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

dc.contributor.authorOta, Motonori
dc.contributor.authorKoike, Ryotaro
dc.contributor.authorAmemiya, Takayuki
dc.contributor.authorTenno, Takeshi
dc.contributor.authorRomero, Pedro R.
dc.contributor.authorHiroaki, Hidekazu
dc.contributor.authorDunker, A. Keith
dc.contributor.authorFukuchi, Satoshi
dc.contributor.departmentCenter for Computational Biology and Bioinformatics, School of Medicine
dc.date.accessioned2025-06-10T06:42:45Z
dc.date.available2025-06-10T06:42:45Z
dc.date.issued2013
dc.description.abstractIntrinsically 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 3.2Å 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.
dc.eprint.versionAuthor's manuscript
dc.identifier.citationOta M, Koike R, Amemiya T, et al. An assignment of intrinsically disordered regions of proteins based on NMR structures. J Struct Biol. 2013;181(1):29-36. doi:10.1016/j.jsb.2012.10.017
dc.identifier.urihttps://hdl.handle.net/1805/48585
dc.language.isoen_US
dc.publisherElsevier
dc.relation.isversionof10.1016/j.jsb.2012.10.017
dc.relation.journalJournal of Structural Biology
dc.rightsPublisher Policy
dc.sourcePMC
dc.subjectAmino acid sequence
dc.subjectProtein conformation
dc.subjectProtein stability
dc.titleAn assignment of intrinsically disordered regions of proteins based on NMR structures
dc.typeArticle
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