Probing electrostatic interactions and structural changes in highly charged protein polyanions by conformer-selective photoelectron spectroscopy

Size and charge-state dependence of detachment energies of polyanionic silver clusters

The electronic properties of silver clusters (N up to 800) charged by attachment of up to z = 7 excess electrons are investigated. As an essential preparation step, the technique of in-trap electron attachment to size-selected monoanions within a linear Paul trap is applied. By taking advantage of tunable laser pulses, the photoelectron spectra allow us to evaluate details of the electronic structure of polyanionic metal clusters, giving a multidimensional dataset. The subsequent analysis based on the liquid drop model provides information about the atomic structure and the bulk work function at a hitherto unknown quality.

Ion mobility resolved photo-fragmentation to discriminate protomers

RATIONALE

Among the sources of structural diversity in biomolecular ions, the co-existence of protomers is particularly difficult to take into account, which in turn complicates structural interpretation of gas-phase data.

METHODS

We investigated the sensitivity of gas-phase photo-fragmentation measurements and ion mobility spectrometry (IMS) to the protonation state of a model peptide derivatized with chromophores. Accessible interconversion pathways between the different identified conformers were probed by tandem ion mobility measurement. Furthermore, the excitation coupling between the chromophores has been probed through photo-fragmentation measurements on mobility-selected ions. All results were interpreted based on molecular dynamics simulations.

RESULTS

We show that protonation can significantly affect the photo-fragmentation yields. Especially, conformers with very close collision cross sections (CCSs) may display dramatically different photo-fragmentation yields in relation with different protonation patterns.

CONCLUSIONS

We show that, even if precise structure assignment based on molecular modeling is in principle difficult for large biomolecular assemblies, the combination of photo-fragmentation and IMS can help to identify the signature of protomer co-existence for a population of biomolecular ions in the gas phase. Such spectroscopic data are particularly suitable to follow conformational changes.

Isomeric Effect of Mercaptobenzoic Acids on the Synthesis, Stability, and Optical Properties of Au25(MBA)18 Nanoclusters

We report a simple size focusing, two-step "bottom-up" protocol to prepare water-soluble Au₂₅(MBA)₁₈ nanoclusters, using the three isomers of mercaptobenzoic acids (p/m/o-MBA) as capping ligands and Me₃NBH₃ as a mild reducing agent. The relative stability of the gas-phase multiply deprotonated Au₂₅(MBA)₁₈ ions was investigated by collision-induced dissociation. This permitted us to evaluate the possible isomeric effect on the Au-S interfacial bond stress. We also investigated their optical properties. The absorption spectra of Au₂₅(MBA)₁₈ isomers were very similar and showed bands at 690, 470, and 430 nm. For all Au₂₅(MBA)₁₈ isomeric clusters, no measurable one-photon excited fluorescence under UV-vis light was found, in neither solid- nor solution-state. The two-photon excited emission spectra and first hyperpolarizabilities of the clusters were also determined. The results are discussed in terms of the possible isomeric effect on excitations within the metal core and the possibility of charge transfer excitations from the ligands to the metal nanocluster.

Spontaneous Reshaping and Splitting of AgCl Nanocrystals under Electron Beam Illumination

AgCl is photosensitive and thus often used as micromotors. However, the dynamics of individual AgCl nanoparticle motion in liquids upon illumination remains elusive. Here, using liquid cell transmission electron microscope (TEM), AgCl nanocrystals reshaping and splitting spontaneously in an aqueous solution under electron beam illumination are observed. It is found that the AgCl nanocrystals are negatively charged in the liquid environment, where the charge induces a repulsive Coulomb force that reshapes and stretches those nanocrystals. Upon extensive stretching, the AgCl nanocrystal splits into small nanocrystals and each nanocrystal retracts back into cuboid shapes due to the cohesive surface. This analysis shows that each nanocrystal maintains a single crystal rocksalt structure during splitting. The splitting of AgCl nanocrystals is analogous to the electrified liquid droplets or other reported the Coulomb fission phenomenon, but with distinctive structural properties. Revealing of the dynamic behavior of AgCl nanocrystals opens the opportunity to explore their potential applications as actuators for nanodevices.

Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry

Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.

