Exploring the Mechanism of IR-UV Double-Resonance for Quantitative Spectroscopy of Protonated Polypeptides and Proteins

Experimental techniques and terminology in gas-phase ion spectroscopy

This perspective gives an overview of the action spectroscopy methods for measurements of electronic, vibrational, and rotational spectra of mass-selected ions in the gas phase. We classify and give a short overview of the existing experimental approaches in this field. There is currently a plethora of names used for, essentially, the same techniques. Hence within this overview, we scrutinized the notations and suggested terms to be generally used. The selection was either driven by making the name unique and straightforward or the term being the most broadly used one. We believe that a simplification and a unification of the notation in ion spectroscopy can make this field better accessible for experts outside the mass spectrometry community where the applications of gas-phase action ion spectroscopy can make a large impact.

Tracking local and global structural changes in a protein by cold ion spectroscopy

Characterization of native structures of proteins in the gas phase remains challenging due to the unpredictable conformational changes the molecules undergo during desolvation and ionization. We spectroscopically studied cryogenically cooled protonated protein ubiquitin and its microhydrated complexes prepared in the gas phase in a range of charge states under different ionization conditions. The UV spectra appear vibrationally resolved for the unfolded protein, but become redshifted and smooth for the native-like structures of ubiquitin. This spectroscopic change results from the H-bonding of the hydroxyl of Tyr to the amide group of Glu-51 in the compact structures; the minimum length of this bond was estimated to be ∼1.7 Å. IR spectroscopy reflects the global structural change by observing redshifts of free NH/OH-stretch vibrational transitions. Evaporative cooling of microhydrated complexes of ubiquitin keeps the protein chilly during ionization, enabling native-like conformers with up to eight protons to survive in the gas phase.

Gas-Phase Resonance Raman Spectroscopy Combined with IR-Laser Ablation of a Droplet Beam: Local Structural Analysis of Myoglobin

Gas phase spectroscopy is a powerful tool for examining fundamental chemical structures and properties free from solvent molecules. We developed a gas-phase resonance Raman spectroscopy combined with IR-laser ablation of a droplet beam, which allowed us to elucidate local structures around chromophores in gas-phase proteins and DNAs. To demonstrate the potential of this approach, we applied this method to myoglobin, one of the heme proteins, and elucidated its structures in the gas phase and in aqueous solution. The experimental spectra are compared with calculated spectra of stable heme structures for the structural determination. These results show the oxidation/spin states of the Fe atom in myoglobin in the gas phase and were compared with the aqueous solution from the obtained resonant Raman spectra. The present method gives an important tool to investigate the gas-phase structure of large biomolecules.

IR multiple photon dissociation spectroscopy of MO2+ (M = V, Nb, Ta)

A laser vaporization cluster source is coupled to the Fourier-transform ion cyclotron resonance mass spectrometer beamline of the free-electron laser for intracavity experiments. Gas phase metal ions and their oxides (VO₂ ⁺, NbO₂ ⁺, and TaO₂ ⁺) are formed and spectroscopically characterized using IR multiple-photon dissociation spectroscopy via loss of atomic oxygen and overcoming fragmentation energies of 3 eV-6 eV. The signal is observed for all MO₂ ⁺ fundamental modes: the symmetric and anti-symmetric ν₁ and ν₃ stretch modes in the 900 cm^-1-1000 cm^-1 range and the ν₂ bending mode in the 300 cm^-1-450 cm^-1 range. A remarkable substructure is observed for the bending vibration, which is at least partly due to the rovibrational substructure.

Far-IR Absorption of Neutral Polycyclic Aromatic Hydrocarbons (PAHs): Light on the Mechanism of IR-UV Ion Dip Spectroscopy

Gas-phase IR-UV double-resonance laser spectroscopy is an IR absorption technique that bridges the gap between experimental IR spectroscopy and theory. The IR experiments are used to directly evaluate predicted frequencies and potential energy surfaces as well as to probe the structure of isolated molecules. However, a detailed understanding of the underlying mechanisms is, especially in the far-IR regime, still far from complete, even though this is crucial for properly interpreting the recorded IR absorption spectra. Here, events occurring upon excitation to vibrational levels of polycyclic aromatic hydrocarbons by far-IR radiation from the FELIX free electron laser are followed using resonance-enhanced multiphoton ionization spectroscopy. These studies provide detailed insight into how ladder climbing and anharmonicity influence IR-UV spectroscopy and therefore the resulting IR signatures in the far-IR region. Moreover, the potential energy surfaces of these low-frequency delocalized modes are investigated and shown to have a strong harmonic character.

