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.     

Self-assembly of supramolecular architectures and polymers by orthogonal metal complexation and hydrogen-bonding motifs

A modular construction kit with two orthogonal noncovalent binding sites for self-assembly of supramolecular architectures is presented. The heteroditopic building blocks contain a terpyridine (tpy) unit for coordination of metal ions and a Hamilton receptor for multiple H-bonding of cyanuric acid derivatives. The association constants of ligand binding of M(II) complexes (M=Ru, Zn, Fe, and Pt) with a dendritic end cap were determined to be in the range of 10(2) and 10(4) L mol(-1) in chloroform. The capabilities for binding of metal ions were investigated by (1)H NMR and UV/Vis spectroscopy. The Fe complexes are most appropriate for the generation of discrete and high-ordered architectures due to their strong tendency to form FeL(2) complexes. Superstructures are readily formed in a one-pot procedure at room temperature. No mutual interactions between the orthogonal binding motifs were observed, and this demonstrates the highly specific nature of each binding process. Decomplexation experiments were carried out to examine the reversibility of Fe-tpy coordination. Substitution of the terminal end cap with a homoditopic bis-cyanurate linkage leads to formation of an iron-containing supramolecular strand. Formation of coordination polymers was confirmed by viscosity measurements. The supramolecular polymer strands can be reversibly cleaved by addition of a terminating cyanuric acid building block, and this proves the dynamic nature of this noncovalent polymerization process.     

Hydrogen/deuterium exchange mass spectrometry identifies two highly protected regions in recombinant full‐length prion protein amyloid fibrils

Understanding the structural basis that distinguishes the amyloid form of the prion protein from its monomeric homologue is of crucial importance to elucidate the mechanism of the lethal diseases related to this protein. Recently, an in vitro conversion system was established which reproduces the transition of recombinant prion protein PrP(23–230) from its native α‐helical rich form into an aggregated amyloid β‐sheet rich form with physicochemical properties reminiscent to those of the disease‐related isoform of the prion protein, PrP^Sc. To study the tertiary and quaternary structural organization within recombinant amyloid fibrils from mouse, mPrP(23–231)^βf; bovine, bPrP(23–230)^βf; and elk, ePrP(23–230)^βf; we utilized hydrogen/deuterium (H/D) exchange analyzed by matrix‐assisted laser desorption/ionization (MALDI) and nano‐electrospray (nano‐ESI) mass spectrometry. No significant differences were found by measuring the deuterium exchange kinetics of the aggregated fibrillar forms for mPrP(23–231)^βf, bPrP(23–230)^βf and ePrP(23–230)^βf, indicating a similar overall structural organization of the fibrils from all three species. Next, we characterized the solvent accessibility for the soluble and fibrillar forms of the mouse prion protein by hydrogen exchange, pepsin proteolysis and nano‐ESI ion trap mass spectrometry analysis. In its amyloid form, two highly protected regions of mPrP(23–231) comprising residues [24–98] and [182–212] were identified. The residues between the two highly protected stretches were found to be more solvent exposed, but less than in the soluble protein, and might therefore rather form part of a fibrillar interface. Copyright © 2009 John Wiley & Sons, Ltd.     

Helix formation in synthetic polymers by hydrogen bonding with native saccharides in protic media

Water-soluble poly(m-ethynylpyridine)s were designed to realize saccharide recognition in protic media. UV/Vis, 1H NMR, and fluorescence measurements revealed that the polymer forms a helical higher order structure by solvophobic interactions between the ethynylpyridine units in the protic medium. The resulting pore in the helix behaves like a binding pocket in proteins, by taking advantage of inwardly directed hydrogen-bonding functional groups of the polymers. Molecular recognition of native saccharides by the polymers was investigated by circular dichroism (CD). The chirality of the saccharide was transferred to the helical sense of the polymers, accompanied by the appearance of induced CDs (ICDs) in the absorptive region of the polymers. In MeOH/water (10/1), mannose and allose showed intense ICDs, and the apparent association constant between the polymer and D-mannose was 14 M(-1).     

