NMR research

Funded PhD Projects

The following PhD projects come with funding (at the time of writing) to cover tutition fees and living expenses. Please note that they may not be available to students from outside the UK or the European Union. We strive to keep this page up to date, but please contact the supervisor of any PhD opportunity you wish to apply for. They will be able to provide current information on any funding restrictions. A more extensive list of projects, both with and without funding, is available.

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Screening of chemical libraries using iPS models for investigating the role of prion protein in Alzheimer’s disease

Background

AD has been identified as a protein misfolding disease (proteopathy). The disease is caused by accumulation of two major amyloids: a rounded “amyloid plaque” outside cells and “neurofibrillary tangles” inside cells. A number of theories have been developed to describe the cause and characteristics of AD although the exact cause is still not fully understood.1,2,3,4,5

Recently, it has been reported that cellular prion protein, PrPC, binds to Aβ1-42 oligomer and inhibits the long-term potentiation (LTP) in mice.6 Antibodies targeting the 94-104 region in PrPC blocks the inhibition of LTP triggered by soluble Aβ1-42 oligomer.7,8 PrPC has also been reported to affect the formation of the Aβ oligomers by modulating the function of β-secretase (BACE-1).9
Several lines of research has pointed to the nature of amyloid formation in AD having some synergies with prion formation in TSE (transmissible spongiform encaphlopathy, a family of fatal neurodegenerative diseases caused by conformational change of soluble prion protein, PrPC, into its insoluble counterpart, PrPSc, including scrapie in goats, mad cow disease in cattle and CJD in human). Although fundamental differences between these two diseases exist, the prion hypothesis10 articulates that the amyloidosis process of Aβ and Tau could well be prion-like. This is because it is suggested that the amyloid plaques such as Aβ and Tau, are formed via seeding of oligomers; and amyloidosis in one cell can trigger the nearby cells within tissue/organs to form plaques despite of the fact that AD is not transmissible from individual to individual.

Suggested role of prion protein in Alzheimer's disease

Fig. 1 Suggested role of prion protein, PrPc, in Alzheimer's disease. PrPc binds, regulates activity of BACE in cleavage of amyloid precursor protein (APP); PrPc acts as receptor for Aβ dimer. PrPc forms a complex with Fyn (probably with the help of Cav-1); and the complex regulates Tau hyperphosphoration, hence Tangle formation.

The close relationship amongst PrPC, Aβ and Tau was unveiled in recently studies. It was found that PrPC is enriched in postsynaptic densities, and the Aβ-PrPC interaction leads to activation of the Src tyrosine kinase Fyn and neuronal demise.11 Aβ engagement of PrPC-Fyn signalling yielded phosphorylation of the NR2B subunit of NMDARs. Fyn can mediate Aβ/Tau-induced toxicity.12 New evidence has showed that soluble Aβ and the Aβ1-42 dimer in particular can bind to PrPC at neuronal dendritic spines where it forms a quadruple complex with Fyn via Cav-1. This results in the activation of the Fyn kinase, which in turn triggers aberrant missorting and hyperphosphorylation of Tau, hence tangle formation.13,14 (Figure 1)

Henceforth, PrPC seems to be an important piece of the jigsaw in the AD landscape. Together with the amyloid and Tau theory, it could provide solutions to some unsolved questions in AD aetiology. Understanding the role PrPC in AD is extremely important and could shine lights on developing new diagnostics and drugs to combat AD.

Aims and Objectives

The aims of the project are:
• Develop and optimise iPS cellular model from epithelium cells from healthy and Alzheimer patient
• Study the interaction between PrPC and its interacting partners such as A, mGlu5, and NMDAR etc.
• Screen chemical libraries for compounds interfering the interactions
• Investigate the mode-of-action of initial hits

Project Plan

Year 1 - Develop and optimise iPS cellular model from epithelium cells from healthy and Alzheimer patient

Epithelium cells from healthy and Alzheimer patients will be reprogrammed and then differentiated into young neurons and cortical neurons and level of expression of PrPC and its interacting partners will be assessed using Western blotting and ICC and flow cytometry.

