Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.
Protein Sci. 2017 Sep 08;:
Authors: Shen Y, Roche J, Grishaev A, Bax A
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) JHN-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) JHN-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) JHN-H? coupling constants for IDPs, and for identifying locations that deviate from fully random behavior. This article is protected by copyright. All rights reserved.
PMID: 28884933 [PubMed - as supplied by publisher]
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...
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Abstract
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Sequential nearest-neighbor effects on computed 13Cα chemical shifts
Abstract To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of 13Cα chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue α/β protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed 13Cα chemical...
Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins.
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