Front Quad

Dr John Vakonakis

Dr John Vakonakis

  • Tutorial Fellow in Biochemistry


I studied Biology as an undergraduate (BSc, 1999) at the University of Crete, Greece, followed by a PhD in the Biochemistry of Circadian Clocks (2004) at Texas A&M University, USA. It was at that time that I developed a strong interest for understanding biological processes at the atomic level. This interest brought me to Oxford in 2005, where I did postdoctoral research on how the extracellular environment of animal tissues is organised. In 2009 I joined the Swiss Light Source where I researched the formation of centrosome cell organelles, before starting my own lab in back in Oxford in 2010, as a Wellcome Trust Research Fellow. I joined Lincoln College in 2013.

College teaching

I teach Lincoln biochemists on Biological Chemistry and Biophysics in the first year of the course, and on Structural Biology, Biophysical Methods, and Data Analysis in years 2/3. Many of these tutorials are linked with the Biophysical Methods lectures I give at the Department of Biochemistry. In the fourth year of the Biochemistry course, the other Lincoln tutors and I support our students in writing their MSc (Part II) dissertations and in preparing to defend their work.

I also teach first year Biological Chemistry to Medics and Biomedical Sciences students at Lincoln.


My research seeks to understand the mechanisms behind biological system; put simply, I want to learn ‘how’ living organisms function. At the most fundamental level, this ‘how’ is an interplay between molecular structures, atomic forces, and chemistry. Thus, my laboratory uses cutting edge biophysical tools, including X-ray crystallography, nuclear magnetic resonance, and electron microscopy, to probe living systems. A major research focus recently has been the malaria parasite and how it modifies the human cells it invades. We hope to answer this question at the most detailed, atomic level, which may help the development of novel antimalarial drugs.

Select publications

Structural analysis of P. falciparum KAHRP and PfEMP1 complexes with host erythrocyte spectrin suggests a model for cytoadherent knob protrusions. Cutts EE, Laasch N, Reiter DM, Trenker R, Slater LM, Stansfeld PJ, Vakonakis I. PLoS Pathog. 13, 2017, e1006552, doi: 10.1371/journal.ppat.1006552.

The Caenorhabditis elegans protein SAS-5 forms large oligomeric assemblies critical for centriole formation. Rogala KB, Dynes NJ, Hatzopoulos GN, Yan J, Pong SK, Robinson CV, Deane CM, Gönczy P, Vakonakis I. eLife 4, 2015, e07410, doi: 10.7554/eLife.07410.

A Plasmodium falciparum PHIST protein binds the virulence factor PfEMP1 and co-migrates to knobs on the host cell surface. Oberli A, Slater LM, Cutts E, Brand F, Mundwiler-Pachlatko E, Rusch S, Masik MFG, Erat MC, Beck HP, Vakonakis I. FASEB J. 28, 2014, 4420-33, doi: 10.1096/fj.14-256057.

The Caenorhabditis elegans centriolar protein SAS-6 can form a spiral that is consistent with imparting a 9-fold symmetry. Hilbert M, Erat MC, Hachet V, Guichard P, Blank ID, Flückiger I, Slater L, Lowe ED, Hatzopoulos GN, Steinmetz MO, Gönczy P, Vakonakis I. Proc. Natl. Acad. Sci. U.S.A. 110, 2013 11373-8, doi: 10.1073/pnas.1302721110.

Structural Basis of the 9-Fold Symmetry of Centrioles. Kitagawa D, Vakonakis I, Olieric N, Hilbert M, Keller D, Olieric V, Bortfeld M, Erat MC, Flückiger I, Gönczy P, Steinmetz MO. Cell. 144, 2011, 364-75, doi: 10.1016/j.cell.2011.01.008.