Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

  1. Haroldas BagdonasORCID Logo,
  2. Daniel UngarORCID Logo and
  3. Jon AgirreORCID Logo

Submitting author affiliation: University of York, York, United Kingdom

Beilstein Arch. 2020, 202083. https://doi.org/10.3762/bxiv.2020.83.v1

Published 20 Jul 2020

  • Preprint

Abstract

The heterogeneity, mobility and complexity of glycans in glycoproteins have been, and currently remain, significant challenges in structural biology. Those aspects present unique problems to the two most prolific techniques: X-ray crystallography and cryo-electron microscopy. At the same time, advances in mass spectrometry have made it possible to get deeper insights on precisely the information that is most difficult to recover by structure solution methods: full-length glycan composition, including linkage details for the glycosidic bonds. These developments have given rise to glycomics. Thankfully, several large scale glycomics initiatives have stored results in publicly-available databases, some of which can be accessed through API interfaces. In the present work, we will describe how the Privateer carbohydrate structure validation software has been extended to harness results from glycomics projects, and its use to greatly improve the validation of 3D glycoprotein structures.

Keywords: Glycomics; Privateer; Glycoinformatics; X-ray Crystallography; Electron cryo-microscopy

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When a peer-reviewed version of this preprint is available, this information will be updated in the information box above. If no peer-reviewed version is available, please cite this preprint using the following information:

Bagdonas, H.; Ungar, D.; Agirre, J. Beilstein Arch. 2020, 202083. doi:10.3762/bxiv.2020.83.v1

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