Tag-Free, Temperature Dependent Infrared Spectra of the GFP Chromophore: Revisiting the Question of Isomerism

We report infrared spectra of a model chromophore of green fluorescent protein, prepared in an ion trap at temperatures ranging from 30 K to room temperature. We compare the changes in the infrared spectrum with predicted infrared spectra for the Z and E isomers of this molecule, and we confirm that the molecule exists as the Z isomer at low temperatures. We revisit the question whether or not it can thermally isomerize in the temperature range of this experiment, and we find no evidence for isomerization.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

Ion traps in modern mass spectrometry

This review is devoted to trapping mass spectrometry wherein ions are confined by electromagnetic fields for prolonged periods of time within limited volume, with mass measurement taking place within the same volume. Three major types of trapping mass spectrometers are discussed, specifically radiofrequency ion trap, Fourier transform ion cyclotron resonance and Orbitrap. While these three branches are intricately interwoven with each other over their recent history, they also differ greatly in their fundamentals, roots and historical origin. This diversity is reflected also in the difference of viewpoints from which each of these directions is addressed in this review. Following the theme of the issue, we focus on developments mainly associated with the country of Germany but, at the same time, we use this review as an illustration of the rapidly increasing globalization of science and expanding multi-national collaborations.

Peptide Bond Ultraviolet Absorption Enables Vibrational Cold-Ion Spectroscopy of Nonaromatic Peptides

Peptide-bond VUV absorption is inherent to all proteins and peptides. Although widely exploited in top-down proteomics for photodissociation, this absorption has never been spectroscopically characterized in the gas phase. We have measured VUV/UV photofragmentation spectrum of a single peptide bond in a cryogenically cold protonated dipeptide. Although the spectrum appears to be very broadband and structureless, vibrational pre-excitation of this and even larger cold peptides significantly increases the UV dissociation yield for some of their photofragments. We use this effect to extend the technique of IR-UV photofragmentation vibrational spectroscopy, developed for aromatic peptides, to nonaromatic ones and demonstrate measurements of conformation-specific and nonspecific IR spectra for di- to hexa-peptides.

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.

Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A

Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.

Charge-state Resolved Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of Ubiquitin Ions in the Gas Phase

In this study, we obtained for the first time the direct infrared multiple photon dissociation (IRMPD) spectra of ubiquitin ions in the range 2700-3750 cm-1. Ubiquitin ions with different charge states showed absorption in the two regions of 2940-3000 cm-1 and 3280-3400 cm-1. The increase of the charge state of ubiquitin ions broadened the absorption peak on the high-frequency side in the second region, indicating some hydrogen bonds were weakened due to Coulomb interaction. It is also found that the relative intensity of the absorption peak in the first region compared to the absorption peak in the second region increased with increasing charge state, making the IRMPD spectra charge-state resolved. Although it is usually reasonable to suggest the origin of the absorption in the range 2940-3000 cm-1 as the C-H bond stretching modes, the results show significantly reduced absorption after the deuteration of all labile hydrogen atoms. A possible explanation for this is that the coupling coefficients between the C-H vibrational mode and other selective modes decreased greatly after the deuteration, reducing the rate of energy redistribution and probability of consecutive IR absorption.

Photoionization of the Buckminsterfullerene Cation

Photoionization of a buckminsterfullerene ion is investigated using an ion trap and a merged beam setup coupled to synchrotron radiation beamlines and compared to theoretical calculations. Absolute measurements derived from the ion trap experiment allow discrepancies concerning the photoionization cross section of C₆₀⁺ to be solved.

