title: Comparison of residual alpha- and beta-structures between two intrinsically disordered proteins by using NMR.
abstract: 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.
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
authors.forename: Yu-ichi
authors.initials: Y
authors.lastname: Ono
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
authors.forename: Manami
authors.initials: M
authors.lastname: Miyashita
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
authors.forename: Yumi
authors.initials: Y
authors.lastname: Ono
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan.
authors.forename: Honoka
authors.initials: H
authors.lastname: Okazaki
authors.affiliation: NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan.
authors.forename: Satoru
authors.initials: S
authors.lastname: Watanabe
authors.affiliation: NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan.
authors.forename: Naoya
authors.initials: N
authors.lastname: Tochio
authors.affiliation: NMR Pipeline Methodology Team, RIKEN Systems and Structural Biology Center, Tsurumi, Yokohama 230-0045, Japan.
authors.forename: Takanori
authors.initials: T
authors.lastname: Kigawa
authors.affiliation: Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano, Tokyo 164-8530, Japan. Electronic address: cnishimura@thu.ac.jp.
authors.forename: Chiaki
authors.initials: C
authors.lastname: Nishimura
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D003461:Crystallography; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D019590:Nucleocapsid Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D064531:Peripherins / Q000737:chemistry* / Q000648:ultrastructure*; D017433:Protein Structure, Secondary; D029867:Xenopus Proteins / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D000596:Amino Acids; D019590:Nucleocapsid Proteins; D064531:Peripherins; C579002:Prph2 protein, Xenopus; D029867:Xenopus Proteins; C000590691:measles virus nucleocapsid protein
keywords: Amide–proton exchange; Intrinsically disordered protein; N(tail) protein; NMR; Peripherin-2; Protein dynamics