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Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.

Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.

Authors :
Shen Y
Roche J
Grishaev A
Bax A
Source :
Protein science : a publication of the Protein Society [Protein Sci] 2018 Jan; Vol. 27 (1), pp. 146-158. Date of Electronic Publication: 2017 Oct 25.
Publication Year :
2018

Abstract

Using fine-tuned hydrogen bonding criteria, a library of coiled peptide fragments has been generated from a large set of high-resolution protein X-ray structures. This library is shown to be an improved representation of ϕ/ψ torsion angles seen in intrinsically disordered proteins (IDPs). The ϕ/ψ torsion angle distribution of the library, on average, provides good agreement with experimentally observed chemical shifts and <superscript>3</superscript> J <subscript>HN-Hα</subscript> coupling constants for a set of five disordered proteins. Inspection of the coil library confirms that nearest-neighbor effects significantly impact the ϕ/ψ distribution of residues in the coil state. Importantly, <superscript>3</superscript> J <subscript>HN-Hα</subscript> coupling constants derived from the nearest-neighbor modulated backbone ϕ distribution in the coil library show improved agreement to experimental values, thereby providing a better way to predict <superscript>3</superscript> J <subscript>HN-Hα</subscript> coupling constants for IDPs, and for identifying locations that deviate from fully random behavior.<br /> (© 2017 The Protein Society. This article is a U.S. Government work and is in the public domain in the USA.)

Details

Language :
English
ISSN :
1469-896X
Volume :
27
Issue :
1
Database :
MEDLINE
Journal :
Protein science : a publication of the Protein Society
Publication Type :
Academic Journal
Accession number :
28884933
Full Text :
https://doi.org/10.1002/pro.3292