Projet de thèse en Physique pour les Sciences du Vivant
Sous la direction de Martin Blackledge.
Thèses en préparation à l'Université Grenoble Alpes , dans le cadre de École doctorale physique , en partenariat avec Institut de Biologie Structurale (laboratoire) et de Groupe dynamique et cinétique des processus moleculaires (equipe de recherche) depuis le 26-09-2017 .
Intrinsically disordered proteins (IDPs) represent a significant population of all proteomes, for which standard structural biology is not adapted due to their inherent conformational disorder. The development of molecular descriptions of the behaviour of IDPs is a key challenge for contemporary structural biology, in particular because they are involved in many human diseases such as neurodegeneration and viral infection. Most importantly, molecular recognition in IDPs remains very poorly understood. In order to understand how these proteins carry out their function, and to provide crucial aid in the development of potential inhibitors, atomic resolution movies' of the dynamics and interaction modes of these proteins are necessary. The PhD candidate will join an active group in this field, combining high field NMR spectroscopy, with single molecule fluorescence spectroscopy (FRET), small angle X-ray and neutron scattering as well as state of the art molecular simulation, to develop a complete picture of the structural and dynamical basis of molecular function and malfunction in IDPs. In addition to providing the basic understanding such interactions, the rational conception of molecular inhibitors of IDPs involved in disease relies on the development of a more precise understanding of their action and remains one of the unsolved challenges of chemical biology. The methods will be applied this to describe the role of protein flexibility in interactions involving IDPs that control replication and transcription in pathogenic viruses, as well as highly dynamic proteins involved in nuclear transport.
Investigating the relationship between intrinsic protein disorder and biological function: Mapping interaction trajectories at atomic resolution using nuclear magnetic resonance spectroscopy and molecular simulation
Despite the success of structural genomic projects, designed to develop a deeper understanding of protein function from three-dimensional structures, such approaches often overlook a crucial aspect. Proteins are inherently dynamic, exhibiting conformational freedom on timescales from picoseconds to hours, implicating structural rearrangements that are essential for their biological function. Nuclear Magnetic Resonance (NMR) spectroscopy is highly sensitive to conformational fluctuations occurring on all time-scales, and provides atomic resolution information throughout the entire molecule. Our group develops methods to quantitatively describe the nature and timescale of these motions with the aim of determining their role in biological function. The thesis project proposed here concerns the fascinating and poorly understood class of intrinsically disordered proteins (IDPs) that represent extreme examples where protein flexibility plays a determining role in biological function. IDPs occupy a significant population of all proteomes for which standard structural biology is simply not adapted, due to their inherent conformational disorder. The development of meaningful descriptions of the behaviour of IDPs is therefore a key challenge for contemporary structural biology. Most importantly, molecular recognition mechanisms in IDPs remain poorly understood. The structural plasticity of IDPs is thought to provide advantageous functional modes that are inaccessible to folded proteins, however, essentially nothing is known about the actual mechanisms governing functional interactions involving IDPs within physiological complexes. The development of experimental and analytical approaches to describe their interaction modes, is therefore of paramount importance and lies at the interface of physics, chemistry and biology. In addition to providing the basic understanding of such interactions, the future rational conception of molecular inhibitors of IDPs involved in disease relies on the development of a more precise understanding of their action. This is particularly important because such a significant fraction of the human proteome and of our associated pathogens fall beyond the realm of classical structure-function paradigms. In order to fully understand how these proteins carry out their function, and how they avoid, or eventually succumb to malfunction, atomic resolution movies' of the dynamics and interaction modes of these proteins are necessary. Nuclear Magnetic Resonance spectroscopy provides the optimal tool to reach this goal, providing highly sensitive probes to describe the conformations sampled by the flexible protein, the associated dynamic modes and timescales, and the interaction kinetics and conformational changes when forming physiological complexes, all this atomic resolution information is necessary to understand the molecular basis of these fascinating biological machines. The PhD candidate will join an active group in this field (see references below), combining high-field solution state NMR, in particular recently developed NMR relaxation- and paramagnetic relaxation-based approaches, with single molecule fluorescence spectroscopy (FRET), small angle X-ray and neutron scattering, as well as state of the art molecular simulation, to develop a complete picture of the structural and dynamical basis of molecular function and malfunction in IDPs. The candidate will also study the effects of the molecular environment, and even study the behaviour of IDPs in live cells using high resolution NMR spectroscopy. The methods developed by the candidate will be applied this to describe the role of protein flexibility in interactions involving IDPs that control replication and transcription in pathogenic viruses, as well as highly dynamic proteins involved in nuclear transport. More generally the methodology will be transferrable to other complex biomolecular systems comprising structured and highly disordered components. The project will thus necessarily provide valuable physical, technical and biologically important results. Very little is currently known about the relationship between primary sequence and function in intrinsically disordered proteins, and we are at the very beginning of developments that are defining a largely unexplored domain of protein biology - it is a very exciting time to work in this field.