Year 2 - Study the interaction between PrPC and its interacting partners such as A, mGlu5, and NMDAR etc; screen chemical libraries for compounds interfering the interactions

Pairwise interaction studies between PrPC and its interacting partners will be carried out using doubly labelled fluorescence tags and the ability of small molecules in interfering such interactions will be assess. Hit compounds will be selected for further studies.

Year 3 - Investigate the mode-of-action of initial hits

The mode-of-action of selected hits will be thoroughly studied using a range of techniques such as RNAi screening and pull-down assays.

For more information

For more information, please contact Prof Beining Chen via email (b.chen@sheffield.ac.uk). To apply online for this studentship, click here.

References

1Braak, H ; Braak, E ; 1991. Acta Neuropathlogia, 82(4): 239-259;
2Bachmeier, C.; Paris, D.; Beaulieu-Abdelahad, D. et al. 2013, Neurodegen. Dis. 11(1): 13-21;
3Suh, Y.H.; Checler, F. 2002. Pharmcological Reviews. 3: 469-525;
4Hardy, J.; Allsop, D. 1991. Trends in Pharm. Sci. 12(10): 383-388;
5Um, J.W; Nygaard, H. B.; & Stephen M Strittmatter, S. M.; Nature NeuroSci. 2012, 15(9):1227-1235.;
6Larson, M.; Sherman, M. A.; Amar, F.; & Lesne, S.E. J. 2012. NeuroSci. 32(47): 16857-16871
7Benilova, I.; Karran, E.; & Bart De Strooper, B. D. Nature NeuroSci. 2012, 15(3): 349-357.;
8Sisodia, S.S.; St George-Hyslop, P.H. 2002. Nature Reviews Neuroscience. 3(4): 281-290.
9Esler, W.P; Wolfe, M.S. 2001. Science, 293(5534): 1449-1454;
10Griffiths, H. H and Hooper, N. M. et al. (2011) J. Biol.Chem. 286(38): 33489-33500.;
11Freir, D.B.; Nicoll, A.J.; Klyubin, I., Panico, S. & Collinge, J. 2011. Nat Commun 2:336.;
12Ittner, L.M.; Ke, Y.D; & Götz, J. et al. 2010. Cell 142:387–397.;
13Walsh, D.M.; Klyubin, I.; Selkoe, D.J. et al. 2002. Nature 416:535–539.;
14Williamson, R.; Scales, T.; & Anderton, B.H, 2002. J Neurosci 22:10–20.

Dissecting and Quantifying Catalytic Effects

Summary

This project is part of EU Training Network MMBio (Molecular Tools for Nucleic Acid Manipulation for Biological Intervention; see http://www.bioc.cam.ac.uk/hollfelder/Research/mmbio). It is funded for 3 years by the EU, so applicants must be not have been resident in the UK for more than 1 year out of the last 3 years. The position can be started immediately, and ideally by October 2017 at the latest. Applicants should have (or expect to obtain) at least the equivalent of a 2.1 honours masters level degree in an appropriate subject.

Details

The focus of this project will be to disentangle the key features that lead to efficient catalysis of phosphate ester cleavage. The ESR will be exposed to a series of diverse applications ranging from synthetic preparation of modified recognition moieties, characterisation of the assembly of secondary structure, and reaction mechanism investigations that will provide a full insight into all aspects of creating an artificial catalyst that is conceptually based on natural systems. The student will be supported throughout the project with training, mentoring and career development opportunities.

Dissecting and Quantifying Catalytic Effects

As the X groups that surround the binding site on the Zn ion are changed from H to NH2, the complex becomes much more reactive for cleaving RNA like molecules. Can we make even better environments at the active site?

