Developing Electron Paramagnetic Resonance Spectroscopy for Studying Biomolecular Structures and Dynamics under Native Conditions

Global PhD Scholarship - St Andrews and Bonn - Chemistry

(Bode-Schiemann)

The University of St Andrews and the University of Bonn are pleased to offer a scholarship funded by both institutions, to support an exceptional student undertaking doctoral research in the following project:

Developing Electron Paramagnetic Resonance Spectroscopy for Studying Biomolecular Structures and Dynamics under Native Conditions

Structural investigation of biomolecules is fundamental to the elucidation of their functional mechanisms. In the dogma of modern structural biology, structure determines biomolecular function. However, increasing evidence shows that also flexibility and dynamics are important for biological function and have implications for dysfunction and disease. In addition, biomolecular function is governed by the interaction between biomolecules leading to the formation of large complexes within cells. Thus, the investigation of biological structures of ever-increasing complexity requires methods on the relevant length-scale and the ability to follow complex formation within cells.

This project will employ electron paramagnetic resonance (EPR) spectroscopy that has been making increasingly important contributions to studies of structure and dynamics over the past decade. EPR can provide nanometre distances between specific points of the biomolecular assembly and monitor changes in the structure and flexibility of the biomolecule. EPR detects the quantum mechanical spin of unpaired electrons. While all matter contains electrons, these are rarely unpaired as this leads to the high reactivity associated with ‘free radicals’. However, chemists have developed tools to introduce stable radicals selectively at strategic positions that can be arbitrarily chosen and thus are able to site-selectively label the biomolecule with a spin. The exclusive and exquisite sensitivity of EPR for electron spins gives the method a very high structural contrast and makes it very appealing in complicated systems where other methods lack resolution. Nevertheless, the method has the drawbacks that the system is commonly studied in isolation (in vitro) and lacks biological context. Furthermore, the spin-labels available commonly require cooling to very low temperatures for achieving good resolution and the molecules are often needed in concentrations that exceed physiological conditions by far.

This project will combine several recent achievements made by EPR researchers in Bonn, St Andrews and elsewhere. The use of bespoke triarylmethyl (TAM)-based spin labels developed in Bonn has allowed measurements in cells, despite the reducing environment and miniscule volume available. This type of strategy has been shown also to bring experiments at ambient temperature within grasp. In parallel, St Andrews researchers have been able to perform experiments at much lower concentrations using only 200 nanograms of sample. The new experimental approaches will be combined to demonstrate distance measurements at physiological concentrations, ambient temperature and in the biological context of the interior of a cell.

Room temperature measurements depend on a sufficiently slow rotational reorientation to not average the dipolar interaction between spins. This holds for both very large complexes and membrane anchored systems. The pathogen Yersinia circumvents the host’s immune system by the use of a Type III secretion system and its YopO protein activates upon actin binding. This leads to a large scale conformational change while also immobilising the protein. YopO is an ideal target for room temperature in cell measurements but several other opportunities exist if YopO were to prove intractable (e.g. bacterial surface proteins, nucleic acid binding/remodelling enzymes, amino sugar transferases). The scholar will synthesise the TAM spin-label and produce proteins constructs that will be TAM labelled. The conditions of the experiment shall be optimised before targeting both room temperature and intracellular measurements. Observing structural transitions under native conditions will pave the way for widespread application of this approach.

The project will be managed jointly between the School of Chemistry at St Andrews and the Institute for Physical and Theoretical Chemistry at Bonn. The student will be supervised by Dr Bela Bode (St Andrews) and Professor Olav Schiemann (Bonn).

Informal enquiries regarding this scholarship may be addressed to the co-supervisors ([Email Address Removed]; [Email Address Removed]).

Geographical criteria

• No restrictions.

Domicile for fee status

• No restrictions.

Level of study

• Postgraduate Research (Doctoral)
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Year of entry

• 2022-2023 academic year.
• If beginning at the University of Bonn, the student may start their degree at any point in the academic year 2022-2023 prior to a final entry date of 27 May 2023. Entry points for students beginning at St Andrews for this project are:
• 27 October
• 27 January
• 27 May

Schools

• School of Chemistry

Additional criteria

• Applicants must not already (i) hold a doctoral degree; or (ii) be matriculated for a doctoral degree at either the University of St Andrews or the University of Bonn (or another institution).

Scholarship application deadline

• Applicants should submit their application to the co-supervisors by 15 June 2022.

When will I hear if my application has been successful?

• You will be notified of the outcome of your application by 15 July 2022. Awards are subject to final signatures of contractual relationships between the parties and are not an indication of admission to the doctoral programme. Successful scholarship applicants must apply to both institutions and meet all relevant entry requirements for admission including any immigration requirements that may be in place.

Next steps

• Once notified, successful candidates should proceed to fulfil the application requirements for each University and must meet all normal entry requirements for admission – please see the advice on applying for research degree programmes. Applications should indicate that the applicant is the recipient of a Global PhD Scholarship St Andrews and Bonn (Bode-Schiemann).