PhD position:

'Putting a spin on structural biology –

Biomedical applications of pulsed high field electron paramagnetic resonance.'

This collaborative project between the laboratories of Prof Graham Smith and Dr Bela Bode aims to drive world-leading laboratory-built pulse high-field EPR instrumentation into biomedically relevant applications. Structural biology is investigating ever more complex systems. It emerges that often capturing the essential biological context is crucial for in vitro studies to become relevant to structure and function in vivo. While there is a range of extremely powerful structural techniques including cryo-EM, crystallography and NMR the addition of biological context (in the form of interacting proteins, nucleic acids, cofactors and metabolites) will most often compromise the structural resolution. Electron paramagnetic resonance (EPR) spectroscopy is an emerging method in the field of structural biology. Pulse dipolar EPR techniques such as PELDOR (also called DEER) and RIDME allow reliable nanometre distance measurements between two or more paramagnetic centres. These paramagnetic centres can be native metal ions or radical cofactors, but most commonly they are deliberately introduced by site-directed mutagenesis and site-specific spin-labelling. One particular advantage of EPR is that it is only sensitive to the spin centres and can thus be used with systems of tremendous complexity without being overwhelmed by the number of overlapping or unresolved signals. EPR has been shown to yield highly reliable results that are especially useful when docking quaternary structures from substructures, validating structural models or tracing conformational transitions. A major challenge in these measurements is posed by the sensitivity of EPR methods. However, St Andrews has been pursuing higher sensitivity (1). The HIPER spectrometer (2) developed in St Andrews offers more than an order of magnitude increase in sensitivity relative to the most used commercial instrumentation - making PELDOR measurements at physiological concentrations possible - and this opens up a new field in biomolecular science. Together with collaborators from the Biomedical Sciences Research Complex (BSRC) St Andrews we aim to exploit this hardware to make decisive progress understanding in the structure-function relationships of nucleic acid binding proteins, mechanosensation (3), and bacterial surface proteins by studying protein nucleic acid interactions, structural transitions in membrane proteins and protein-protein interactions.
The St Andrews-Dundee EPR grouping has an outstanding track record in EPR applications especially for biological distance measurements. Expertise ranges from production of optimised samples (mutagenesis, protein deuteration, reconstitution of membrane proteins) to data analysis and structural modelling and interpretation. St Andrews has the UK’s largest density of state-of-the-art pulse EPR facilities dedicated to structural biology applications.
This project will exploit the combined expertise of the Bode laboratory, driving methodology for biological EPR spectroscopy, and the mmwave and high-field EPR group being world leaders in the development of EPR instruments. The prospective student will receive training in a wide range of skills: molecular biology and mutagenesis, protein purification, spin-labelling, hands on EPR on laboratory built instruments and data analysis.
(1) Wort et al. (2019) Angew Chem Int Ed 131: 11807-11811.
(2) Giannoulis et al. (2018) Phys Chem Chem Phys 20: 2151-2154.
(3) Kapsalis et al. (2019) Nat Commun 10: 4619.
For a detailed description see FindAPhD. Please note BBSRC eligibility requirements (UK nationals and EU nationals resident in the UK for 3+ years). The deadline for applications is the 6th of January 2020.