Correlation of the structural information obtained for europium-chelate ensembles from gas-phase photoluminescence and ion-mobility spectroscopy with density-functional computations and ligand-field theory

We report a combined investigation of europium(iii)9-oxo-phenalen-1-one (PLN) coordination complexes, [Eu(PLN)₄AE]⁺ with AE = Mg, Ca, and Sr, using gas-phase photoluminescence, trapped ion-mobility spectrometry and density-functional computations. In order to sort out the structural impact of the alkali earth dications on the photoluminescence spectra, the experimental data are compared to the predicted ligand-field splittings as well as to the collision cross-sections for different isomers of [Eu(PLN)₄AE]⁺. The best fitting interpretation is that one isomer family predominantly contributes to the recorded luminescence. The present work demonstrates the complexity of the coordination patterns of multicenter lanthanoid chelates involved in dynamical equilibria and the pertinence of using isolation techniques to elucidate their photophysical properties.

Multiple electron capture from isolated protein poly-anions in collision with slow highly charged ions

Multiply charged ions very efficiently capture several electrons from trapped mass/charge selected protein poly-anions, producing dominantly charge-reduced proteins and small neutral losses.

TEMPO-Assisted Free Radical-Initiated Peptide Sequencing Mass Spectrometry (FRIPS MS) in Q-TOF and Orbitrap Mass Spectrometers: Single-Step Peptide Backbone Dissociations in Positive Ion Mode

The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. 85, 7044-7051 (30)). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research. Graphical Abstract ᅟ.

Tandem ion mobility spectrometry coupled to laser excitation

This manuscript describes a new experimental setup that allows to perform tandem ion mobility spectrometry (IMS) measurements and which is coupled to a high resolution time-of-flight mass spectrometer. It consists of two 79 cm long drift tubes connected by a dual ion funnel assembly. The setup was built to permit laser irradiation of the ions in the transfer region between the two drift tubes. This geometry allows selecting ions according to their ion mobility in the first drift tube, to irradiate selected ions, and examine the ion mobility of the product ions in the second drift tube. Activation by collision is possible in the same region (between the two tubes) and between the second tube and the time-of-flight. IMS-IMS experiments on Ubiquitin are reported. We selected a given isomer of charge state +7 and explored its structural rearrangement following collisional activation between the two drift tubes. An example of IMS-laser-IMS experiment is reported on eosin Y, where laser irradiation was used to produce radical ions by electron photodetachment starting from doubly deprotonated species. This allowed measuring the collision cross section of the radical photo-product, which cannot be directly produced with an electrospray source.

Radical-driven peptide backbone dissociation tandem mass spectrometry

In recent years, a number of novel tandem mass spectrometry approaches utilizing radical-driven peptide gas-phase fragmentation chemistry have been developed. These approaches show a peptide fragmentation pattern quite different from that of collision-induced dissociation (CID). The peptide fragmentation features of these approaches share some in common with electron capture dissociation (ECD) or electron transfer dissociation (ETD) without the use of sophisticated equipment such as a Fourier-transform mass spectrometer. For example, Siu and coworkers showed that CID of transition metal (ligand)-peptide ternary complexes led to the formation of peptide radical ions through dissociative electron transfer (Chu et al., 2000. J Phys Chem B 104:3393-3397). The subsequent collisional activation of the generated radical ions resulted in a number of characteristic product ions, including a, c, x, z-type fragments and notable side-chain losses. Another example is the free radical initiated peptide sequencing (FRIPS) approach, in which Porter et al. and Beauchamp et al. independently introduced a free radical initiator to the primary amine group of the lysine side chain or N-terminus of peptides (Masterson et al., 2004. J Am Chem Soc 126:720-721; Hodyss et al., 2005 J Am Chem Soc 127: 12436-12437). Photodetachment of gaseous multiply charged peptide anions (Joly et al., 2008. J Am Chem Soc 130:13832-13833) and UV photodissociation of photolabile radical precursors including a C-I bond (Ly & Julian, 2008. J Am Chem Soc 130:351-358; Ly & Julian, 2009. J Am Soc Mass Spectrom 20:1148-1158) also provide another route to generate radical ions. In this review, we provide a brief summary of recent results obtained through the radical-driven peptide backbone dissociation tandem mass spectrometry approach.