Structure elucidation of highly polar basic degradants by on-line hydrogen/deuterium exchange hydrophilic interaction chromatography coupled to tandem mass spectrometry

A hydrophilic interaction liquid chromatography (HILIC) method was used to separate a commonly used pharmaceutical starting material, 4-aminomethylpyridine (4-AMP), and its degradants. The structures of the major degradants were characterized and elucidated without prior isolation by accurate mass measurement, MS/MS analysis and on-line hydrogen/deuterium (H/D) exchange experiments. The mass spectra obtained from H/D exchange experiments are particularly useful to differentiate structural isomers, to elucidate the fragmentation pathways, and to aid in structure elucidation in the absence of MS/MS fragmentation information. The impact of deuterium oxide and temperature on HILIC separation has also been explored here. The integration of H/D exchange with HILIC has been described here for the first time and has been demonstrated to be a powerful structure elucidation tool via the study of degradants in 4-AMP.     

Hierarchical self-assembly of a bow-shaped molecule bearing self-complementary hydrogen bonding sites into extended supramolecular assemblies

The bow-shaped molecule 1 bearing a self-complementary DAAD-ADDA (D=donor A=acceptor) hydrogen-bonding array generates, in hydrocarbon solvents, highly ordered supramolecular sheet aggregates that subsequently give rise to gels by formation of an entangled network. The process of hierarchical self-assembly of compound 1 was investigated by the concentration and temperature dependence of UV-visible and (1)H NMR spectra, fluorescence spectra, and electron microscopy data. The temperature dependence of the UV-visible spectra indicates a highly cooperative process for the self-assembly of compound 1 in decaline. The electron micrograph of the decaline solution of compound 1 (1.0 mM) revealed supramolecular sheet aggregates forming an entangled network. The selected area electronic diffraction patterns of the supramolecular sheet aggregates were typical for single crystals, indicative of a highly ordered assembly. The results exemplify the generation, by hierarchical self-assembly, of highly organized supramolecular materials presenting novel collective properties at each level of organization.     

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.     

Epitope mapping of 7S cashew antigen in complex with antibody by solution‐phase H/D exchange monitored by FT‐ICR mass spectrometry

The potential epitope of a recombinant food allergen protein, cashew Ana o 1, reactive to monoclonal antibody, mAb 2G4, has been mapped by solution‐phase amide backbone H/D exchange (HDX) monitored by Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS). Purified mAb 2G4 was incubated with recombinant Ana o 1 (rAna o 1) to form antigen:monoclonal antibody (Ag:mAb) complexes. Complexed and uncomplexed (free) rAna o 1 were then subjected to HDX‐MS analysis. Five regions protected from H/D exchange upon mAb binding are identified as potential conformational epitope‐contributing segments. Copyright © 2015 John Wiley & Sons, Ltd.     

Conditions for deuterium exchange mediated by iridium complexes formed in situ

A series of iridium-based complexes formed in situ, containing pyridine, phosphines, triphenylarsine, triphenylstibine, and triphenylamine as ligands, has been screened for ability to mediate ortho-exchange of hydrogen in a series of model substrates. Improved incorporation into a number of substrate classes has been achieved. The electronic properties and number of ligands at the metal centre are instrumental in determining which catalysts are best suited to exchange in any given substrate.     

Hydrogen/deuterium exchange in parallel with acid/base induced protein conformational change in electrospray droplets

