Dr Jon Agirre

Royal Society Olga Kennard Research Fellow

Tel: 01904 32 8252  Office: B/K/065 (Biology, Campus West)
Email: jon.agirre@york.ac.uk

Computational methods in structural glycobiology

In our group, we create computer programs that help model and understand atomic structures of biomolecules. We are particularly interested in carbohydrates and their interactions with proteins. We favour a combination of Python for prototyping, C++ for number crunching, HTML and Javascript for representation. We are a friendly, diverse and very international bunch, and our ambition is to put YSBL at the forefront of crystallographic and cryoEM method development.

Research

Sugars - little image

‌‌We primarily work on the development of new methods for carbohydrate structure detection, refinement and validation. Using a YSBL-designed fingerprinting engine, we can create syntheses of different sugars and their environment, and then use that information for detecting features in a crystallographic or cryoEM map. This is precisely what the Sails software does. After they are built, structures can be refined and validated with the aid of Privateer, the first sugar-specific validation software to check ring conformation, stereochemistry, linkage torsions, nomenclature and fit to unbiased electron density maps. Additionally, Privateer produces vector diagrams (SVG) for glycans - these are compliant with the latest specification of the Standard Symbol Nomenclature for Glycans (SNFG). Privateer can be obtained through CCP4.

Together with Stuart McNicholas, and with key input from Gideon Davies, we have developed Glycoblocks, which is a schematic 3D representation for glycans and their interactions.‌ This representation is available within CCP4mg, the CCP4 molecular graphics program. As both are part of the CCP4 suite, CCP4mg can use the interactive 2D glycan diagrams and validation information generated by Privateer

Biography

I completed a degree in Computer Engineering (UPV/EHU, Donostia, Spain) in 2002, then moved on to doctoral training in structural virology, receiving my PhD in 2009 (Biophysics Unit, Bilbao, Spain). At the end of my PhD, I visited Prof. Jorge Navaza at the Institut de Biologie Structurale Jean-Pierre Ebel in Grenoble (2009, crucially funded by an EMBO short-term fellowship). I then obtained a 2-year fellowship (UPV/EHU) to do structural work on ion channels and their regulation by calmodulin, during which time I visited Prof. Félix Rey at the Institut Pasteur in Paris (2011, funded by UPV/EHU) to finish some dangling work from my PhD.

Between 2011 and 2012, I received priceless one-to-one training in crystallographic and cryoEM method development from Prof. Jorge Navaza, who was at the time visiting UPV/EHU (funded by Ikerbasque, Basque Foundation for Science). Informal and question-driven, these discussions were paramount in orientating my future career. In 2013, I went on to postdoctoral research with Profs Keith Wilson and Kevin Cowtan here in the Department of Chemistry where, in close collaboration with Prof. Gideon Davies, I produced most of the software I am currently recognised for. I also learned heaps of crystallography from Prof. Eleanor Dodson, who naturally filled Prof. Navaza's shoes and further expanded my training. In 2017, I was awarded a career-defining Royal Society University Research Fellowship to work on new methodologies for carbohydrate structure modelling, refinement, validation and representation. This fellowship has allowed me to build my own research group in York, and is providing me with outstanding training and career development opportunities. 

My team

‌‌PhD students

  • Mihaela Atanasova
    Funded by EPSRC, co-supervised by Kevin Cowtan and Paul Walton (Chemistry)

  • Haroldas Bagdonas
    Funded by The Royal Society, co-supervised by Dani Ungar (Biology)

  • Manal Alzahrani
    Funded by Saudi Ministry of Education. co-suppervised by Jamie Blaza and Gideon Davies (Chemistry)

‌‌Masters students

  • Iwan Hill
    Co-supervised by Tony Wilkinson (Chemistry)

  • Will Rochira
    Co-supervised by Kevin Cowtan (Chemistry)

Visitors

  • Alba Nin-Hill (April-June 2019, Universitat de Barcelona)

Upcoming events

I shall be taking part in the following events in the near future:

  • [organising] "CCP4 Study Weekend 2020", 7-9 January 2020 in Nottingham, UK. Tentative topic: model building and validation. Also, Mihaela will be speaking at this meeting.

Recent past events:

  • [speaking] "25 years of cryoelectron microscopy in Spain: a tribute to José L. Carrascosa", 12-13 June 2019 in Madrid, Spain.

  • [speaking] "25th international symposium on glycoconjugates", 25-31 August 2019 in Milano, Italy.

  • [attending] CCP4 developers meeting, 26-28 March 2019 in Abingdon, UK.

  • [attending] Royal Society course on Leadership effectiveness, 12-15 March 2019 in Chicheley Hall, UK.

  • [speaking] Invited talk at CIC bioGUNE, 1 March 2019 in Bilbao, Spain.

  • [attending] CCP4 Study Weekend 2019, 8-10 January 2019 in Nottingham, UK.

  • [speaking] Invited talk at Strubi, Wellcome Trust Centre for Human Genetics, 8 November 2018 in Oxford, UK.

Publications

Selected recent articles

  • Structural glycobiology in the age of electron cryo-microscopy. Mihaela Atanasova, Haroldas Bagdonas and Jon Agirre. Current Opinion in Structural Biology, in press. Post-print on OSF Preprints.
  • The molecular basis of endolytic activity of a multidomain alginate lyase from Defluviitalea phaphyphila, a representative of a new lyase family, PLxx. Shiqi Ji, Samuel Dix, Adli Aziz, Svetlana Sedelnikova, Patrick Baker, John Rafferty, Per Bullough, Svetomir Tzokov, Jon Agirre, Fu-Li Li and David Rice. Journal of Biological Chemistry, 2019, in press. 
  • Automating tasks in protein structure determination with the Clipper Python module. Stuart McNicholas, Tristan Croll, Tom Burnley, Colin Palmer, Scott Hoh, Huw Jenkins, Eleanor Dodson, Kevin Cowtan and Jon Agirre. Protein Science, 2018, 27(1), 207-216.
  • Strategies for carbohydrate model building, refinement and validation. Jon Agirre. Acta Crystallographica D, 2017, D73, 171-186.
  • Glycoblocks: a schematic 3D representation for glycans and their interactions. Stuart McNicholas and Jon Agirre. Acta Crystallographica, 2017, D73, 187-194.
  • Carbohydrate structure: the rocky road to automation. Jon Agirre, Gideon Davies, Keith Wilson and Kevin Cowtan. Current Opinion in Structural Biology, 2017, 44, 39-47.
  • Carbohydrate anomalies in the PDB. Jon Agirre, Gideon Davies, Keith Wilson and Kevin Cowtan. Nature Chemical Biology, 2015, 11, 303.
  • Privateer: software for the conformational validation of carbohydrate structures. Jon Agirre, Javier Iglesias-Fernández, Carme Rovira, Gideon Davies, Keith Wilson and Kevin Cowtan. Nature Structural & Molecular Biology, 2015, 22(11), 833-834.


For a more complete list, please check my Google Scholar profile.

Teaching

  • Core 3: Molecules & Reactions (CHE00017C) - I run small-group tutorials for Dalton college.

  • Core 4a: Molecules in Action (CHE00016I) - I run small-group tutorials for Dalton college.

  • Data Analysis (BIO00058M) - I lead the 'Analysing and using 3D structures in molecular bioscience research' strand, composed of two lectures and five practical sessions.

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Photo credit: Suzy Harrison

York Research Database link

Funding and support

My team's activities are supported (financially and/or logistically) by:

EPSRC Logo

University of York new logo

CCP-em logo

CCP Biosim logo