (ZF-TEDOR) experiments. These restraints enabled us to calculate the high-resolution MAS NMR structure of GNNQQNY nanocrystals, which closely matches the known X-ray crystal structure, thus validating our approach. Anticipating severe spectral degeneracies in studying polymorphic fibrils, we also introduce a novel FSR-RFDR pulse sequence which effectively deconvolves overlapped resonances, enabling precise distance measurements even in complex spectra. Our validated method, which includes specific labeling and the FSR-RFDR sequence, establishes a robust pipeline for future structural studies of heterogeneous amyloid fibrils, advancing our understanding of polymorphism at the atomic level.