Comparison of residual alpha- and beta-structures between two intrinsically disordered proteins by using NMR

• The value of chemical shift was sensitive for detection of residual secondary structures.
• Protection of amide–proton exchange was more significant in beta-hairpin than in helix.
• Remaining structure of measles virus nucleoprotein was less compared to peripherin-2.
• Signal intensity of intrinsically disordered protein was random as a function of sequence.
• Alpha- and beta-structures were observed in the residual structures for both proteins.

Intrinsically disordered proteins contain some residual structures, which may fold further upon binding to the partner protein for function. The residual structures observed in two intrinsically disordered proteins, including the C-terminal segment of peripherin-2 (63 residues) and measles virus nucleocapsid protein Ntail (125 residues), were compared using NMR. Differences in the chemical shifts of alpha-, beta- and carbonyl carbons between the observed structure and calculated random coil revealed the existence of a helix and some possible beta-structures in both proteins. The intensity of signals in the C-terminal segment of peripherin-2 in NMR spectra was informative and locally low, particularly in the middle and N-terminal parts: this suggested the broadening of the signals caused by the formation of residual structures in those areas. Furthermore, the protection of exchange of amide protons was significantly observed at the N-terminus. Conversely, the intensities of signals for Ntail were random beyond the overall areas of protein, and indicated no characteristic pattern. Only a faint protection of amide–proton exchange in Ntail was observed in the C-terminus. It was concluded that Ntail was more intrinsically disordered than the C-terminal segment of peripherin-2. The combination of chemical shifts with the amide–proton exchanges and signal intensities was useful for the analyses of the remaining secondary structures. The beta-structure might be more detectable by the protection of amide–proton exchange than the helical structure, although the changes in chemical shifts were sensitive for the detection of elements of both secondary structures.