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

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 ?/? torsion angles seen in intrinsically disordered proteins (IDPs). The ?/? torsion angle distribution of the library, on average, provides good agreement with experimentally observed chemical shifts and 3JHN-H? coupling constants for a set of five disordered proteins. Inspection of the coil library confirms that nearest-neighbor effects significantly impact the ?/? distribution of residues in the coil state. Importantly, 3JHN-H? coupling constants derived from the nearest-neighbor modulated backbone ? distribution in the coil library show improved agreement to experimental values, thereby providing a better way to predict 3JHN-H? coupling constants for IDPs, and for identifying locations that deviate from fully random behavior. This article is protected by copyright. All rights reserved.




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