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1	Apports de l'échange hydrogène/deutérium couplé à la spectrométrie de masse en protéomique structurale pour la caractérisation de complexes multi-protéiques. / Hydrogen/deuterium exchange coupled to mass spectrometry in structural proteomics Terral, Guillaume 08 July 2016 (has links) Ce travail de thèse porte sur développement de méthodes en spectrométrie de masse structurale pour l’analyse de protéines recombinantes et de leurs complexes associés. L’objectif central s’est porté sur des développements méthodologiques en échange hydrogène/deutérium couplé à la spectrométrie de masse (HDX-MS). Les techniques biophysiques de caractérisation structurale à haute résolution comme la cristallographie ou la RMN se heurtent régulièrement à des problèmes de productions de cristaux, de taille de complexes analysables ou encore de quantité de matériel nécessaire importante. Le développement de méthodes spécifiques HDX-MS a permis de réaliser une caractérisation structurale de systèmes protéiques variés, et réfractaires aux approches haute résolution. La combinaison de cette approche à différents outils de MS structurale est aussi illustrée, et montre tout son intérêt pour l’obtention d’informations à résolution augmentée. / This thesis work focuses on development of structural mass spectrometry methods for the analysis of recombinant proteins and their associated complex. The central objective has focused on the development of hydrogen/deuterium exchange coupled to mass spectrometry approaches (HDX-MS). The high resolution biophysical techniques for structural characterization such as crystallography or NMR regularly face problems of crystal productions, size analyzable complex or quantity of material required. The development of specific HDX-MS methods allowed the characterization of various, and refractory protein systems to high resolution approaches. The combination of this approach with complementary structural MS tools is also illustrated, and shows its interest to obtain increased resolution information. Spectrométrie de masse structurale Échange hydrogène/deutérium Spectrométrie de masse native Protéines Anticorps thérapeutiques Ribonucléoprotéines Structural mass spectrometry Hydrogen/deuterium exchange Native mass spectrometry Proteins Therapeutic antibodies Ribonucleoproteins 543
2	The Development and Application of Mass Spectrometry-based Structural Proteomic Approaches to Study Protein Structure and Interactions Makepeace, Karl A.T. 26 August 2022 (has links) Proteins and their intricate network of interactions are fundamental to many molecular processes that govern life. Mass spectrometry-based structural proteomics represents a powerful set of techniques for characterizing protein structures and interactions. The last decade has witnessed a large-scale adoption in the application of these techniques toward solving a variety of biological questions. Addressing these questions has often been coincident with the further development of these techniques. Insight into the structures of individual proteins and their interactions with other proteins in a proteome-wide context has been made possible by recent developments in the relatively new field of chemical crosslinking combined with mass spectrometry. In these experiments crosslinking reagents are used to capture protein-protein interactions by forming covalent linkages between proximal amino acid residues. The crosslinked proteins are then enzymatically digested into peptides, and the covalently-coupled crosslinked peptides are identified by mass spectrometry. These identified crosslinked peptides thus provide evidence of interacting regions within or between proteins. In this dissertation the development of tools and methods that facilitate this powerful technique are described. The primary arc of this work follows the development and application of mass spectrometry-based approaches for the identification of protein crosslinks ranging from those which exist endogenously to those which are introduced synthetically. Firstly, the development of a novel strategy for comprehensive determination of naturally occurring protein crosslinks in the form of disulfide bonds is described. Secondly, the application of crosslinking reagents to create synthetic crosslinks in proteins coupled with molecular dynamics simulations is explored in order to structurally characterize the intrinsically disordered tau protein. Thirdly, improvements to a crosslinking-mass spectrometry method for defining a protein-protein interactome in a complex sample is developed. Altogether, these described approaches represent a toolset to allow researchers to access information about protein structure and interactions. / Graduate Mass Spectrometry Structural Proteomics Crosslinking Cross-linking Disulfide bonds Proteomics Tau Mitochondria Method development Molecular dynamics Protein chemistry Protein crosslinking Protein cross-linking Shotgun proteomics Bottom-up proteomics Data-dependent acquisition DDA Protein-protein interactome Interactome Interactomics Proteinase K Trypsin Higher-order crosslinking Machine learning Feature engineering Yeast Yeast mitochondria Algorithms Data analysis Surface modification Molecular modelling Non-specific digest Structural mass spectrometry Structural biology Biochemistry LC-MS

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Apports de l'échange hydrogène/deutérium couplé à la spectrométrie de masse en protéomique structurale pour la caractérisation de complexes multi-protéiques. / Hydrogen/deuterium exchange coupled to mass spectrometry in structural proteomics

The Development and Application of Mass Spectrometry-based Structural Proteomic Approaches to Study Protein Structure and Interactions