UV and IR Spectroscopy of Cryogenically Cooled, Lanthanide-Containing Ions in the Gas Phase

We measure UV and IR spectra in the gas phase for EuOH⁺, EuCl⁺, and TbO⁺ ions, which are produced by an electrospray ionization source and cooled to ∼10 K in a cold, 22-pole ion trap. The UV photodissociation (UVPD) spectra of these ions show a number of sharp, well-resolved bands in the 30000-38000 cm^-1 region, although a definite assignment of the spectra is difficult because of a high degree of congestion. We also measure an IR spectrum of the EuOH⁺ ion in the 3500-3800 cm^-1 region by IR-UV double-resonance spectroscopy, which reveals an OH stretching band at 3732 cm^-1. We perform density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations of these ions in order to examine the nature of the transitions. The DFT results indicate that the states of highest-spin multiplicity (octet for EuOH⁺ and EuCl⁺ and septet for TbO⁺) are substantially more stable than other states of lower-spin multiplicity. The TD-DFT calculations suggest that UV absorption of the EuOH⁺ and EuCl⁺ ions arises from Eu(4f) → Eu(5d,6p) transitions, whereas electronic transitions of the TbO⁺ ion are mainly due to the electron promotion of O(2p) → Tb(4f,6s). The UVPD results of the lanthanide-containing ions in this study suggest the possibility of using lanthanide ions as "conformation reporters" for gas-phase spectroscopy for large molecules.

Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features

Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer.

Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry

Characterization of all gas-phase charge sites of natively sprayed proteins and peptides is demonstrated using 193 nm UVPD. The high sequence coverage offered by UVPD is exploited for the accurate determination of charge sites in protein systems up to 18 kDa, allowing charge site to be studied as a function of protein conformation and the presence of disulfide bonds. Charging protons are found on both basic sidechains and on the amide backbone of less basic amino acids such as serine, glutamine, and proline. UVPD analysis was performed on the 3+ charge state of melittin, the 5+ to 8+ charge states of ubiquitin, and the 8+ charge state of reduced and oxidized β-lactoglobulin. The location of charges in gas-phase proteins is known to impact structure; molecular modeling of different charge site motifs of 3+ melittin demonstrates how placement of protons in simulations can dramatically impact the predicted structure of the molecule. The location of positive charge sites in ubiquitin and β-lactoglobulin are additionally found to depend on the presence or absence of salt-bridges, columbic repulsion across the length of the peptide, and protein conformation. Charge site isomers are demonstrated for ubiquitin and β-lactoglobulin but found to be much less numerous than previously predicted.

Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate

Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.

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.

UV and IR Spectroscopy of Cold H2O(+)-Benzo-Crown Ether Complexes

The H2O(+) radical ion, produced in an electrospray ion source via charge transfer from Eu(3+), is encapsulated in benzo-15-crown-5 (B15C5) or benzo-18-crown-6 (B18C6). We measure UV photodissociation (UVPD) spectra of the (H2O·B15C5)(+) and (H2O·B18C6)(+) complexes in a cold, 22-pole ion trap. These complexes show sharp vibronic bands in the 35 700-37 600 cm(-1) region, similar to the case of neutral B15C5 or B18C6. These results indicate that the positive charge in the complexes is localized on H2O, giving the forms H2O(+)·B15C5 and H2O(+)·B18C6, in spite of the fact that the ionization energy of B15C5 and B18C6 is lower than that of H2O. The formation of the H2O(+) complexes and the suppression of the H3O(+) production through the reaction of H2O(+) and H2O can be attributed to the encapsulation of hydrated Eu(3+) clusters by B15C5 and B18C6. On the contrary, the main fragment ions subsequent to the UV excitation of these complexes are B15C5(+) and B18C6(+) radical ions; the charge transfer occurs from H2O(+) to B15C5 and B18C6 after the UV excitation. The position of the band origin for the H2O(+)·B18C6 complex (36323 cm(-1)) is almost the same as that for Rb(+)·B18C6 (36315 cm(-1)); the strength of the intermolecular interaction of H2O(+) with B18C6 is similar to that of Rb(+). The spectral features of the H2O(+)·B15C5 complex also resemble those of the Rb(+)·B15C5 ion. We measure IR-UV spectra of these complexes in the CH and OH stretching region. Four conformers are found for the H2O(+)·B15C5 complex, but there is one dominant form for the H2O(+)·B18C6 ion. This study demonstrates the production of radical ions by charge transfer from multivalent metal ions, their encapsulation by host molecules, and separate detection of their conformers by cold UV spectroscopy in the gas phase.