We want to generate a reaction centre that is reactive enough to catalyse the cleavage of natural phosphate di-ester substrates at a practical rate in vivo. To achieve this, we need to dissect and quantify the effect of different local features on the activity of metal ion complexes, and to explore the impact that catalysis has on the transition state. Methods: We will test the impact of replacing amino groups (which currently support the most active complexes we have developed to date) with other H-bond donors. These substitutions allow delivery of specific local solvating groups that can enhance the intrinsic reactivity of the system. This polyfunctional behaviour mimics active sites; it will be important to explore a range of structures to be able to dissect the contributions of several (possibly competing) interactions. We will also probe how these interactions affect the transition state so that we can simultaneously assay for activity with a close analogue of RNA and explore how the transition state varies through the charge development at the leaving group.

For more information

Please contact Prof. N. H. Williams via email (N.H.Williams@Sheffield.ac.uk).

Recognition Activated Catalysts

Summary

This project is part of EU Training Network MMBio (Molecular Tools for Nucleic Acid Manipulation for Biological Intervention; see http://www.bioc.cam.ac.uk/hollfelder/Research/mmbio). It is funded for 3 years by the EU, so applicants must be not have been resident in the UK for more than 1 year out of the last 3 years. The position can be started immediately, and ideally by October 2017 at the latest. Applicants should have (or expect to obtain) at least the equivalent of a 2.1 honours masters level degree in an appropriate subject.

Details

This project aims to create RNA/DNA cleaving agents capable of highly localised activity, and to harness the intrinsic recognition features of the targets to achieve this. Such selective DNA cleaving agents could find relevant applications against cancer, bacteria and viruses. The ESR will be exposed to a series of diverse applications ranging from synthetic preparation of modified recognition moieties, characterisation of secondary structure formation, and reaction mechanism investigations that provide a complete picture of creating an artificial catalyst that is conceptually based on natural systems. The student will be supported throughout the project with training, mentoring and career development opportunities.

dinuclear complex

This dinuclear complex is very active for cleaving RNA like molecules, and relies on bringing together two metal ions and several H-bond donors. Can this be achieved by recognition rather than covalent bonds?

We want to prepare RNA or DNA cleaving agents that create the active form of a metal ion based catalyst by inducing a specific secondary structure as part of the sequence selective recognition of specific targets. If this proof of concept can be demonstrated, it opens up the scope to control activity through allosteric interactions, and relates to the widely described use of remote binding interactions to affect enzyme activity through conformational changes. Metal binding units will be conjugated to different positions of RNA and DNA recognising moieties that provide predictable secondary structures. Cleavage activity will require the combination of at least two units, and these will be positioned so that that they are remote in the resting state of the catalyst, but brought into proximity as part of the substrate recognition event. To maximise the hierarchy of the binding/activation events, complementary binding units will be explored so that the final assembly event to bring in the second functionality only occurs once the right sequence has been sequestered.

For more information

Please contact Prof. N. H. Williams via email (N.H.Williams@Sheffield.ac.uk)

FRET@ the short end

Supervisor: Dr Tim Craggs

Single-molecule Biophysics Lab – University of Sheffield

An exciting opportunity has arisen to join the Single-molecule Biophysics Lab at the University of Sheffield. Research in the lab involves the development and application of single-molecule fluorescence techniques to addressing crucial questions across physics, chemistry and the life sciences. You will join a multidisciplinary environment, which benefits from many national and international collaborations (Florida, Madrid, Bristol, Leeds). One project is detailed below but other projects are also available.

Project title: FRET@ the short end

Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful tool for monitoring distances between 40-100 Å. However, there is a need to extend the sensitivity to shorter distances which would enable the study of important conformational changes in smaller proteins and de novo protein structure determination by FRET. The dynamic range of a dye pair is characterized by the Förster radius (R0), defined as the inter-dye distance at which the FRET efficiency is 50%. Popular single-molecule dye pairs have Förster radii in the 50–65 Å range, ruling them out for detecting shorter distances (20-40 Å). This project will involve characterising a range of FRET pairs and linker chemistries to develop both ensemble and single-molecule assays for measuring these shorter distances.

