Mass Spectrometry (MS) and Ion Mobility - Mass Spectrometry (IM-MS) can be used to investigate protein structure and dynamics and are ideally positioned to study intrinsically disordered and amyloidogenic proteins, whose diverse conformational space and/or oligomeric state is hard to track accurately. This thesis uses hybrid MS approaches including IM-MS, Cross-linking IM-MS and ECD-FT-ICR MS to probe the structure of alpha-Synuclein and Amyloid-beta (Abeta). For alpha-Synuclein, the effect of solution pH and ionisation polarity on the species observed by MS and IM-MS is investigated. Conformational families observed by Cross-linking IM-MS provides a link between the solution and gas phase structures of alpha-Synuclein observed here and our data correlates with that reported by other groups. MS, IM-MS and HDX-MS are used to probe alpha-Synuclein during the early stages of aggregation. A specific aggregation competent conformer is not observed suggesting that the solution constituents remain conformationally dynamic. We observe shifts in the species observed by MS and IM-MS between samples and our data contributes to an array of conflicting structural studies indicating that alpha-Synuclein adopts a diverse range of species with significant variation. For Abeta(1-42) and Abeta(1-40) Collision Induced Unfolding and ETD/ETcaD demonstrate that Abeta(1-42) adopts a compact conformation bound by intramolecular interactions. Changes to the Abeta(1-42) and Abeta(1-40) ATDs following SID are correlated to known structure influencing intermolecular interactions and demonstrate the large structural difference between Abeta(1-42) and Abeta(1-40) despite differing by only two C-terminal amino acids. IM-MS is used to classify the mode of action of anti-aggregation drug candidates on Abeta(1-42). The anti-aggregation capacity of the retro-inverso peptide, RI-OR2 is shown to result from inducing the compaction or extension of Abeta(1-42), preventing the adoption of an aggregation competent structure. In contrast, the flavonoid Rutin is shown to act solely through inducing Abeta(1-42) compaction. This thesis demonstrates the power of MS based methods to investigate the diverse range of structures of intrinsically disordered aggregating proteins implicated in disease.

This dissertation expounds on the investigations of the structure and chemistry of peptides and supramolecular host-guest systems in the gas phase. These investigations used two different kinds of analytical instrument: Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and ion mobility mass spectrometry (IM-MS, IMS). These investigations were complemented by chemical modeling. The FTICR was used to radially trap ions with its 4.7 T magnet, which allowed the ions to undergo sustained off-resonance irradiation collision-induced dissociation (SORI-CID). A subsequent event then measured the collision cross sections (σ) of the targeted precursor ion and one of the selected product ions. These experiments were repeated multiple times to measure σ for as many precursor/product pairs as possible. A similar kind of experiment was performed in the IM-MS instrument, through in-source collision-induced dissociation and size-based ion separation in the instrument’s mobility region. When the precursor/product σ ratios were compared, the values obtained by both methods were in good agreement with each other. Application of the FTICR-based technique to [2.2.2]-cryptand+Cs+ caused the externally bound Cs+ to migrate into the cryptand’s cavity. Further development of the FTICR-based technique allowed me to perform the post-SORI σ measurements in a time-resolved fashion. Data collected in this manner revealed that collisionally activated peptides refold over a 5 – 10 second timescale, as determined by their σ shrinking with time. These experiments allowed for observation of a peptide refolding. The IM-MS instrument was applied to a supramolecular chemistry problem surrounding cucurbit[7]uril (CB7), and its ability to bind two identical guests within its cavity. Literature precedent and conventional wisdom suggested that only one guest would bind within CB7’s cavity while the other guest would be bound externally. When ion mobility cross sections (Ω) were obtained for [CB7 + Guest2]2+ systems, it was discovered that both guests could be bound within CB7’s cavity. This was possible because the guests possessed the correct shape and chemistry to favor dispersive interactions between CB7’s cavity and the adjacent guest, and ion-dipole interactions with CB7’s carbonyl-lined portal.

No description available.

No description available.

Ce travail de thèse a été focalisé sur le développement d’approches MS et IM-MS supramoléculaires pour la caractérisation fine des interactions protéine/ligand et pour l’analyse de mélanges protéiques complexes. La maîtrise des instruments de MS supramoléculaire ainsi que les optimisations instrumentales et méthodologiques réalisées ont permis d’étendre le potentiel des approches MS et IM-MS pour la caractérisation d’assemblages moléculaires particulièrement complexes. Nous avons ainsi pu suivre la cinétique de formation de complexes protéine/ligand ainsi que les changements conformationnels qui y sont associés, montrant l’intérêt du couplage IM-MS en recherche pharmaceutique. De plus, ce travail a porté sur l’étude de complexes de très hauts poids moléculaires et l’évaluation de l’IM-MS pour obtenir des informations structurales sur ces complexes. Nous avons ainsi permis de repousser certaines limites de la MS et de placer cette technique au cœur des études de biologie structurale. / The aim of this thesis was the development of different supramolecular approaches, like MS and IM-MS, to characterize precisely protein/ligand interaction and to analyze complex mixtures of proteins. Understanding of supramolecular MS instruments and instrumental and methodological optimizations were allowed the development of MS and IM-MS to characterize very high mass supramolecular assembly. Thus, we were able to follow by kinetic the formation of protein/ligand interaction as well as associated conformational modifications, showing the interest of IM-MS coupling in pharmaceutical research. Furthermore, this work deals with the study of high mass complexes and assessment of IM-MS to obtain structural information on these complexes. As a consequence, we have pushed away some limits of MS allowing the use of this technique in structural biology.

Mitteilungen des URZ 1/2003

Mitteilungen des URZ 1/2003