Gas phase hydrogen/deuterium exchange reactions of fluorophenyl anions

Hydrogen/deuterium (H/D) exchange reactions of fluorophenyl and difluorophenyl anions (C₆H₄F^?, o-C₆H₃F ₂ ^? , m-C₆H₃F ₂ ^? , p-C₆H₃F ₂ ^? ) have been studied using the flowing afterglow-selected ion flow tube technique. The C₆H₄F^? anion exchanges all hydrogens for deuterium upon reaction with D₂O. The difluorophenyl anions o-, m-, and p-C₆H₃F ₂ ^? exchange three, two, and one hydrogen, respectively, with D₂O, whereas they undergo one, two, and three H/D exchanges, respectively, with CH₃OD. The structures of the anions and the isotope exchange dynamics within the intermediate ion-dipole complexes are discussed using ab initio molecular orbital calculations. Calculated values for the proton affinities of the most stable anions are 385.2, 378.0, 371.9, and 378.2 kcal/mol for C₆H₄F^?, o-C₆H₃F ₂ ^? , m-C₆H₃F ₂ ^? , and p-C₆H₃F ₂ ^? , respectively, in excellent agreement (within 2 kcal/mol) with the previous experimental values for the acidities of the corresponding fluorobenzenes. The H/D exchange results are explained by the energy differences of the intermediate DO^? and CH₃O^? species within the ion-dipole complexes; CH₃O^? is mobile within the “hot” intermediate complex, whereas DO^? is nearly “frozen” within the complex and cannot migrate across the barriers caused by the fluorine atoms or by the π electrons.     

Gas phase hydrogen/deuterium exchange of arginine and arginine dipeptides complexed with alkali metals

The hydrogen/deuterium (H/D) exchange of protonated and alkali-metal cationized Arg-Gly and Gly-Arg peptides with D(2)O in the gas phase was studied using electrospray ionization quadropole ion trap mass spectrometry. The Arg-Gly and Gly-Arg alkali metal complexes exchange significantly more hydrogens than protonated Arg-Gly and Gly-Arg. We propose a mechanism where the peptide shifts between a zwitterionic salt bridge and nonzwitterionic charge solvated conformations. The increased rate of H/D exchange of the alkali metal complexes is attributed to the peptide metal complexes' small energy difference between the salt-bridge conformation and the nonzwitterionic charge-solvated conformation. Implications for the applicability of this mechanism to other zwitterionic systems are discussed.     

Gas-phase hydrogen/deuterium exchange and conformations of deprotonated flavonoids and gas-phase acidities of flavonoids

Gas-phase hydrogen/deuterium (H/D) exchange was used to probe the conformations, gas-phase acidities, and sites of deprotonation of isomeric flavonoid aglycons and glycosides. The flavonoids in each isomer series were differentiated on the basis of their relative rate constants and total numbers of exchanges. For example, flavonoids that possess neohesperidose-type disaccharides may undergo faster and far more extensive exchange than isomeric rutinoside flavonoids. The structural factors that promote or prevent H/D exchange were identified and correlated with collisionally activated dissociation (CAD) patterns and/or molecular modeling data (both high-level ab initio acidity calculations and conformational analysis with molecular dynamics (MD) simulations), thus providing a framework for the use of H/D exchange reactions in the structural elucidation of new flavonoids.     

Isolation of isomers based on hydrogen/deuterium exchange in the gas phase

A method to isolate isomers in a Fourier transform ion cyclotron resonance mass spectrometer on the basis of their different hydrogen/deuterium exchange rates has been developed and applied to the protonated serine octamer cluster. Isolation allows interrogation of each isomer by infrared multi-photon dissociation to determine any differences in the building blocks that form these clusters. The experimental results strongly support previous assignments of an all-zwitterion structure to the slower-exchanging isomer and an all-neutral structure to its faster- exchanging counterpart.     

Gas phase hydrogen / deuterium exchange in electrospray ionization mass spectrometry as a practical tool for structure elucidation

Two methods for gas phase hydrogen/deuterium exchange have been developed for the analysis of small molecules. Hydrogen/deuterium exchange has been implemented by making simple modifications to the plumbing for the nebulizer and curtain gases on a nebulization-assisted electrospray ion source. The nebulizer gas exchange method has demonstrated deuterium exchange levels of 84–97% for a variety of molecules representing a wide range of structural classes containing up to 51 potentially exchangeable hydrogens; this allowed determination of the number of exchangeable hydrogens for all of the molecules studied containing ≤ 25 labile hydrogens (M _r ≤ 3000). ND₃ gas consumption is minimized in the nebulizer method by toggling the nebulizer from air to ND₃ for only a few scans of the total sample elution period. The curtain gas exchange method is more variable, yielding exchange levels of 32–98% for the same set of molecules; this was still sufficient to allow determination of > 70% of the molecules studied containing ≤ 25 labile hydrogens. Gas consumption is minimized in the curtain method by replacing ≤ 10% of the curtain gas flow with ND₃. Neither the nebulizer nor curtain exchange method requires the use of deuterated or aprotic solvents at typical 2 μL/min flow rates.     

