The advent of electrospray ionization enabled the study of intact protein complexes via MS. For example, in the mid-1990s, the observation that viruses can survive after entering the gas-phase and still retain activity was shown. Advances in sample preparation methodologies, mainly native MS, allowed for the preservation of large non-covalently bound complexes, which led to structural characterization studies that were previously unachievable. However, native MS suffers from complications arising from inherent heterogeneity and severe salt adduction. Consequently, the spectra can consist of broad and overlapping peaks that may even preclude the ability to obtain a mass measurement. This dissertation will focus on a gas-phase technique to address highly complex native MS scenarios that give rise to poorly resolved signals using the E. coli ribosome as one model system. Moreover, brief discussion of improvements made on our QToF platform (SCIEX 5600) will be compared with other state-of-the-art instruments. Lastly, other applications to our ion/ion reaction workflow will be explored.

Proteins are synthesised as linear polymeric chains. The subtle energetic interplay of interatomic interactions results in chain folding, through which proteins may acquire defined structures. This spatial organisation is encoded by the protein sequence itself; the so-called thermodynamic hypothesis formulated by Anfinsen in 1961. A defined structure is often considered a pre-requisite to protein function, but widespread existence of intrinsically disordered proteins (IDPs) has prompted a re- evaluation of the ways biological function may be encoded into polypeptide chains. Furthermore, proteins often exist as part of multi-component entities, where regulation of assembly is integral to their properties. The interplay between disorder, oligomerisation and function is the focus of this thesis. Some IDPs fold conditionally upon interacting with a partner protein; a process known as coupled folding and binding. What are the biophysical advantages and consequences of disorder in the context of these interactions? A common feature of IDPs is their sequence composition bias, with charged residues being often over-represented. It is therefore tempting to speculate that electrostatic interactions may play a major role in coupled folding and binding reactions. Surprisingly, the opposite was found to be true. Charge-charge interactions only contributed about an order of magnitude to the association rate constants of two contrasting model systems. The lack of pre-formed binding interfaces-a consequence of disorder-might preclude electrostatic acceleration from complementary patches. By looking at the role of the sequence, many studies have taken a protein-centric approach to understanding disorder. Yet there is paucity of data about the effect of extrinsic factors on interactions involving disordered partners. Investigating the role of co-solutes, it was discovered that the kinetic and thermodynamic profiles of coupled folding and binding reactions were sensitive to ion-types. This effect followed the Hofmeister series, and occurred at physiological concentrations of salt. The sensitivity of coupled folding and binding reactions-a consequence of the lack of stability of IDPs-might be advantageous. Given the role of ions in biology, this 'biophysical sensing' could be a mechanism of physiological relevance, allowing modulation of protein-protein interactions involving disordered partners in response to changes in their environments. In cells, signalling networks are often multi-layered, and involve competing protein-protein interactions. The interplay between the biophysical characteristics of the components, and the behaviour of the network were investigated in a model tripartite system composed of folded and disordered proteins. The BCL-2 family regulates the intrinsic pathway of apoptosis through control of mitochondrial outer-membrane permeabilisation; a result of BAK and BAX oligomerisation. Through a shared homology motif (termed BH3), the subtle balance of their interactions determines cellular fate at the molecular level. Characterisation of the model under simple biochemical conditions revealed large differences in affinities among binary interactions; the consequence of the lifetime of the complexes, not their speed of association. A membrane-like environment, re-created using detergents, allows the oligomerisation of BAK and BAX in vitro. Furthermore, investigation of the tripartite system under detergent conditions showed that regulation of the network was the result of competing hetero- and homo-oligomerisation events. Relationships to their biophysical properties were gained by probing their energy landscapes using protein folding techniques. The connection between the biophysical properties of the components of the network and their interactions provides a molecular explanation for the regulation of apoptosis. This thesis offers insights into the ways structured assemblies and environmentally responsive disorder elements may encode functions into proteins.

No description available.

<p dir="ltr">Multiply-charged ions of intact biomolecules generated from electrospray ionization (ESI) have drawn researchers' interest in the field of native mass spectrometry (MS) for decades because these ions carry mass and charge information of the intact molecules and interactions among different units. However, the confinement of multiple charge states in a narrow range of <i>m/z</i> makes mass and charge assignments challenging, especially for analytes with a mass greater than 100 kDa. Gas-phase ion/ion reactions have proven to be powerful techniques that facilitate the interpretation of mass spectra of natively sprayed macromolecular analytes by manipulating the masses and charges of ions detected.</p><p dir="ltr">The proton-transfer reaction (PTR) is the most used gas-phase ion/ion reaction method. It utilizes perfluorinated PTR reagents to "grab" protons away from the analyte ions, thereby reducing their charges. A novel charge state manipulation technique called "ion parking," based on PTR, has been developed. In this method, ion signals are accumulated to one or a range of charge states by selectively inhibiting reactions between the target charge state and the PTR reagents via resonance excitation.</p><p dir="ltr">The multiply-charged ion attachment (MIA) reaction is another gas-phase ion/ion reaction approach. It utilizes the significant <i>m/z</i> displacement caused by the attachment of multiply-charged reagent ions, and it has been proven useful for mass analysis of heterogeneous macromolecular analytes with a mass greater than 1 MDa.</p><p dir="ltr">All gas-phase ion/ion reaction techniques require mutual storage of ions in opposite polarities within an electrodynamic quadrupole ion trap, such as a 3D quadrupole ion trap (QIT) or a linear quadrupole ion trap (LIT). Electrodynamic ion traps use high-voltage (HV) drive radio frequencies (RF) to trap ions in a quadrupolar field, typically employing a sinusoidal waveform (sine wave). A digital quadrupole ion trap (DIT) is an unconventional electrodynamic ion trap that uses a digital waveform (square wave) as the drive RF. The high agility of square waves makes DIT an ideal mass analyzer for studying high <i>m/z</i> ions resulting from gas-phase ion/ion reactions. This dissertation describes the development of a novel home-built digital dual-trap mass spectrometer and ion/ion chemistry studies of large biomolecules within the instrument.</p>