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Issue 31, 2018
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Prediction of disulfide dihedral angles using chemical shifts

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Abstract

Cystine residues result from the formation of disulfide bonds between pairs of cysteine residues. This cross linking of the backbone is essential for the structure and activity of peptides and proteins. The conformation of a cystine side chain can be described using five dihedral angles, χ1, χ2, χ3, χ2′, and χ1′, with cystines favouring certain combinations of these angles. 2D NMR spectroscopy is ideally suited for structure determination of disulfide-rich peptides, because of their small size and constrained nature. However, only limited information of the cystine side chain conformation can be determined by NMR spectroscopy, leading to ambiguity in the deduced 3D structures. Resolving accurate structures is important as disulfide-rich peptides have proven to be promising drug candidates in a number of fields, either as bioactive leads or scaffolds. Using a database of NMR chemical shifts combined with crystallographic structures, we have developed a method called DISH that uses support vector machines to predict the dihedral angles of cysteine side chains. It is able to successfully predict χ2 angles with 91% accuracy, and has improved performance over existing prediction methods for χ1 angles, with 87% accuracy. For 81% of cysteine residues, DISH successfully predicted both the χ1 and χ2 angles. By revisiting published solution structures of peptides determined using NMR spectroscopy, we assessed the impact of additional cystine dihedral restraints on the quality of 3D models. DISH improved the resolution and accuracy, highlighting the potential for improving the understanding of structure–activity relationships and rational development of peptide drugs.

Graphical abstract: Prediction of disulfide dihedral angles using chemical shifts

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Publication details

The article was received on 28 Mar 2018, accepted on 02 Jul 2018 and first published on 05 Jul 2018


Article type: Edge Article
DOI: 10.1039/C8SC01423J
Chem. Sci., 2018,9, 6548-6556
  • Open access: Creative Commons BY-NC license
    All publication charges for this article have been paid for by the Royal Society of Chemistry

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    Prediction of disulfide dihedral angles using chemical shifts

    D. A. Armstrong, Q. Kaas and K. J. Rosengren, Chem. Sci., 2018, 9, 6548
    DOI: 10.1039/C8SC01423J

    This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Material from this article can be used in other publications provided that the correct acknowledgement is given with the reproduced material and it is not used for commercial purposes.

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