Postgraduate research opportunities

Identifying chemical probes to characterise intrinsically disordered drug targets through novel ion mobility-based screening capabilities

Ion mobility mass spectrometry will be used to characterise an intrinsically disordered protein that is involved in cancer. Screening methods will be developed to identify small molecules that affect the behaviour of the protein, to be used as chemical probes for its validation as a suitable drug target.

Number of places

1

Funding

Home fee, Stipend

Opens

4 February 2021

Duration

42 months

Eligibility

Minimum 2.1 degree (or equivalent) in chemistry or a related subject.

Open to all UK nationals.

Project Details

It was long thought that each protein has a specific 3-dimensional fold or conformation that is required for it to carry out its function in the cell. More recently, it has been discovered that a subset of proteins, called intrinsically disordered proteins (IDPs), exist in a range of conformations under physiological conditions, and interconvert rapidly between these conformations. IDPs are heavily involved in cell signalling networks that control cellular replication and are therefore overrepresented in diseases such as cancer. They are therefore often considered attractive drug targets, but their dynamic behaviour makes them difficult to study with traditional structural biology methods. New techniques are required to characterise these proteins, leading to better understanding of their behaviour which will result in increased drugability of IDPs and hence better therapies for disease.

Ion mobility mass spectrometry (IMMS) is a widely applicable, low-resolution method that measures the range of conformations in which an IDP exists, and can report on any preference of the IDP for a compact or extended shape. The IDP’s response to different solution conditions such as salt concentration or pH can be measured, and its interaction modes with cellular binding partners can be delineated. For example, it can be deduced whether the IDP folds upon binding, or retains dynamic behaviour as part of the protein complex. Moreover, the structural effect of small molecule inhibitors or modulators on the IDP can be uncovered.

During this project, IMMS will be used to interrogate the behaviour of an IDP in its unbound state, and to uncover its mode of action with its cellular binding partners. Methods will subsequently be developed to screen libraries of small molecules to search for compounds that affect the conformational distribution of the IDP, and hence its ability to bind to its partner. These molecules will be used as chemical probes to delineate the effect of different conformational groups on the function of the IDP in question, for example, which conformation is required for protein complex formation.

The project will be based in the lab of Dr Rebecca Beveridge, which houses excellent IMMS infrastructure, and will be carried out in collaboration with Waters (Wilmslow, UK).

Techniques used:

Mass spectrometry, ion mobility, size exclusion chromatography, capillary electrophoresis, related analytical techniques.

References:

Beveridge, R., Covill, S., Pacholarz, K. J., Kalapothakis, J. M., MacPhee, C. E., & Barran, P. E. (2014). A mass-spectrometry-based framework to define the extent of disorder in proteins. Analytical chemistry, 86(22), 10979-10991.

Beveridge, R., Migas, L. G., Das, R. K., Pappu, R. V., Kriwacki, R. W., & Barran, P. E. (2019). Ion mobility mass spectrometry uncovers the impact of the patterning of oppositely charged residues on the conformational distributions of intrinsically disordered proteins. Journal of the American Chemical Society, 141(12), 4908-4918.

Beveridge, R., Migas, L. G., Kriwacki, R. W., & Barran, P. E. (2019). Ion Mobility Mass Spectrometry Measures the Conformational Landscape of p27 and its Domains and how this is Modulated upon Interaction with Cdk2/cyclin A. Angewandte Chemie, 131(10), 3146-3150.

Conditions: (e.g. experience in a specific technique, qualification)

We are looking for a motivated candidate who will ideally have experience in protein chemistry and/ or mass spectrometry.

Funding Details

Funding is available to cover tuition fees for Home UK applicants for 3.5 years (from 1st of October 2021), as well as paying a stipend at the Research Council rate (estimated £15,667).

How to apply

To apply please send your C.V., a cover letter and details of two referees to Rebecca Beveridge. The cover letter should outline why you’re interested in this project and describe your relevant experience.