Capping Motif for Peptide Helix Formation

It is known that a C-terminal lysine stabilizes helix formation in polyalanine peptides that have seven or more residues. Using a combination of cold ion spectroscopy and DFT calculations, we demonstrate that even a three-residue peptide, Ac-Phe-Ala-LysH(+), adopts a structure in which the lysine side chain forms three hydrogen bonds with backbone carbonyls, reproducing the capping motif of larger polyalanine helices. This is confirmed by comparison with Ac-Phe-(Ala)5-LysH(+), which forms a 310 helix containing the same structural feature. In both molecules, we identified the vibrational bands of the N- and C-terminal amide NH stretches, which lack strong hydrogen bonds with carbonyls and consequently appear in a characteristic region above 3400 cm(-1). A similar pattern is also present in the even longer peptide Ac-Phe-(Ala)10-LysH(+), illustrating the generality of this capping motif. The two longer peptides contain additional, characteristic amide NH stretch bands below 3400 cm(-1), which form the core of the helix.

Persistence of dual free internal rotation in NH4(+)(H2O)·Hen=0-3 ion-molecule complexes: expanding the case for quantum delocalization in He tagging

To explore the extent of the molecular cation perturbation induced by complexation with He atoms required for the application of cryogenic ion vibrational predissociation (CIVP) spectroscopy, we compare the spectra of a bare NH4(+)(H2O) ion (obtained using infrared multiple photon dissociation (IRMPD)) with the one-photon CIVP spectra of the NH4(+)(H2O)·He1-3 clusters. Not only are the vibrational band origins minimally perturbed, but the rotational fine structures on the NH and OH asymmetric stretching vibrations, which arise from the free internal rotation of the -OH2 and -NH3 groups, also remain intact in the adducts. To establish the location and the quantum mechanical delocalization of the He atoms, we carried out diffusion Monte Carlo (DMC) calculations of the vibrational zero point wave function, which indicate that the barriers between the three equivalent minima for the He attachment are so small that the He atom wave function is delocalized over the entire -NH3 rotor, effectively restoring C3 symmetry for the embedded -NH3 group.

Vibrational spectroscopy of isolated copper(ii) complexes with deprotonated triglycine and tetraglycine peptides

The gas-phase vibrational predissociation spectra of deprotonated copper–triglycine and deprotonated copper–tetraglycine are presented and analyzed.

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.

Solution dependence of the collisional activation of ubiquitin [M + 7H](7+) ions

The solution dependence of gas-phase unfolding for ubiquitin [M + 7H](7+) ions has been studied by ion mobility spectrometry-mass spectrometry (IMS-MS). Different acidic water:methanol solutions are used to favor the native (N), more helical (A), or unfolded (U) solution states of ubiquitin. Unfolding of gas-phase ubiquitin ions is achieved by collisional heating and newly formed structures are examined by IMS. With an activation voltage of 100 V, a selected distribution of compact structures unfolds, forming three resolvable elongated states (E1-E3). The relative populations of these elongated structures depend strongly on the solution composition. Activation of compact ions from aqueous solutions known to favor N-state ubiquitin produces mostly the E1 type elongated state, whereas activation of compact ions from methanol containing solutions that populate A-state ubiquitin favors the E3 elongated state. Presumably, this difference arises because of differences in precursor ion structures emerging from solution. Thus, it appears that information about solution populations can be retained after ionization, selection, and activation to produce the elongated states. These data as well as others are discussed.

New Method for Double-Resonance Spectroscopy in a Cold Quadrupole Ion Trap and Its Application to UV-UV Hole-Burning Spectroscopy of Protonated Adenine Dimer

A novel method for double-resonance spectroscopy in a cold quadrupole ion trap is presented, which utilizes dipolar resonant excitation of fragment ions in the quadrupole ion trap. Photofragments by a burn laser are removed by applying an auxiliary RF to the trap, and a probe laser detects the depletion of photofragments by the burn laser. By scanning the wavelength of the burn laser, conformation-specific UV spectrum of a cold ion is obtained. This simple and powerful method is applicable to any type of double-resonance spectroscopy in a cold quadrupole ion trap and was applied to UV-UV hole-burning spectroscopy of protonated adenine dimer. It was found that protonated adenine dimer has multiple conformers/tautomers, each with multiple excited states with drastically different excited state dynamics.

