Proteins, Lipids, and Water in the Gas Phase

Dodecyl maltoside protects membrane proteins in vacuo

Molecular dynamics simulations have been used to characterize the effects of transfer from aqueous solution to a vacuum to inform our understanding of mass spectrometry of membrane-protein-detergent complexes. We compared two membrane protein architectures (an α-helical bundle versus a β-barrel) and two different detergent types (phosphocholines versus an alkyl sugar) with respect to protein stability and detergent packing. The β-barrel membrane protein remained stable as a protein-detergent complex in vacuum. Zwitterionic detergents formed conformationally destabilizing interactions with an α-helical membrane protein after detergent micelle inversion driven by dehydration in vacuum. In contrast, a nonionic alkyl sugar detergent resisted micelle inversion, maintaining the solution-phase conformation of the protein. This helps to explain the relative stability of membrane proteins in the presence of alkyl sugar detergents such as dodecyl maltoside.

Lipidomics applications for discovering biomarkers of diseases in clinical chemistry

Lipids are the fundamental components of biological membranes as well as the metabolites of organisms. Lipids play diverse and important roles in biologicals. The lipid imbalance is closely associated with numerous human lifestyle-related diseases, such as atherosclerosis, obesity, diabetes, and Alzheimer's disease. Lipidomics or lipid profiling is a system-based study of all lipids aiming at comprehensive analysis of lipids in the biological system. Lipidomics has been accepted as a lipid-related research tool in lipid biochemistry, clinical biomarker discovery, disease diagnosis, and in understanding disease pathology. Lipidomics will not only provide insights into the specific functions of lipid species in health and disease, but will also identify potential biomarkers for establishing preventive or therapeutic programs for human diseases. This review presents an overview of lipidomics followed by in-depth discussion of its application to the study of human diseases, including extraction methods of lipids, analytical technologies, data analysis, and clinical research in cancer, neuropsychiatric disease, cardiovascular disease, kidney disease, and respiratory disease. We describe the current status of the identification of metabolic biomarkers in different diseases. We also discuss the lipidomics for the future perspectives and their potential problems. The application of lipidomics in clinical studies may provide new insights into lipid profiling and pathophysiological mechanisms.

Molecular dynamics of electrosprayed water nanodroplets containing sodium bis(2-ethylhexyl)sulfosuccinate

The behavior of aqueous solutions of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) subject to electrospray ionization (ESI) has been investigated by molecular dynamics (MD) simulations at three temperatures (350, 500 and 800 K). We consider several types of water nanodroplets containing AOTNa molecules and composed of a fixed number of water molecules (1000), N(AOT)(0) AOT(-) anions (N(AOT)(0) =  0, 5, 10) and N(Na)(0) sodium ions (N(Na)(0) =  0, 5, 10, 15, 20): in a short time scale (less than 1 ns), the AOTNa molecules, initially forming direct micelles in the interior of the water nanodroplets, are observed in all cases to diffuse nearby the nanodroplet surface, so that the hydrophilic heads and sodium ions become surrounded by water molecules, whereas the alkyl chains lay at the droplet surface. Meanwhile, evaporation of water molecules and of solvated sodium ions occurs, leading to a decrease of the droplet size and charge. At 350 K, no ejection of neutral or charged surfactant molecules is observed, whereas at 500 K, some fragmentation occurs, and at 800 K, this event becomes more frequent. The interplay of all these processes, which depend on the values of temperature, N(AOT)(0) and N(Na)(0) eventually leads to anhydrous charged surfactant aggregates with prevalence of monocharged ones, in agreement with experimental results of ESI mass spectrometry. The quantitative analysis of the MD trajectories allows to evidence molecular details potentially useful in designing future ESI experimental conditions.

Extracting structural information from charge-state distributions of intrinsically disordered proteins by non-denaturing electrospray-ionization mass spectrometry

Intrinsically disordered proteins (IDPs) exert key biological functions but tend to escape identification and characterization due to their high structural dynamics and heterogeneity. The possibility to dissect conformational ensembles by electrospray-ionization mass spectrometry (ESI-MS) offers an attracting possibility to develop a signature for this class of proteins based on their peculiar ionization behavior. This review summarizes available data on charge-state distributions (CSDs) obtained for IDPs by non-denaturing ESI-MS, with reference to globular or chemically denatured proteins. The results illustrate the contributions that direct ESI-MS analysis can give to the identification of new putative IDPs and to their conformational investigation.

