Protein side chain flexibility is essential for protein function and an impediment for drug design and protein docking algorithms, but side chain flexibility is difficult to analyse by X-ray crystallography or cryo-electron microscopy. Using solution NMR spectroscopy, multiple side chain conformations are evident from averaged scalar couplings and NOEs. The present project explores the use of pseudocontact shifts (PCS) to determine the spatial orientation of solvent-exposed long side-chains of residues such as lysine, where scalar couplings cannot be measured due to spectral overlap and NOEs are weak due to solvent exposure and reduced correlation times arising from side-chain mobility. PCSs are observed in NMR spectra as changes in the chemical shifts generated by paramagnetic tags. PCSs provide structural information at long distances from the tag. Using PCSs generated from two different lanthanide tagging sites established in ubiquitin previously [1], we investigated the localization space of the atoms of long side chains.
Reference
[1] Pearce, B.J.G., Jabar, S., Loh, C.-T., Szabo, M., Graham, B. and Otting, G. (2017) Structure restraints from heteronuclear pseudocontact shifts generated by lanthanide tags at two different sites. J. Biomol. NMR 68, 19-32.