Assessment of amide I spectroscopic maps for a gas-phase peptide using IR-UV double-resonance spectroscopy and density functional theory calculations

The spectroscopy of amide I vibrations has become a powerful tool for exploring protein structure and dynamics. To help with spectral interpretation, it is often useful to perform molecular dynamics (MD) simulations. To connect spectroscopic experiments to simulations in an efficient manner, several researchers have proposed "maps," which relate observables in classical MD simulations to quantum spectroscopic variables. It can be difficult to discern whether errors in the theoretical results (compared to experiment) arise from inaccuracies in the MD trajectories or in the maps themselves. In this work, we evaluate spectroscopic maps independently from MD simulations by comparing experimental and theoretical spectra for a single conformation of the α-helical model peptide Ac-Phe-(Ala)5-Lys-H(+) in the gas phase. Conformation-specific experimental spectra are obtained for the unlabeled peptide and for several singly and doubly (13)C-labeled variants using infrared-ultraviolet double-resonance spectroscopy, and these spectra are found to be well-modeled by density functional theory (DFT) calculations at the B3LYP/6-31G** level. We then compare DFT results for the deuterated and (13)C(18)O-labeled peptide with those from spectroscopic maps developed and used previously by the Skinner group. We find that the maps are typically accurate to within a few cm(-1) for both frequencies and couplings, having larger errors only for the frequencies of terminal amides.

Development of Ultraviolet-Ultraviolet Hole-Burning Spectroscopy for Cold Gas-Phase Ions

A new ultraviolet-ultraviolet hole-burning (UV-UV HB) spectroscopic scheme has been developed for cold gas-phase ions in a quadrupole ion trap (QIT) connected with a time-of-flight (TOF) mass spectrometer. In this method, a pump UV laser generates a population hole for the ions trapped in the cold QIT, and a second UV laser (probe) monitors the population hole for the ions extracted to the field-free region of the TOF mass spectrometer. Here, the neutral fragments generated by the UV dissociation of the ions with the second laser are detected. This UV-UV HB spectroscopy was applied to protonated dibenzylamine and to protonated uracil. Protonated uracil exhibits two strong electronic transitions; one has a band origin at 31760 cm(-1) and the other at 39000 cm(-1). From the UV-UV HB measurement and quantum chemical calculations, the lower-energy transition is assigned to the enol-keto tautomer and the higher-energy one to the enol-enol tautomer.

Cryogenically cooled octupole ion trap for spectroscopy of biomolecular ions

We present here the design of a linear octupole ion trap, suitable for collisional cryogenic cooling and spectroscopy of large ions. The performance of this trap has been assessed using ultraviolet (UV) photofragmentation spectroscopy of protonated dipeptides. At the trap temperature of 6.1 K, the vibrational temperature of the ions reaches 9.1 K, although their estimated translational temperature is ~150 K. This observation suggests that, despite the significant translational heating by radio-frequency electrical field, vibrational cooling of heavy ions in the octupole is at least as efficient as in the 22-pole ion traps previously used in our laboratory. In contrast to the 22-pole traps, excellent radial confinement of ions in the octupole makes it convenient for laser spectroscopy and boosts the dissociation yield of the stored ions to 30%. Overlap of the entire ion cloud by the laser beam in the octupole also allows for efficient UV depletion spectroscopy of ion-He clusters. The measured electronic spectra of the dipeptides and the clusters differ drastically, complicating a use of UV tagging spectroscopy for structural determination of large species.

Bioresponsive controlled release from mesoporous silica nanocontainers with glucometer readout

A portable and quantitative biosensing platform for monitoring proteins and small molecules without the need for sample separation and washing is developed by using a commercialized personal glucose meter based on bioresponsive controlled release of glucose from aptamer-gated mesoporous silica nanocontainers.