Electron photodetachment dissociation for structural characterization of synthetic and bio-polymer anions

Tandem mass spectrometry (MS-MS) is a generic term evoking techniques dedicated to structural analysis, detection or quantification of molecules based on dissociation of a precursor ion into fragments. Searching for the most informative fragmentation patterns has led to the development of a vast array of activation modes that offer complementary ion reactivity and dissociation pathways. Collisional activation of ions using atoms, molecules or surface resulting in unimolecular dissociation of activated ions still plays a key role in tandem mass spectrometry. The discovery of electron capture dissociation (ECD) and then the development of other electron-ion or ion/ion reaction methods, constituted a significant breakthrough, especially for structural analysis of large biomolecules. Similarly, photon activation opened promising new frontiers in ion fragmentation owing to the ability of tightly controlled internal energy deposition and easy implementation on commercial instruments. Ion activation by photons includes slow heating methods such as infrared multiple photon dissociation (IRMPD) and black-body infrared radiative dissociation (BIRD) and higher energy methods like ultra-violet photodissociation (UVPD) and electron photo detachment dissociation (EPD). EPD occurs after UV irradiation of multiply negatively charged ions resulting in the formation of oxidized radical anions. The present paper reviews the hypothesis regarding the mechanisms of electron photo-detachment, radical formation and direct or activated dissociation pathways that support the observation of odd and even electron product ions. Finally, the value of EPD as a complementary structural analysis tool is illustrated through selected examples of synthetic polymers, oligonucleotides, polypeptides, lipids, and polysaccharides.

Multiple Electron Ejection from Proteins Resulting from Single-Photon Excitation in the Valence Shell

One-photon multiple ionization is a signature of dynamical electron correlations in atoms and small molecules, as observed in the Auger process when Auger electron emission follows core-shell ionization. In such a process, the high energy needed to remove several electrons is due to the strong Coulombic attraction between the last departing electron(s) and the ionic core. Multiply negatively charged molecules offer the possibility to overcome the Coulombic attraction, opening the way for multielectron photodetachment following valence shell excitation. Here photodetachment studies have been performed on electrosprayed protein polyanions using vacuum ultraviolet synchrotron radiation coupled to a radiofrequency ion trap. Double, triple, and quadruple electron emissions from protein polyanions resulting from single-photon excitation in the valence shell were observed with ionization thresholds below 20 eV photon energy. This suggests the existence of large electronic correlations in proteins between weakly bound electrons standing on distant sites. Besides, the resulting multiradical polyanions appear to be remarkably stable, an important issue in radiobiology.

Excited states of multiply-charged anions probed by photoelectron imaging: riding the repulsive Coulomb barrier

Recent progress towards understanding the repulsive Coulomb barrier in multiply-charged anion using photoelectron spectroscopy is discussed.

A quantitative measure of electrostatic perturbation in holo and apo enzymes induced by structural changes

Biological pathways are subject to subtle manipulations that achieve a wide range of functional variation in differing physiological niches. In many instances, changes in the structure of an enzyme on ligand binding germinate electrostatic perturbations that form the basis of its changed catalytic or transcriptional efficiency. Computational methods that seek to gain insights into the electrostatic changes in enzymes require expertise to setup and computing prowess. In the current work, we present a fast, easy and reliable methodology to compute electrostatic perturbations induced by ligand binding (MEPP). The theoretical foundation of MEPP is the conserved electrostatic potential difference (EPD) in cognate pairs of active site residues in proteins with the same functionality. Previously, this invariance has been used to unravel promiscuous serine protease and metallo-β-lactamase scaffolds in alkaline phosphatases. Given that a similarity in EPD is significant, we expect differences in the EPD to be significant too. MEPP identifies residues or domains that undergo significant electrostatic perturbations, and also enumerates residue pairs that undergo significant polarity change. The gain in a certain polarity of a residue with respect to neighboring residues, or the reversal of polarity between two residues might indicate a change in the preferred ligand. The methodology of MEPP has been demonstrated on several enzymes that employ varying mechanisms to perform their roles. For example, we have attributed the change in polarity in residue pairs to be responsible for the loss of metal ion binding in fructose 1,6-bisphosphatases, and corroborated the pre-organized state of the active site of the enzyme with respect to functionally relevant changes in electric fields in ketosteroid isomerases.

Soret Band of the Gas-Phase Ferri-Cytochrome c

We report the first visible spectrum of a heme-protein in the gas phase. The aim of this work was to provide a reference for the optical absorption of an isolated heme-protein to better understand the influence of protein conformation and fluctuation and of solvent on its optical properties. After laser irradiation of gas-phase cytochrome c (cyt c), electron emission is observed. Electron photodetachment yield of cyt c 6- was recorded in the region of the Soret band of the porphyrin group, showing a maximum at 410 nm. Our results are compared with optical spectra of gas-phase heme and of cyt c in solution. We discuss the influence of the polypeptide chain and of the solvent on both the position and the broadening of the Soret band. Action spectrum of gas-phase cyt c is close to the absorption of native cyt c in solution, suggesting an efficient protection of the heme group from solvent accessibility by the polypeptide chain and similar interactions between the two moieties in solution and the gas phase.

