Comprehensive NOE characterization of a partially folded large fragment of staphylococcal nuclease Δ131Δ, using NMR methods with improved resolution

Comprehensive NOE results from detailed structural characterization of a 131 residue partially folded fragment of staphylococcal nuclease (Δ131Δ) made possible by NMR methods with improved resolution are presented. The resulting NOE patterns reflect sampling of both α and β regions of Φ,φ conformational space, yet demonstrate significant preferences for both native-like and non-native-like rum and potentially helical conformations. Together with data from studies of the unfolded state of the drkN SH3 domain, NOE patterns observed for partially folded or unfolded proteins are summarized. It is surprising that few long-range NOEs were observed in Δ131Δ. The two longest-range NOEs are both native-like; one of these, an (i,i + 5) NOE, provides evidence for a Schellman capping motif for helix termination. Many aliphatic-aliphatic and aliphatic-amide NOEs, which are not normally observed in folded proteins, were detected. We have ruled out significant contributions from spin-diffusion for a number of these NOEs and suggest that one source may be sampling of non-prolyl cis peptide bond configurations in the disordered state of Δ131Δ.