PhD student profiles


Jack Paton
Wellcome Trust 4-year Interdisciplinary PhD Programme, beginning in Autumn 2012

Project title
Studies of co-translational folding by NMR spectroscopy.

Principle investigator: Professor John Christodoulou, ISMB, UCL
Co-investigator: Dr Renos Savva, ISMB, Birkbeck

I graduated with an MSci in Chemistry from the University of Bristol in 2012. As an undergraduate, I completed a summer project with Dr Craig Butts in 2011, where I exploited NMR techniques to assign the stereochemistry and precise atomic level structure of small synthetic molecules. I then worked with Prof Matthew Crump in the final year of my degree, where I investigated the interaction between insulin-like growth factor 2 (IGF2) and various mutants of its receptor, IGF2R, using surface plasmin resonance, before being accepted onto the Wellcome Trust interdisciplinary programme in 2012.

Rotation 1
Characterisation of the interaction between the intrinsically disordered protein α-synuclein and 70S ribosomes using NMR spectroscopy. Supervised by Prof John Christodoulou.

Rotation 2
Computational modelling of a drug-resistant mutant of HIV2 reverse transcriptase, to identify the cause of resistance at an atomic level. Supervised by Prof Peter Coveney.

Rotation 3
Synthesis of metallo-porphyrin complexes and investigation of their binding to membrane lipid analogues, to develop a system that can detect specific phospholipids in the lipid bilayer. Supervised by Dr Salvador Tomas.

PhD Project
Co-translational folding is the study of the acquisition of native structure of a protein as it emerges vectorially from the ribosome during biosynthesis. The evolution of the folding pathway as a function of chain length (Figure 1) indicates a fundamental difference between protein folding in vivo and the classical in vitro experiments that have been carried out over the years. This indicates that our understanding of protein folding, although richly developed, is in need of a stronger biological context. My PhD project is concerned with the development of a ribosome-bound nascent chain system that can be used to understand the protein folding process on the ribosome. My work involves investigation of the properties of candidate proteins, including folding studies in isolation, using urea denaturation methods alongside circular dichroism and NMR techniques to determine whether a protein would be suitable for study as a translation stalled variant. This is complemented with rigorous biochemical assays of nascent chain samples to ensure that I can produce a pure and stable solution of a translation stalled protein attached to an intact 70S ribosome. Once an ideal system has been identified and conditions for the nascent chain optimised, the sample will be produced with isotopic enrichment for study using NMR spectroscopy, to acquire residue specific information on structure and folding in a co-translational environment.
figure 1
Figure 1: Schematic diagram showing the co-translational acquisition of structure of a nascent polypeptide chain, coupled with its emergence from the ribosomal tunnel during biosynthesis. The black line indicates a hypothetical pathway that may be taken by a protein with comparable folding and translation rates.

Mutation V111I in HIV-2 Reverse Transcriptase Increases the Fitness of the Nucleoside Analogue-Resistant K65R and Q151M Viruses. Deuzing, IP; Charpentier, C; Wright, DW; Matheron, S; Paton, J; Frentz, D; van de Vijver, DA; Coveney, PV; Descamps, D; Boucher, CAB; Beerens, N; Journal of Virology, 2015, 89:833-843.

The H50Q Mutation Induces a 10-fold Decrease in the Solubility of alpha-Synuclein. Porcari, R; Proukakis, C; Waudby, CA; Bolognesi, B; Mangione, PP; Paton, JF; Mullin, S; Cabrita, LD; Penco, A; Relini, A; Verona, G; Vendruscolo, M; Stoppini, M; Tartaglia, GG; Camilloni, C; Christodoulou, J; Schapira, AH; Bellotti, V; Journal of Biological Chemistry, 2015, 4:2395-2404.




Institute of Structural and Molecular Biology, University of London
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