Native mass spectrometry characterization of intact nanodisc lipoprotein complexes

We describe here the analysis of nanodisc complexes by using native mass spectrometry (MS) to characterize their molecular weight (MW) and polydispersity. Nanodiscs are nanoscale lipid bilayers that offer a platform for solubilizing membrane proteins. Unlike detergent micelles, nanodiscs are native-like lipid bilayers that are well-defined and potentially monodisperse. Their mass spectra allow peak assignment based on differences in the mass of a single lipid per complex. Resultant masses agree closely with predicted values and demonstrate conclusively the narrow dispersity of lipid molecules in the nanodisc. Fragmentation with collisionally activated dissociation (CAD) or electron-capture dissociation (ECD) shows loss of a small number of lipids and eventual collapse of the nanodisc with release of the scaffold protein. These results provide a foundation for future studies utilizing nanodiscs as a platform for launching membrane proteins into the gas phase.

Characterization of rhinovirus subviral A particles via capillary electrophoresis, electron microscopy and gas-phase electrophoretic mobility molecular analysis: Part I

During infection, enteroviruses, such as human rhinoviruses (HRVs), convert from the native, infective form with a sedimentation coefficient of 150S to empty subviral particles sedimenting at 80S (B particles). B particles lack viral capsid protein 4 (VP4) and the single-stranded RNA genome. On the way to this end stage, a metastable intermediate particle is observed in the cell early after infection. This subviral A particle still contains the RNA but lacks VP4 and sediments at 135S. Native (150S) HRV serotype 2 (HRV2) as well as its empty (80S) capsid have been well characterized by capillary electrophoresis. In the present paper, we demonstrate separation of at least two forms of subviral A particles on the midway between native virions and empty 80S capsids by CE. For one of these intermediates, we established a reproducible way for its preparation and characterized this particle in terms of its electrophoretic mobility and its appearance in transmission electron microscopy (TEM). Furthermore, the conversion of this intermediate to 80S particles was investigated. Gas-phase electrophoretic mobility molecular analysis (GEMMA) yielded additional insights into sample composition. More data on particle characterization including its protein composition and RNA content (for unambiguous identification of the detected intermediate as subviral A particle) will be presented in the second part of the publication.

Do charge state signatures guarantee protein conformations?

The extent to which proteins in the gas phase retain their condensed-phase structure is a hotly debated issue. Closely related to this is the degree to which the observed charge state reflects protein conformation. Evidence from electron capture dissociation, hydrogen/deuterium exchange, ion mobility, and molecular dynamics shows clearly that there is often a strong correlation between the degree of folding and charge state, with the most compact conformations observed for the lowest charge states. In this article, we address recent controversies surrounding the relationship between charge states and folding, focussing also on the manipulation of charge in solution and its effect on conformation. 'Supercharging' reagents that have been used to effect change in charge state can promote unfolding in the electrospray droplet. However for several protein complexes, supercharging does not appear to perturb the structure in that unfolding is not detected. Consequently, a higher charge state does not necessarily imply unfolding. Whilst the effect of charge manipulation on conformation remains controversial, there is strong evidence that a folded, compact state of a protein can survive in the gas phase, at least on a millisecond timescale. The exact nature of the side-chain packing and secondary structural elements in these compact states, however, remains elusive and prompts further research.

Conformational distribution of bradykinin [bk + 2 H]2+ revealed by cold ion spectroscopy coupled with FAIMS

We employ cold ion spectroscopy (CIS) in conjunction with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to study the peptide bradykinin in its doubly protonated charge state ([bk + 2 H](2+)). Using FAIMS, we partially separate the electrosprayed [bk + 2 H](2+) ions into two conformational families and selectively introduce one of them at a time into a cold ion trap mass spectrometer, where we probe them by UV photofragment spectroscopy. Although the two conformational families have distinct electronic spectra, some cross-conformer contamination can be observed under certain conditions. We demonstrate that this contamination comes from isomerization of ions energized during and/or after their separation and not from incomplete separation of the initially electrosprayed conformations in the FAIMS stage. By varying the injection voltage of the ions into our mass spectrometer, we can intentionally induce isomerization to produce what seems to be a gas phase equilibrium distribution of conformers. This distribution is different from the one produced initially by electrospray, indicating that some of the conformers are kinetically trapped and may be related to conformers that are more favored in solution.