Gas-phase hydrogen/deuterium exchange of adenine nucleotides

Gas-phase hydrogen/deuterium exchange reactions of (de)protonated (sodiated) adenosine-5'-mono-, di- and triphosphate ions with CD(3)OD, CD(3)CO(2)D and ND(3) were achieved using a combination of electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry. The reaction kinetics are dependent on factors such as the charge state, the phosphate chain length, the properties of the exchange reactants and the sodium content. The results indicate that the overall H/D exchange may involve specific sites even if endowed with high energetic barriers. The enhanced reactivity exhibited by adenosine polyphosphate ions compared with adenosine-5'-monophosphate suggests a critical role of the polyphosphate chain in rendering conformationally accessible remote H-donor sites. Low-energy collision-induced dissociation of (sodiated) adenine nucleotides anions supports the aptitude of the (poly)phosphate chain in probing distant sites via the intermediacy of a cyclic structure.     

Gas phase hydrogen deuterium exchange reactions of a model peptide: FT-ICR and computational analyses of metal induced conformational mutations

We utilized gas phase hydrogen/deuterium (H/D) exchange reactions and ab initio calculations to investigate the complexation between a model peptide (Arg-Gly-AspRGD) with various alkali metal ions. The peptide conformation is drastically altered upon alkali metal ion complexation. The associated conformational changes depend on both the number and type of complexing alkali metal ions. Sodium has a smaller ionic diameter and prefers a multidentate interaction that involves all three amino acids of the peptide. Conversely, potassium and cesium form different types of complexes with the RGD. The [RGD + 2Cs − H]⁺ species exhibit the slowest H/D exchange reactivity (reaction rate constant of 6 × 10⁻¹³ cm³molecule⁻¹s⁻¹ for the fastest exchanging labile hydrogen with ND₃). The reaction rate constant of the protonated RGD is two orders of magnitude faster than that of the [RGD + 2Cs − H]⁺. Addition of the first cesium to the RGD reduces the H/D exchange reaction rate constant (i.e., D₀) by a factor of seven whereas sodium reduces this value by a factor of thirty. Conversely, addition of the second alkali metal ions has the opposite effect; the rate of D₀ disappearance for all [RGD + 2Met − H]⁺ species (MetNa, K, and Cs) decreases with the alkali metal ion size.     

Rate and extent of gas-phase hydrogen/deuterium exchange of bradykinins: evidence for peptide zwitterions in the gas phase

The gas-phase H/D exchange of bradykinin [M + H]⁺, [M + Na]⁺, [M + 2H]²⁺, and [M + H + Na]²⁺ ions; des-Arg¹-bradykinin, des-Arg⁹-bradykinin, and bradykinin fragment 2-7 [M + H]⁺ ions; and O-methylbradykinin [M + H]⁺ and [M + 2H]²⁺ ions with D₂O have been examined by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry at 9.4 T. The different peptides vary widely in exchange rate and extent of deuterium incorporation. H/D exchange was slowest and deuterium incorporation was least for bradykinin [M + H]⁺, [M + H + Na]²⁺ and bradykinin methyl ester [M + 2H]²⁺ ions. In contrast, H/D exchange and extent of deuteration are higher for des-Arg¹-bradykinin, des-Arg⁹-bradykinin, and bradykinin fragment 2-7 [M + H]⁺ ions; and highest for bradykinin [M + Na]⁺ and [M + 2H]²⁺, and O-methylbradykinin [M + H]⁺. Because the most likely site of protonation is the guanidino group of arginine, the above reactivity pattern strongly supports a zwitterion form for protonated gas-phase bradykinin.     

Use of on-line hydrogen/deuterium exchange to facilitate metabolite identification

Biotransformation studies performed on an investigational compound (I, represented by R1-CH(NH(2))-CO-N(R2)-CH(2)-S-R3) led to the identification of five metabolites (M1-M5). Based on LC/MS (liquid chromatography/mass spectrometry) analysis which included the use of H(2)O and D(2)O in the mobile phases, they were identified as the sulfoxide (M1), sulfone (M2), carbamoyl glucuronide (M3), N-glucuronide (M4), and N-glucoside (M5) metabolites, respectively. The structure of M3, a less commonly seen carbamoyl glucuronide metabolite, was established using on-line H/D (hydrogen/deuterium) exchange experiments conducted by LC/MS. H/D exchange experiments were also used to distinguish the S-oxidation structures of M1 and M2 from hydroxylation. Herein, the application of deuterium oxide as the LC/MS mobile phase for structural elucidation of drug metabolites in biological matrices is demonstrated.     

