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 ³ J_HN-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, ³ J_HN-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 ³ J_HN-H? coupling constants for IDPs, and for identifying locations that deviate from fully random behavior.

SUBMITTER: Shen Y 

PROVIDER: S-EPMC5734315 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature