Native Biomolecules in the Gas Phase? The Case of Green Fluorescent Protein

Mass spectrometric stochastic dynamic 3D structural analysis of mixture of steroids in solution - Experimental and theoretical study

There is explored, herein, functional relation: Experimental mass spectrometric phenomenon, obeying a certain scientific law ⇔ 3D molecular conformations and electronic structures of analytes obtained for quantum chemical theories. The paper answers to questions: (a) What evidence claims these actual relations among measurable and theoretical parameters, experimental factors and molecular properties; (b) how the provided evidence is collected and used; and (c) how empirical proof relates to assign and explain mass spectrometric phenomena of steroids afforded by our innovative stochastic dynamic mass spectrometric formula, D″_SD = 2.6388.10^-17.(<I²>-<I>²), quantum chemical 3D conformations, electronic structures and energetics of molecules, respectively. The paper address issue concerning empirical evidence at very high-to-exact level of assignment of 3D molecular conformations of steroids to experimental mass spectrometric fragment ions, accounting precisely for (i) effect of protonation; (ii) intramolecular rearrangement for A-D rings of steroidal skeleton and proton transfer effect, if any; in addition to (iii) examination of enantiomers of steroids in mixture with different stereochemistry, (R) and (S), of a set of six atoms of the molecular backbone of hydrocortisone (1), deoxycorticosterone (2), progesterone (3) and methyltestosterone (4), respectively. Results from testosterone (5) are discussed, as well. There are used ultra-high resolution atmospheric pressure chemical ionization mass spectrometric data on analytes (1)-(4) at ng.(mL)^-1 concentration levels in mixtures in solution obtained for positive operation mode. High accuracy static and molecular dynamic quantum chemical computations and chemometrics are also utilized. Experimental 3D structural parameters of steroids obtained for stochastic dynamic diffusion theory are correlated with available crystallographic data.

Adapting a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Gas-Phase Fluorescence Spectroscopy Measurement of Trapped Biomolecular Ions

Gas-phase fluorescence spectroscopy is still in its infancy, which demands further instrumental developments. In this study, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), equipped with a lab-developed data acquisition system, was coupled to a tunable femtosecond laser and a state-of-the-art optical system for fluorescence studies of mass-selected ions. For excitation, a laser beam was focused (beam size < 1.0 mm) into the cylindrical ICR cell. A wire mesh replaced the back trapping plate, allowing ∼10% of the fluorescence emitted from trapped ions to be collected by a lens installed beside the wire mesh. The collected fluorescence light was then transmitted outside of the mass spectrometer via fiber optics. A novel accumulation during detection (ADD) scheme was developed to increase the duty cycle of gas-phase fluorescence spectroscopy experiments. With ADD, >90% duty cycle for mass spectrometry and fluorescence experiments could be achieved. This instrument was able to perform fluorescence experiments on various ions, from simple rhodamine dyes to large biomolecules (i.e., peptides and proteins) labeled with dyes of various optical properties. A fluorescence lifetime measurement of trapped rhodamine 6G cations was also performed, yielding a value of 5.97 ± 0.23 ns. This setup has a broad mass range and decent fluorescence spectroscopy performance (i.e., the emission spectrum of rhodamine 6G can be acquired with good S/N in a minute). Finally, this setup also allows more challenging gas-phase fluorescence spectroscopy experiments, for example, of low quantum yield fluorophores and large biomolecules in their native state that appear at high m/z, which may not be doable with quadrupole ion traps (QIT).

Gas-phase hydration of the lysozyme ion produced by infrared-laser ablation of a droplet beam studied by photodissociation and fluorescence spectroscopy

Biomolecules function in an aqueous environment. Elucidation of the hydration structures of biomolecules is hence important to understand their functions. Here, we investigated the hydration structure of lysozyme (Lys) in the gas phase by photodissociation and fluorescence spectroscopy in combination with droplet-beam laser ablation mass spectrometry. We found that water molecules are held inside and on the surface of the Lys molecule, and the hydration structure around the tryptophan residue changes by photoexcitation. This study provides a novel method to observe the hydration structures of large biomolecules at the molecular level.

Fluorescence-Based Detection of the Desolvation Process of Protein Ions Generated in an Aqueous Electrospray Plume

A new experimental setup to study laser-induced fluorescence from analytes at different locations in an electrospray plume has been developed. The high fluorescence collection efficiency (∼2%) of the setup, along with a sensitive charge coupled device (CCD) detector, enabled the study of low ion concentrations (down to ∼fM) in the plume. The use of small electrospray tip inner diameters (<1 μm) facilitated the fast desolvation of gaseous protein ions in an aqueous electrospray plume. Fluorescence spectra were acquired from specific locations along the plume axis in different aqueous electrospray plumes with three different analytes: a rhodamine dye and two proteins (ubiquitin and apomyoglobin) labeled with rhodamine dyes. To confirm the presence of gaseous ions, pure gas-phase fluorescence spectra were acquired in the vacuum of a modified ion trap mass spectrometer. These spectra were used to fit to confirm the presence of gaseous species in the corresponding spectra obtained from the electrospray plume. This study shows that with small inner diameter spray capillaries, gaseous protein ions generated at atmospheric pressure in an electrospray plume can be detected with fluorescence-based techniques. Fluorescence measurements can be used to study their structure in the electrospray plume, and the dynamics as they transition from solution to the gas phase and in the early stages after desolvation from charged droplets. Other techniques can also be applied to further study gaseous biomolecular structures under ambient conditions immediately after desolvation.

Breaking the Brightness Barrier: Design and Characterization of a Selected-Ion Fluorescence Measurement Setup with High Optical Detection Efficiency

A quadrupole ion trap (QIT) mass spectrometer has been modified and coupled with tunable laser excitation and highly sensitive fluorescence detection systems to perform fluorescence studies on mass-selected ions. Gaseous ions, generated using nanoelectrospray ionization (nano-ESI), are trapped in the QIT that allows optical access for laser irradiation. The emitted fluorescence is collected from a 5.0 mm diameter hole drilled into the ring electrode of the QIT and is directed toward the detection setup. Due to the small inner diameter (7.07 mm) of the ring electrode and a relatively large opening for fluorescence collection, a fluorescence collection efficiency of 2.3% is achieved. After some losses in transmission, around 1.8% of the emitted fluorescence reaches the detectors, more than any other similar instrument reported in the literature. This improved fluorescence collection translates to a much shorter measurement time for a fluorescence signal. Another key feature of this setup is the ability to perform a variety of fluorescence experiments on trapped ions including excitation and emission spectroscopy, lifetime measurement, and ion imaging. The capabilities of the instrument are demonstrated by measuring fluorescence spectra of dyes and biomolecules labeled with dyes in a range of different excitation and emission wavelengths, quantum yields, m/z, and different polarities. A fluorescence lifetime measurement and ion image of trapped rhodamine 6G cations are also shown. With a wide array of functionality and high fluorescence detection performance, this setup provides an opportunity to study biomolecular structures and photophysics of fluorophores in well-controlled environments.

Inspecting fluctuation and coordination around chromophore inside green fluorescent protein from water to nonpolar solvent

Green fluorescent protein (GFP) is a widely used biomarker that demands systematical rational approaches to its structure function redesign. In this work, we mainly utilized atomistic molecular dynamics simulations to inspect and visualize internal fluctuation and coordination around chromophore inside GFP, from water to nonpolar octane solvent. We found that GFP not only maintains its β-barrel structure well into the octane, but also sustains internal residue and water coordination to position the chromophore stably while suppress dihedral fluctuations of the chromophore, so that functional robustness of GFP is achieved. Our accompanied fluorescence microscope measurements accordingly confirmed the GFP functioning into the octane. Furthermore, we identified that crucial water sites inside GFP along with permeable pores on the β-barrel of the protein are largely preserved from the water to the octane solvent, which allows sufficiently fast exchanges of internal water with the bulk or with the water layer kept on the surface of the protein. By additionally pulling GFP from bulk water to octane, we suggest that the GFP function can be well maintained into the nonpolar solvent as long as, first, the protein does not denature in the nonpolar solvent nor across the polar-nonpolar solvent interface; second, a minimal set of water molecules are in accompany with the protein; third, the nonpolar solvent molecules may need to be large enough to be nonpermeable via the water pores on the β-barrel.

Installation, validation, and application examples of two instrumental setups for gas-phase HDX-MS analysis of peptides and proteins

Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by reaction with the highly basic reagent ND₃, enabling conformational analysis of protein states that are pertinent to the native solution-phase. Here, we describe two different instrumental approaches to enable gas-phase HDX-MS for analysis of peptides and proteins on high-resolution Q-TOF mass spectrometers. We include a description of the procedure and equipment required for successful installation as well as suggested procedures for testing, validation, and troubleshooting of a gas-phase HDX-MS setup. In the two described approaches, gas-phase HDX-MS are performed either immediately after ESI in the cone exit region by leading N₂-gas over a deuterated ND₃/D₂O solution, or by leading purified ND₃-gas into different traveling wave ion guides (TWIG) of the mass spectrometer. We envision that a detailed description of the two gas-phase HDX-MS setups and their practical implementation and validation can pave the way for gas-phase HDX-MS to become a more routinely used MS technique for structural analysis of peptides and proteins.

Mass spectrometry beyond the native state

Native mass spectrometry allows the study of proteins by probing in vacuum the interactions they form in solution. It is a uniquely useful approach for structural biology and biophysics due to the high resolution of separation it affords, allowing the concomitant interrogation of multiple protein components with high mass accuracy. At its most basic, native mass spectrometry reports the mass of intact proteins and the assemblies they form in solution. However, the opportunities for more detailed characterisation are extensive, enabled by the exquisite control of ion motion that is possible in vacuum. Here we describe recent developments in mass spectrometry approaches to the structural interrogation of proteins both in, and beyond, their native state.

Gas-phase protein conformation/multimer ion formation by electrospray ion mobility-mass spectrometry: bovine insulin and ubiquitin

Ion mobility-mass spectrometry (IMMS) is a very attractive method for studies in structural biology because of the ability of rapid isolation by nearly simultaneous m/z characterization and size separation, leading to an emergence of IMMS as a complimentary biochemical tool. Earlier, we developed a method based on varying the protein concentration in solution prior to electrospray ionization (ESI) with subsequent m/z selection and dissociation of protein multimers by IMMS of cytochrome c. The focus of this work will be to correctly distinguish truly different ion conformations formed by ESI versus homomultimeric complexes with the same m/z for well-studied proteins bovine ubiquitin and insulin. These proteins were chosen due to their large difference in solution phase structures: insulin tightly bound by disulfide linkages, and ubiquitin-a protein that may adopt a range of states from compact to extended. Our preliminary results, as with cytochrome c reveal false negatives for protein oligomer formation and false positives for protein conformational states. In addition, these results will be couched in terms of the need for quantification of IMMS analysis of proteins given the total area under IMMS peaks can also distinguish conformation versus aggregation as higher order oligomers have more mass per ion.This article is part of the themed issue 'Quantitative mass spectrometry'.

Native Mass Spectrometry in Fragment-Based Drug Discovery

The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.

Leveraging ultraviolet photodissociation and spectroscopy to investigate peptide and protein three-dimensional structure with mass spectrometry

Recent advances in mass spectrometry and lasers have facilitated the development of novel experiments combining the benefits of both technologies.

Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin

We explore conformational space of triply protonated bradykinin. Three conformational families are mobility-separated and spectroscopically characterized. Kinetically trapped structures are identified via annealing.

Proteins with highly similar native folds can show vastly dissimilar folding behavior when desolvated

Proteins can be exposed to vastly different environments such as the cytosol or membranes, but the delicate balance between external factors and intrinsic determinants of protein structure, stability, and folding is only poorly understood. Here we used electron capture dissociation to study horse and tuna heart Cytochromes c in the complete absence of solvent. The significantly different stability of their highly similar native folds after transfer into the gas phase, and their strikingly different folding behavior in the gas phase, can be rationalized on the basis of electrostatic interactions such as salt bridges. In the absence of hydrophobic bonding, protein folding is far slower and more complex than in solution.