The complexation of protonated peptides with saccharides in the gas phase decreases the rates of hydrogen/deuterium exchange reactions

Gas-phase noncovalently bound complexes are probed by hydrogen/deuterium exchange. The complexes, composed of a protonated amino acid and a monosaccharide, are investigated to observe the effects of complexation on the rates of exchange. Rate constants are determined and compared for complexed and uncomplexed amino acids. The overall rate constant, which corresponds to exchange of a specific number of hydrogens, is deconvoluted to yield site-specific rate constants. Complexation of amino acids with saccharides significantly decreases the rate constants of the exchange. Results of molecular orbital calculations are provided to explain the decrease in the rates.     

Studying protein-carbohydrate interactions by amide hydrogen/deuterium exchange mass spectrometry

Protein-carbohydrate interactions play a significant role in biological processes. Presented here is the novel application of amide hydrogen/deuterium exchange mass spectrometry (amide exchange-MS) to the study of the interaction between a protein and its carbohydrate substrate. The degree of deuterium incorporation into hen egg lysozyme was monitored with and without substrate to verify that a carbohydrate can provide sufficiently stable protection of the amide hydrogen atoms in a protein's backbone from exchange with deuterated solvent. The substrate protected a number of amide hydrogens from exchange, implying that protein-carbohydrate binding systems will be compatible with amide exchange-MS. Endopolygalacturonase-II (EPG-II) from Aspergillus niger, a pectin-degrading enzyme, was chosen as the first carbohydrate-binding system to be extensively studied using quenched amide exchange-MS. Monitoring the changes in deuterium incorporation of EPG-II in the presence and absence of an oligomer of galacturonic acid implied the location of substrate binding. This study demonstrates the ability of amide exchange-MS to investigate protein-carbohydrate interactions.     

Fast gas-phase hydrogen/deuterium exchange observed for a DNA G-quadruplex

The gas-phase hydrogen/deuterium (H/D) exchange kinetics of DNA G-quadruplexes has been investigated using Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The quadruplex [(TGGGGT)4 . 3NH4+] undergoes very fast H/D exchange, in both the positive and in the negative ion modes, compared to DNA duplexes and other quadruplexes tested, and compared to the corresponding single-stranded TGGGGT. Substitution of NH4+ for K+ did not alter this fast H/D exchange, indicating that the hydrogens of the ammonium ions are not those exchanged. However, stripping of the interior cations of the quadruplex by source collision-induced dissociation (CID) in the positive ion mode showed that the presence of the inner cations is essential for the fast exchange to be possible. Molecular dynamics simulations show that the G-quadruplex is very rigid in the gas phase with NH4+ ions inside the tetrads. We suggest that the fast H/D exchange is favored by this rigid quadruplex conformation. This example illustrates that the concept that compact DNA structures exchange H for D slower than unfolded ones is a misconception.     

Improving hydrogen/deuterium exchange mass spectrometry by reduction of the back-exchange effect

The measurement of deuterium incorporation kinetics using hydrogen/deuterium (H/D) exchange experiments is a valuable tool for the investigation of the conformational dynamics of biomolecules in solution. Experiments consist of two parts when using H/D exchange mass spectrometry to analyse the deuterium incorporation. After deuterium incorporation at high D(2)O concentration, it is necessary to decrease the D(2)O concentration before the mass analysis to avoid deuterium incorporation under artificial conditions of mass spectrometric preparation and measurement. A low D(2)O concentration, however, leads to back-exchange of incorporated deuterons during mass analysis. This back-exchange is one of the major problems in H/D exchange mass spectrometry and must be reduced as much as possible. In the past, techniques using electrospray ionization (ESI) had the lowest back-exchange values possible in H/D exchange mass spectrometry. Methods for the measurement of H/D exchange by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) that have been developed since 1998 have some significant advantages, but they could not achieve the back-exchange minima of ESI methods. Here, we present a protocol for H/D exchange MALDI-MS which allows for greater minimization of back-exchange compared with H/D exchange ESI-MS under similar conditions.     

HDXFinder: automated analysis and data reporting of deuterium/hydrogen exchange mass spectrometry

Hydrogen/deuterium exchange in combination with mass spectrometry (H/D MS) is a sensitive technique for detection of changes in protein conformation and dynamics. However, wide application of H/D MS has been hindered, in part, by the lack of computational tools necessary for efficient analysis of the large data sets associated with this technique. We report a novel web-based application for automatic analysis of H/D MS experimental data. This application relies on the high resolution of mass spectrometers to extract all isotopic envelopes before correlating these envelopes with individual peptides. Although a fully automatic analysis is possible, a variety of graphical tools are included to aid in the verification of correlations and rankings of the isotopic peptide envelopes. As a demonstration, the rate constants for H/D exchange of peptides from rabbit muscle pyruvate kinase are mapped onto the structure of this protein.     

