An assignment of intrinsically disordered regions of proteins based on NMR structures

Motonori Ota, Ryotaro Koike, Takayuki Amemiya, Takeshi Tenno, Pedro R. Romero, Hidekazu Hiroaki, A. Dunker, Satoshi Fukuchi

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Intrinsically disordered proteins (IDPs) do not adopt stable three-dimensional structures in physiological conditions, yet these proteins play crucial roles in biological phenomena. In most cases, intrinsic disorder manifests itself in segments or domains of an IDP, called intrinsically disordered regions (IDRs), but fully disordered IDPs also exist. Although IDRs can be detected as missing residues in protein structures determined by X-ray crystallography, no protocol has been developed to identify IDRs from structures obtained by Nuclear Magnetic Resonance (NMR). Here, we propose a computational method to assign IDRs based on NMR structures. We compared missing residues of X-ray structures with residue-wise deviations of NMR structures for identical proteins, and derived a threshold deviation that gives the best correlation of ordered and disordered regions of both structures. The obtained threshold of 3.2. å was applied to proteins whose structures were only determined by NMR, and the resulting IDRs were analyzed and compared to those of X-ray structures with no NMR counterpart in terms of sequence length, IDR fraction, protein function, cellular location, and amino acid composition, all of which suggest distinct characteristics. The structural knowledge of IDPs is still inadequate compared with that of structured proteins. Our method can collect and utilize IDRs from structures determined by NMR, potentially enhancing the understanding of IDPs.

Original languageEnglish
Pages (from-to)29-36
Number of pages8
JournalJournal of Structural Biology
Volume181
Issue number1
DOIs
StatePublished - Jan 2013

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Intrinsically Disordered Proteins
Magnetic Resonance Spectroscopy
Proteins
X-Rays
Biological Phenomena
X Ray Crystallography
Amino Acids

Keywords

  • Deviations
  • Intrinsically disordered proteins
  • Matthews's correlation coefficient
  • Missing residues
  • Nuclear Magnetic Resonance

ASJC Scopus subject areas

  • Structural Biology

Cite this

Ota, M., Koike, R., Amemiya, T., Tenno, T., Romero, P. R., Hiroaki, H., ... Fukuchi, S. (2013). An assignment of intrinsically disordered regions of proteins based on NMR structures. Journal of Structural Biology, 181(1), 29-36. https://doi.org/10.1016/j.jsb.2012.10.017

An assignment of intrinsically disordered regions of proteins based on NMR structures. / Ota, Motonori; Koike, Ryotaro; Amemiya, Takayuki; Tenno, Takeshi; Romero, Pedro R.; Hiroaki, Hidekazu; Dunker, A.; Fukuchi, Satoshi.

In: Journal of Structural Biology, Vol. 181, No. 1, 01.2013, p. 29-36.

Research output: Contribution to journalArticle

Ota, M, Koike, R, Amemiya, T, Tenno, T, Romero, PR, Hiroaki, H, Dunker, A & Fukuchi, S 2013, 'An assignment of intrinsically disordered regions of proteins based on NMR structures', Journal of Structural Biology, vol. 181, no. 1, pp. 29-36. https://doi.org/10.1016/j.jsb.2012.10.017
Ota, Motonori ; Koike, Ryotaro ; Amemiya, Takayuki ; Tenno, Takeshi ; Romero, Pedro R. ; Hiroaki, Hidekazu ; Dunker, A. ; Fukuchi, Satoshi. / An assignment of intrinsically disordered regions of proteins based on NMR structures. In: Journal of Structural Biology. 2013 ; Vol. 181, No. 1. pp. 29-36.
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