Conference by Dr. Jon Agirre

Dr. Jon Agirre (YSBL, Department of Chemistry, University of York, UK)

With over 200,000 atomic structures of biological macromolecules, the Protein Data Bank (PDB) is a key resource in biotechnological and medical research. About 10% of the PDB structures deposited annually contain carbohydrates, either as ligands or covalent modifications to proteins, with N-glycosylation being most frequently modelled. Achieving high precision in structural data – – requires order and homogeneity, two characteristics protein glycosylation is not particularly associated with. Imprecise structural data will often lead to inaccurate atomic modelling, with potentially awful knock-on effects on docking, simulations and misinterpretation of glycochemical features – e.g. the suggestion of unlikely linkages. While the PDB have come a long way towards addressing many of these issues through validation and remediation efforts, it is still extremely important that structural biologists use glycan-specific modelling and validation software prior to deposition in order to make the most of structural data and avoid common pitfalls. The Privateer software is one such tool; first published 10 years ago (2015), it has been developed to detect and address most structural issues affecting poly- and oligosaccharides down to the monosaccharide level, with pyranoside ring conformation being one of the most useful quality indicators. In this talk, I will show how the most common issues can be detected and addressed, leading to the improvement and ultimately extension of deposited atomic models of glycoproteins and protein-carbohydrate complexes.

Short bio: Jon Agirre did an MEng in Computer Science in San Sebastian (Spain), then completed a PhD in Biochemistry in Bilbao (Spain), followed by two postdoctoral short-term fellowships at the IBS Grenoble (France) and Institut Pasteur (France), after which he moved to the University of York, where he started his own group in the Department of Chemistry with the support of a Royal Society University Research Fellowship. After 8 years, he is now lecturer in the department, focusing on validation and improvement of 3D atomic models of glycoproteins and protein-carbohydrate complexes.
 

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