Interfacing multistage mass spectrometry with liquid chromatography or ion mobility separation for synthetic polymer analysis

Synthetic polymers are naturally mixtures of homologs, even in pure form. More complexity is introduced by the presence of different comonomers, end groups and/or macromolecular architectures. The analysis of such systems is substantially facilitated by interfacing mass spectrometry (MS), which disperses based on mass, with an additional level of separation involving either interactive liquid chromatography (LC) or ion mobility (IM) spectrometry, both of which are readily coupled online with electrospray ionization and MS detection. IM-MS separates in the gas phase, post-ionization and, therefore, is ideally suitable for labile and reactive polymers. Its usefulness is illustrated with the characterization of non-covalent siloxane-saccharide complexes, metallosupramolecular assemblies and an air- and moisture-sensitive inorganic polymer, poly(dichlorophosphazene). Conversely, LC-MS which separates in solution phase, before ionization, is most effective for the analysis of polymeric mixtures whose components differ in polarity. Interactive LC conditions can be optimized to disperse by the content of hydrophobic units, as is demonstrated for amphiphilic polyether copolymers and sugar-based nonionic surfactant blends. Both LC-MS and IM-MS can be extended into a third dimension by tandem mass spectrometry (MS(2)) studies on select oligomers, in order to obtain insight into individual end groups and isomeric architectures, comonomer sequences and degree of substitution, for example, by hydrophobic functionalities.

Do electrospray mass spectra of surfactants mirror their aggregation state in solution?

One important feature in the gas phase chemistry of surfactants is to ascertain whether their aggregates produced by electrospray ionization reflect those formed in the starting solution. With this aim, we have performed ESI-MS, ESI-MS/MS and ER-MS spectra of bis(2-ethylhexyl)sulfosuccinate (AOTNa) solutions in different solvents, i.e. water, water/methanol, methanol and n-hexane. The results clearly indicate that, notwithstanding the strongly different aggregation state in solution (direct micelles in water and in water/methanol, molecular dispersion in methanol and reverse micelles in n-hexane) and marked effects of the solvent polarity on the total ionic current, the surfactant aggregates in gas phase show identical structural features. Analogous conclusions can be drawn analyzing the infrared multiple photon dissociation (IRMPD) spectra of AOTNa solutions in water/methanol and n-hexane. Moreover, according to the idea that gas phase can be considered an apolar environment par excellence, data consistently suggest a reverse micelle-like aggregation. Some peculiarities of the mechanisms leading to aggregate formation through electrospray ionization of surfactant solutions in solvent media with different polarity have been also discussed.

Lipid analysis and lipidomics by structurally selective ion mobility-mass spectrometry

Recent advances in mass spectrometry approaches to the analysis of lipids include the ability to incorporate both lipid class identification with lipid structural information for increased characterization capabilities. The detailed examination of lipids and their biosynthetic and biochemical pathways made possible by novel instrumental and bioinformatics approaches is advancing research in fundamental cellular and medical studies. Recently, high-throughput structural analysis has been demonstrated through the use of rapid gas-phase separation on the basis of the ion mobility (IM) analytical technique combined with mass spectrometry (IM-MS). While IM-MS has been extensively utilized in biochemical research for peptide, protein and small molecule analysis, the role of IM-MS in lipid research is still an active area of development. In this review of lipid-based IM-MS research, we begin with an overview of three contemporary IM techniques which show great promise in being applied towards the analysis of lipids. Fundamental concepts regarding the integration of IM-MS are reviewed with emphasis on the applications of IM-MS towards simplifying and enhancing complex biological sample analysis. Finally, several recent IM-MS lipid studies are highlighted and the future prospects of IM-MS for integrated omics studies and enhanced spatial profiling through imaging IM-MS are briefly described.

Mass spectrometry of surfactant aggregates

In contrast with the enormous amount of literature produced during many decades in the field of surfactant aggregation in liquid, liquid crystalline and solid phases, only a few investigations concerning surfactant self- assembling in the gas phase as charged aggregates have been carried out until now. This lack of interest is disappointing in view of the remarkable theoretical and practical importance of the inherent knowledge. The absence of surfactant-solvent interactions makes it easier to study the role of surfactant-surfactant forces in determining their peculiar self-assembling features as well as the ability of these assemblies to incorporate selected solubilizate molecules. Thus, the study of gas-phase surfactant and surfactant-solubilizate aggregates is a research subject which has exciting potential, including mass and energy transport in the atmosphere, origin of life and simulation of supramolecular aggregation in interstellar space. On the other hand, the structural and dynamic properties of surfactant aggregates in the gas phase could be exploited in a number of interesting applications such as atmospheric cleaning agents, transport and protection of pulmonary drugs or biomolecules and as nanoreactors for specialized chemical reactions in confined space. Spectrometric techniques, together with molecular dynamics simulations, have been the principal investigative tools in this field and appearto be particularly suited to gaining fundamental information on the structure and stability of surfactant-based supramolecular aggregates, charge state effects, entrapment of solubilizate molecules, preferential solubilization sites and chemical reactions localized in a single organized aggregate. The main aim of this review is to present the actual state of the art in this novel and exciting research field underlining the knowledge acquired up to now as well as the aspects needing a more deep understanding. Moreover, intriguing departures of the behavior of surfactant solutions under electrospray ionization conditions from that of ionic, polar and apolar analytes will be discussed.