PhD position Blackledge group IBS Grenoble

PhD position starting 2024/2025 in the group of Martin Blackledge at the Insititut de Biologie Structurale (IBS), Grenoble, France

 

NMR STUDIES OF MOLECULAR DYNAMICS AND DISORDER IN THE VIRAL REPLICATION MACHINERY OF SARS-COV-2

 

The nucleoprotein (N) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is important for genome replication, encapsidating the viral genome and regulating gene transcription. The central disordered domain is essential to the function of this highly dynamic protein, interacting with the viral protein nsp3,1 and containing a number of important mutations that are responsible for enhanced viral fitness, and comprising a region that is hyperphosphorylated during the viral cycle. NMR spectroscopy is the tool of choice for studying the conformational behaviour of intrinsically disordered proteins, an abundant class of proteins that are functional in their disordered form. They represent 40% around of all known proteomes and are too dynamic to be studied by crystallography or electron microscopy. The host lab has developed a large number of unique NMR-based tools to help understand the function of this class of proteins at atomic resolution.2–11  We will use state-of-the-art NMR spectroscopy, small angle scattering and electron microscopy, in combination with molecular simulation, to describe the interactions of N with host and viral partner proteins and viral RNA. The results will be correlated with light and electron microscopy, and fluorescence spectroscopy carried out in collaboration. In addition, the druggability of intrinsically disordered regions of the viral replication machinery is an important, but essentially untapped source of new inhibitory strategies that will be addressed by this project.

 

  1. Bessa, L. M. et al. The intrinsically disordered SARS-CoV-2 nucleoprotein in dynamic complex with its viral partner nsp3a.Science Advances 8, eabm4034 (2022).
  2. Bernado, P. et al. A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. Proc Natl Acad Sci 102, 17002–17007 (2005).
  3. Salmon, L. et al. NMR Characterization of Long-Range Order in Intrinsically Disordered Proteins. J. Am. Chem. Soc. 132, 8407–8418 (2010).
  4. Jensen, et al. Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy.Chem. Rev. 114, 6632–6660 (2014).
  5. Abyzov, A. et al. Identification of Dynamic Modes in an Intrinsically Disordered Protein Using Temperature-Dependent NMR Relaxation. J. Am. Chem. Soc. 138, 6240–6251 (2016).
  6. Milles, S. et al. An ultraweak interaction in the intrinsically disordered replication machinery is essential for measles virus function. Science Advances 4, eaat7778 (2018).
  7. Adamski, W. et al. A Unified Description of Intrinsically Disordered Protein Dynamics under Physiological Conditions Using NMR Spectroscopy. J. Am. Chem. Soc. 141, 17817–17829 (2019).
  8. Guseva, S. et al. Measles virus nucleo- and phosphoproteins form liquid-like phase-separated compartments that promote nucleocapsid assembly. Science Advances 6, eaaz7095 (2020).
  9. Camacho-Zarco, et al. Molecular basis of host-adaptation interactions between influenza virus polymerase PB2 subunit and ANP32A. Nature Communications 11, 3656 (2020).
  10. Camacho-Zarco, et al. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins. Chem. Rev. (2022)
  11. Guseva, S. et al. Liquid–Liquid Phase Separation Modifies the Dynamic Properties of Intrinsically Disordered Proteins. J. Am. Chem. Soc. 145, 10548–10563 (2023).

The successful candidate will join a multi-disciplinary team investigating the physical role of highly dynamic proteins involved in viral replication, in particular SARS-CoV-2, influenza and measles. The project lies at the interface of biology, chemistry and physics and will combine state-of-the-art NMR spectroscopy with simulation, fluorescence spectroscopy and imaging, X-ray crystallography, cryo-electron microscopy and small angle scattering.

Capital of the French Alps, Grenoble is a world-renowned scientific hub with a strong international flavour. It is a pleasant city, situated at the foot of three mountain ranges offering many possibilities for cultural, outdoor and sporting activities throughout the year. Grenoble is close to the French riviera, Italy and Switzerland and is served by international airports and a high-speed rail network

Interested candidates (biochemists, chemists or biophysicists) should send a cv and motivation letter to martin.blackledge@ibs.fr