Format

Send to

Choose Destination
Protein Sci. 2018 Jan;27(1):146-158. doi: 10.1002/pro.3292. Epub 2017 Oct 25.

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

Author information

1
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520.
2
National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850.

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 3 JHN-Hα 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, 3 JHN-Hα 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 3 JHN-Hα coupling constants for IDPs, and for identifying locations that deviate from fully random behavior.

KEYWORDS:

3JHN-Hα; IDP; NMR; Ramachandran map; coil library; scalar coupling

PMID:
28884933
PMCID:
PMC5734315
DOI:
10.1002/pro.3292
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Wiley Icon for PubMed Central
Loading ...
Support Center