PhD in chemistry and NMR spectroscopy (M/F)

Job Description

Thesis Subject

Uncovering the roles of prolines in disordered proteins using proline fluorination and new 19F NMR methods.

This thesis will focus on the NMR spectroscopic characterization of short model peptide fragments from disordered proteins that contain both proline and aromatic amino acid residues. Proline displays unusual conformations that regulate overall protein structural properties. It has been shown that the interaction with nearby aromatic residues also play an important role in this, leading to stable, short structural motifs in otherwise highly disordered protein sequences. The conformational dynamics of these motifs are not well understood, however. In this project, we will pursue an original strategy involving unnaturally fluorinated proline variants to edit their properties, thereby interrogating their roles in overall peptide conformational dynamics. We already have established a toolbox of fluorinated prolines with unique spectral properties, as well as advanced computational and NMR spectroscopic means to characterize the fluorinated prolines within peptides.

The principal aim of this project will be to apply and further develop the fluorinated proline toolbox and the newly developed spectroscopic tools to fully characterize the proline-aromatic motifs in disordered proteins. We will use advanced 1H, 19F, 13C and 15N NMR methods to extract spectral information that report on the conformational dynamics. Particularly, 19F NMR will be a powerful reporter on proline and overall peptide dynamics.

Besides short model peptides, we will apply the methodology on a real test-case: the disordered region of the Non-Structural 5A (NS5A) Protein, a protein that is essential for Hepatitis C Virus (HCV) replication via an unknown molecular mechanism. Our lab has previously characterized a disordered segment of this protein, establishing with NMR that residual structural elements exist in it that are essential for binding to the human protein cyclophilin A, an essential step for viral replication. These residual structural elements appear to be regulated by the conformations of several proline residues nearby aromatic residues; but we do not yet understand how. Using the new approaches, we aim to clarify how exactly the conformational dynamics of the proline residues are connected with viral activity.

Your Work Environment

The Integrative Structural Biology CNRS research group investigates the structural basis and molecular mechanism underlying protein biological functions, and the impact of their deregulation in human diseases. In particular, we are interested in intrinsically disordered proteins involved in proteinopathies. At the heart of our work are biophysical multidisciplinary methods for characterizing the structure of proteins, as well as the interactions between them, such as Nuclear Magnetic Resonance spectroscopy, X-ray crystallography and cryo-electron microscopy. Our research is essentially fundamental, but we remain attentive to its application to the development of new therapeutic approaches, the evaluation of the therapeutic potential of various compounds from small molecules to nanobodies, and the study of the mode of action of bioactive molecules.

The group has access to state-of-the-art liquid NMR instrumentation in Lille, including a recently installed 1.2 GHz spectrometer (Avance NEO, cryoprobe), a 900 MHz (Avance NEO, cryoprobe), an 800 MHz (Avance NEO), and a 600 MHz (Avance III HD, 1H-13C-15N-19F QCI cryoprobe). Furthermore, we are part of Infranalytics (https://infranalytics.cnrs.fr/), a national research infrastructure network of NMR, EPR and FT-ICR MS laboratories. This network connects us to all the French specialists in High resolution NMR spectroscopy and allows easy access to additional high field spectrometers and specific hardware. The laboratory possesses state-of-the-art facilities for molecular biology, biochemistry and cell biology.

In this project, you will be part of an international consortium of researchers focusing on fluorinated proline synthesis, NMR spectroscopy and computational chemistry, including Ghent (Belgium), Strasbourg (France), ENS-Paris (France) and Southampton (UK). Yearly meetings are planned between these groups, in which you will be actively involved and present your results. Potential short research visits to some of these groups can be envisaged.

Constraints and risks

Working with High Magnetic Fields
Handling Cryogenic Fluids and Chemicals

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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