Dissociation chemistry of hydrogen-deficient radical peptide anions

The fragmentation chemistry of anionic deprotonated hydrogen-deficient radical peptides is investigated. Homolytic photodissociation of carbon-iodine bonds with 266 nm light is used to generate the radical species, which are subsequently subjected to collisional activation to induce further dissociation. The charges do not play a central role in the fragmentation chemistry; hence deprotonated peptides that fragment via radical directed dissociation do so via mechanisms which have been reported previously for protonated peptides. However, charge polarity does influence the overall fragmentation of the peptide. For example, the absence of mobile protons favors radical directed dissociation for singly deprotonated peptides. Similarly, a favorable dissociation mechanism initiated at the N-terminus is more notable for anionic peptides where the N-terminus is not protonated (which inhibits the mechanism). In addition, collisional activation of the anionic peptides containing carbon-iodine bonds leads to homolytic cleavage and generation of the radical species, which is not observed for protonated peptides presumably due to competition from lower energy dissociation channels. Finally, for multiply deprotonated radical peptides, electron detachment becomes a competitive channel both during the initial photoactivation and following subsequent collisional activation of the radical. Possible mechanisms that might account for this novel collision-induced electron detachment are discussed.

Visible and ultraviolet spectroscopy of gas phase protein ions

Optical spectroscopy has contributed enormously to our knowledge of the structure and dynamics of atoms and molecules and is now emerging as a cornerstone of the gas phase methods available for investigating biomolecular ions. This article focuses on the UV and visible spectroscopy of peptide and protein ions stored in ion traps, with emphasis placed on recent results obtained on protein polyanions, by electron photodetachment experiments. We show that among a large number of possible de-excitation pathways, the relaxation of biomolecular polyanions is mainly achieved by electron emission following photo-excitation in electronically excited states. Electron photodetachment is a fast process that occurs prior to relaxation on vibrational degrees of freedom. Electron photodetachment yield can then be used to record gas phase action spectra for systems as large as entire proteins, without the limitation of system size that would arise from energy redistribution on numerous modes and prevent fragmentation after the absorption of a photon. The optical activity of proteins in the near UV is directly related to the electronic structure and optical absorption of aromatic amino acids (Trp, Phe and Tyr). UV spectra for peptides and proteins containing neutral, deprotonated and radical aromatic amino acids were recorded. They displayed strong bathochromic shifts. In particular, the results outline the privileged role played by open shell ions in molecular spectroscopy which, in the case of biomolecules, is directly related to their reactivity and biological functions. The optical shifts observed are sufficient to provide unambiguous fingerprints of the electronic structure of chromophores without the requirement of theoretical calculations. They constitute benchmarks for calculating the absorption spectra of chromophores embedded in entire proteins and could be used in the future to study biochemical processes in the gas phase involving charge transfer in aromatic amino acids, such as in the mediation of electron transfer or redox reactions. We then addressed the important question of the sensitivity of protein optical spectra to the intrinsic properties of protein ions, including conformation, charge state, etc., and to environmental factors. We report optical spectra for different charge states of insulin, for ubiquitin starting from native and denaturated solutions, and for apo-myoglobin protein. All these spectra are compared critically to spectra recorded in solution, in order to assess solvent effects. We also report the spectra of peptides complexed with metal cations and show that complexation gives rise to new optical transitions related to charge transfer types of excitation. The perspectives of this work include integrative approaches where UV-Vis spectroscopy could, for example, be combined with ion mobility spectrometry and high level calculations for protein structural characterization. It could also be used in spectroscopy to probe biological processes in the gas phase, with different light sources including VUV radiation (to probe different types of excitations) and ultra short pulses with time and phase modulation (to probe and control the dynamics of de-excitation or charge transfer events), and with the derivatization of proteins with chromophores to modulate their optical properties. We also envision that photo-excitation will play an important role in the future to produce intermediates with new chemical and reactive properties. Another promising route is to conduct activated electron photodetachment dissociation experiments.