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Enzyme mechanisms studied by single molecule optical sensing. PhD in Physics and Astronomy SWBio DTP)

  • Full or part time
  • Application Deadline
    Monday, December 02, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

Lead Supervisor
Professor Frank Vollmer, Department of Physics and Astronomy, College of Engineering, Mathematics and Physical Sciences, University of Exeter

Additional Supervisors
- Dr Stefan Bagby, Department of Biology and Biochemistry, University of Bath
- Professor Janet Anders, Department of Physics and Astronomy, College of Engineering, Maths and Physical Sciences, University of Exeter
- Dr Paul Whitley, Department of Biology and Biochemistry, University of Bath

Location: University of Exeter, Streatham Campus, Exeter, EX4 4QJ

Programme Overview
The South West Biosciences Doctoral Training Partnership (SWBio DTP is led by the University of Bristol, together with the Universities of Bath, Cardiff and Exeter, alongside Rothamsted Research.

For more information about the programme structure, please visit

Funding for 2020/21
These studentships are available to UK and EU nationals who have established UK residency (EU nationals must have ordinarily lived in the UK throughout the three years preceding the start of the studentship).

The four core universities (Bath, Bristol, Cardiff and Exeter) have a very limited number of fully-funded four year studentships for EU students who do not meet the residency requirements (1-2 studentships per university)*. Please contact the relevant university for more information.

*These are not available for CASE DTP studentships or Standard DTP studentships with a collaborative partner

Project Description

Ubiquitination is an important post-translational modification involved in modulation and regulation of protein function in many processes in most, if not all, eukaryotic cell types; ubiquitination goes awry in numerous diseases. Ubiquitination involves the covalent attachment to a target protein (the “substrate”) of one molecule, or multiple molecules in chains, of a small protein called ubiquitin (Figure 1). As described below, different types of ubiquitin chains can be assembled; this is important because chain type determines the biological outcome of ubiquitination (e.g. whether the substrate protein is degraded, or its function or location is affected), but currently it is difficult to determine chain type. The aim is to develop a rapid, accurate and user-friendly method to identify the type of ubiquitin chain assembled by any E3 ubiquitin ligase, at the same time providing new insights into ubiquitination mechanism and kinetics.

Ubiquitination, catalysed by ubiquitin ligases, involves covalent conjugation of ubiquitin to the protein substrate via formation of an isopeptide bond between ubiquitin’s C-terminal carboxylate and the substrate’s N-terminal amine or amino group of a lysine residue. In many cases a chain of ubiquitin molecules is assembled on a substrate protein (Figure 1) whereby a ubiquitin monomer is linked to the chain via any one of seven lysines or N-terminus. Ubiquitin chains can involve a single type of lysine linkage or mixed linkages, with each linkage producing a different degree of flexibility and repertoire of conformational states. Since chain type determines biological outcome, this project will provide detailed new insights into the relationships between E3 ligase function and resulting phenotype, and will therefore potentially advance understanding of the relationships between particular ubiquitin ligases and health and disease.

The project will involve a combination of cutting edge physical and biochemical methods. Ubiquitination reactions will be studied using plasmonically enhanced whispering gallery mode (WGM) microcavity sensing (Figure 1). This is the first optical technique capable of directly monitoring structural changes within individual biomolecules such as proteins. A major aim will be establishing whether each type of ubiquitin linkage has a unique WGM signature. Biochemical and chemical biology experiments with Drs Bagby and Whitley at Bath will include ubiquitination assays, and production of ubiquitin and enzymes (ligases and deubiquitinases) modified for immobilisation on gold nanoparticles that are used in WGM sensing. Single molecule WGM sensing studies of ubiquitin chain assembly will be conducted at Exeter with Professor Vollmer’s group.


To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria in line with UKRI guidelines see the following webpage for further details

A fully-funded four year SWBio DTP studentship will cover:

• a stipend at the standard Research Council UK rate; currently £15,009 per annum for 2019-2020
• research and training costs
• tuition fees (at the standard Research Councils UK rate)
• additional funds to support fieldwork, conferences and a 3-month internship

Funding Notes

SWBio DTP funded studentship available for September 2020 entry. The studentship will provide funding of fees and a stipend which is currently £15,009 per annum for 2019-20, on a full time basis.

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