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. 2018 Oct;27(10):1821-1830.
doi: 10.1002/pro.3485. Epub 2018 Oct 3.

Using 1 HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method

Hiroki Okazaki  1 , Naoki Matsuo  2 , Takeshi Tenno  2   3 , Natsuko Goda  2 , Yoshiki Shigemitsu  2 , Motonori Ota  1 , Hidekazu Hiroaki  2   3   4
Affiliations

Using 1 HN amide temperature coefficients to define intrinsically disordered regions: An alternative NMR method

Hiroki Okazaki et al. Protein Sci. 2018 Oct.

Abstract

This report describes a cost-effective experimental method for determining an intrinsically disordered protein (IDP) region in a given protein sample. In this area, the most popular (and conventional) means is using the amide (1 HN ) NMR signal chemical shift distributed in the range of 7.5-8.5 ppm. For this study, we applied an additional step: analysis of 1 HN chemical shift temperature coefficients (1 HN -CSTCs) of the signals. We measured 1 H-15 N two-dimensional NMR spectra of model IDP samples and ordered samples at four temperatures (288, 293, 298, and 303 K). We derived the 1 HN -CSTC threshold deviation, which gives the best correlation of ordered and disordered regions among the proteins examined (below -3.6 ppb/K). By combining these criteria with the newly optimized chemical shift range (7.8-8.5 ppm), the ratios of both true positive and true negative were improved by approximately 19% (62-81%) compared with the conventional "chemical shift-only" method.

Keywords: chemical shift temperature coefficient; hydrogen bond; intrinsically disordered protein; nuclear magnetic resonance.

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Figures

Figure 1
Figure 1
SOFAST‐HMQC spectra of the analyzed proteins recorded at four temperatures: (a) IDP‐B3, (b) IDP‐C1, (c) hUb, (d) mZO1‐PDZ1, (e) hVps4bMIT, (f) hSUMO1, and (g) hSUMO2. For all spectra, signals of 288, 293, 298, and 303 K are shown, respectively, as cyan, green, orange, and red.
Figure 2
Figure 2
Histograms of (a) 1HN‐CSTC and (b) 15NH‐CSTC for residues classified in both structured (light gray) and IDR (black) residues.
Figure 3
Figure 3
(a) MCC curve of IDP discrimination by change of the 1HN‐CSTC threshold. (b) ROC curve of IDP discrimination by 1HN‐CSTC < −3.6 ppb/K as IDR.
See this image and copyright information in PMC

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