Assessment of the repeatability and reproducibility of hydrogen/deuterium exchange mass spectrometry measurements

A system to perform automated hydrogen/deuterium exchange mass spectrometry measurements was constructed using an XYZ robotic autosampler that was capable of performing solvent manipulations and a 4.7 T Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometer. The system included features such as the first demonstration of a ‘dual column’ high‐performance liquid chromatography (HPLC) setup, and a novel digestion strategy. The performance of the system, in terms of the repeatability and reproducibility of the measurement of protein hydrogen/deuterium exchange, was assessed over a 2‐month period. The sensitivity of the measurement of hydrogen exchange towards several parameters was assessed, which allowed their impact on the reproducibility to be discussed. The parameters assessed were the temperature of the HPLC columns and switching valves, the temperature of the quench solutions, the pH of the mobile phase, the pH of the quenched solution, the acid used in the mobile phase and the analytical column used. Copyright © 2008 John Wiley & Sons, Ltd.     

Homogeneous isotope exchange reaction between hydrogen and deuterium

The isotope exchange reaction between hydrogen and deuterium was studied in incident and reflected shock waves over the temperature range 1200–1800 K by vacuum ultraviolet absorption spectroscopy. The observed exchange reaction ensued after long induction periods at rates that proved to account for the amounts of exchange previously seen in single-pulse shock-tube and reflected-wave mass-spectrometric investigations. From the absence of detectable reaction during the induction period, lower bounds of 70 and 45 kcal were placed on the barriers to molecular exchange in four- and six-center transition structures, respectively.     

Local stability of Rhodobacter capsulatus cytochrome c 2 probed by solution phase hydrogen/deuterium exchange and mass spectrometry

The hydrogen/deuterium exchange kinetics of Rhodobacter capsulatus cytochrome c2 have been determined using mass spectrometry. As expected, the relative domain stability was generally similar to that of the cytochrome c2 structural homolog, horse heart cytochrome c, but we were able to find evidence to support the presence of a second, small beta-sheet not found in the horse cytochrome, which stabilizes a structural region dominated by Omega loops. Importantly, we find that the so-called hinge region, comprised of 15 amino acids, which include the methionine sixth heme ligand (M96), is destabilized on oxidation, and this destabilization is propagated to a portion of the second Omega loop, most likely through perturbation of two hydrogen bonds that couple these two domains in the three dimensional structure. The mutation of a lysine at position 93 to proline amplifies the destabilization observed on oxidation of the wild-type cytochrome c2 and results in further destabilization observed in regions 52-60, 75-82, and 83-97. This suggests that hydrogen bond interactions involving two bound waters, the T94 hydroxyl, the front heme propionate and the Y75 hydroxyl, are significantly compromised upon mutation. In summary, these observations are consistent with the approximately 20-fold increase in the movement of the hinge away from the heme face in the oxidized cytochrome c2 as determined by ligand binding kinetics. Thus, H/D exchange kinetics can be used to identify relatively subtle structural features and at least in some cases facilitate the understanding of the structural basis of the dynamic properties of proteins.     

Denaturant sensitive regions in creatine kinase identified by hydrogen/deuterium exchange

The GdmHCl-induced unfolding of creatine kinase (CK) has been studied by hydrogen/deuterium (H/D) exchange combined with mass spectrometry. MM-CK unfolded for various periods in different denaturant concentrations was pulsed-labeled with deuterium to identify different conformational intermediate states. For all denaturation times or GdmHCl concentrations, we observed variable proportions of only two species. The low-mass envelope of isotope peaks corresponds to a species that has gained about 10 deuteriums more than native CK, and the high-mass envelope to a completely deuterated species. To localize precisely the unfolded regions in the states highly populated during denaturation, the protein was digested with two proteases (pepsin and type XIII protease) after H/D exchange and rapid quenching of the reaction. The two sets of fragments obtained were analyzed by liquid chromatography coupled to mass spectrometry to determine the deuterium level in each fragment. Bimodal distributions of deuterium were found for most peptides, indicating that these regions were either folded or unfolded. This behavior is consistent with cooperative, localized unfolding. However, we observed a monomodal distribution of deuterium in two regions (1-12 and 162-186). We conclude that the increment of mass observed in the low-mass species of the intact protein (+10 Da) has its origin in these two segments. These regions, which are very sensitive to low GdmHCl concentrations, are involved in the monomer-monomer interface of CK and their perturbation is likely to weaken the dimeric structure. At higher denaturant concentration, this would induce dissociation of the dimer.