FRET Effieciency and Distance

The novel methods developed here will open up a new range of distance measurements (left plot – red area) enabling precise measurements of DNA and protein conformations (right) for synthetic biology, structure determination and drug discover applications.

Once established, these novel methods will be applied to a range of different systems, including protein-protein interactions in synthetic biology, assay development for allosteric drug discovery, and de novo protein structure determination1.

Skills:

The successful candidate will receive full training in a wide range of biochemical and biophysical techniques, chiefly single-molecule FRET spectroscopy and biomolecular labeling. Skills may also be gained by working closely with our collaborators, with significant scope to develop the project according to individual interests.

Applicants should have (or expect to gain) a 1st or 2.1 class degree in Biochemistry, Chemistry, Biophysics or a related discipline, and be happy to work in a collaborative, multidisciplinary environment. The project is funded for 3 years - applicants must be UK or EU nationals.

For more details about the project, please contact Dr Tim Craggs (t.craggs@sheffield.ac.uk). To apply on-line for this studentship click here.

1. Craggs TD (2017) Nature Methods 14, 123-124

Gas adsorption and host-guest chemistry in flexible metal-organic framework materials

Primary Supervisor: Prof. Lee Brammer, The University of Sheffield, email lee.brammer@sheffield.ac.uk

Co-supervisors: Dr. David Allan and Dr. Chiu Tang, Diamond Light Source

Background

Metal-organic frameworks (MOFs) are a prominent class of hybrid materials that are the subject of intense research activity worldwide for applications related to their porosity, including gas adsorption and separation, catalysis, sensing and drug delivery. MOFs are constructed by linking metal ions or small metal clusters into 2D or 3D frameworks via bridging organic ligands. Their advantage over other porous materials is their potential, arising from modular construction, for extensive tuning of pore size, shape and chemical composition. Of 20-30,000 MOFs reported to date, it is estimated that approximately 100 are flexible. We have recently reported a new continuous ‘breathing’ MOF, in which molecular scale pores can open and close in response to guests. The material shows excellent guest selectivity and potential for gas separation (Nature Chemistry, 2017 (DOI: 10.1038/NCHEM.2747). The PhD project will build upon this discovery in a project that is a collaboration between University of Sheffield and Diamond Light Source, near Oxford.

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Toward artificial photosynthesis

Supervisor: Dr Adrien Chauvet

Summary

This project is in ultrafast spectroscopy. It is funded for 3 years. Applicants must be UK or EU nationals.

Details

The Sun represents an unlimited source of energy that can be harvested and ultimately converted to electricity. Solar energy is therefore the solution to not only depart from the fossil fuels but also to responds to the ever-increasing energy needs of our societies. In this grand scheme, our group is interested in the fundamental understanding of light absorption and conversion by using the latest laser-based techniques.[1]

The project focuses on the study of artificially modified porphyrins by means of ultrafast transient absorption spectroscopy. Porphyrins are the main actors in organic light harvesting complexes, and via artificial structural modifications, can be tuned to absorb in any desired part of the spectrum.[2]

The goal is to investigate the photo-physics, of these porphyrins, in order to better understand the mechanisms of light absorption as well as to identify the best candidates for artificial photosynthesis. Throughout this project, you will learn about the experimental sample preparation and laser manipulation (non-linear optics, ultrashort pulsed laser) as well as learn how to treat the data (Matlab, Igor) and how to interpret it. The student will be supported throughout the project with training, mentoring and career development opportunities.

We are looking for motivated individual interested in high resolution laser-based spectroscopy, preferably with some experience in computer-based analytical tools. For more information about the project, please contact a.chauvet@shefield.ac.uk.

[1] R. Berera, et al. Photosynth. Res. (2009)
[2] C. Brückner, Acc. Chem. Res. (2016)