The exposure of electrospray droplets to vapors of deuterating reagents during droplet desolvation in the interface of a mass spectrometer results in hydrogen/deuterium exchange (HDX) on the sub‐millisecond time scale. Deuterated water is used to label ubiquitin and cytochrome c with minimal effect on the observed charge state distribution (CSD), suggesting that the protein conformation is not being altered. However, the introduction of deuterated versions of various acids (e.g., CD₃COOD and DCl) and bases (ND₃) induces unfolding or refolding of the protein while also labeling these newly formed conformations. The extent of HDX within a protein CSD associated with a particular conformation is essentially constant, whereas the extent of HDX can differ significantly for CSDs associated with different conformations from the same protein. In some cases, multiple HDX distributions can be observed within a given charge state (as is demonstrated with cytochrome c) suggesting that the extent of HDX and CSDs share a degree of complementarity in their sensitivities for protein conformation. The CSD is established late in the evolution of ions in electrospray whereas the HDX process presumably takes place in the bulk of the droplet throughout the electrospray process. Back exchange is also performed in which proteins are prepared in deuterated solvents prior to ionization and exposed to undeuterated vapors to exchange deuteriums for hydrogens. The degree of deuterium uptake is easily controlled by varying the identity and partial pressure of the reagent introduced into the interface. Since the exchange occurs on the sub‐millisecond time scale, the use of deuterated acids or bases allows for transient species to be generated and labeled for subsequent mass analysis. Copyright © 2014 John Wiley & Sons, Ltd.     

Effect of stoichiometry on liquid crystalline supramolecular polymers formed with complementary nucleobase pair interactions

We report herein studies on the liquid crystalline behavior of a series of supramolecular materials that contain different ratios of two complementary symmetrically-substituted alkoxy-bis(phenylethynyl)benzene AA- and BB-type monomers. One monomer has thymine units placed at either end of the rigid mesogenic core, while the other has N⁶-(4-methoxybenzoyl)-adenine units placed on the ends. Differential scanning calorimetric and polarized optical microscopy studies have been carried out on these systems. These studies show that the material's behavior is strongly dependent on its thermal history. As a result, the materials can exhibit, on heating, either a liquid crystalline phase, a crystalline phase, or the coexistence of crystalline and liquid crystalline regions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5049–5059, 2006     

α-proton deuterium exchange of five-coordinate bicycloazastannoxides catalyzed by Et3N

The live-coordinate bicycloawstannowxides (1–6) in the presence of Et₃N has been investigated by ♪1H NMR spectrograph. It has been found that the deuterium exrhange of αCH of five-coordinate bicycloazastannoxides with CD₃0D takes place, which is catalyzed by Et₃N. In the presrnce of Et₃ N(2 pL), the apparent rate constants (koba.) for the deuterium cxchangc in CD₃OD) is determined by ♪1H NMR method, wd the value of k_Oba is in the range of (2.05-10.8) ×10-⁴ s^-1. Thr effect of the substitutes on the rates and the kinetic mechanism are discussed.     

Liquid chromatography/quadrupole time‐of‐flight mass spectrometry in combination with online hydrogen/deuterium exchange technique for structural elucidation of phase I metabolites of iso‐phenylcyclopentylamine in rat bile

MS/MS experiment and accurate mass measurement are powerful tools in metabolite identification. However, sometimes these data do not provide enough information to assign an unambiguous structure to a metabolite. In combination with MS techniques, hydrogen/deuterium (H/D) exchange can provide additional information for structural elucidation by determination of the number of exchangeable hydrogen atoms in a structure. In this study, the principal phase I metabolites of iso‐phenylcyclopentylamine in rat bile were identified by high‐performance liquid chromatography with electrospray ionization quadrupole time‐of‐flight mass spectrometry (ESI‐Q‐TOF‐MS). Since N‐oxidation may occur because of the existence of the primary amino group in the structure, it was difficult to differentiate the hydroxylated metabolites from N‐oxides by ESI‐Q‐TOF‐MS alone. Therefore, online H/D exchange technique was applied to solve this problem. Finally, 25 phase I metabolites were detected and structurally described, in which 11 were confirmed to be N‐oxides. This study demonstrated the effectiveness of high‐resolution mass spectrometry in combination with an online H/D exchange technique in rapid identification of drug metabolites, especially in discriminating hydroxylated metabolites from N‐oxides. Copyright © 2014 John Wiley & Sons, Ltd.     

Higher order structure characterization of protein therapeutics by hydrogen/deuterium exchange mass spectrometry

Characterization of therapeutic drugs is a crucial step in drug development in the biopharmaceutical industry. Analysis of protein therapeutics is a challenging task because of the complexities associated with large molecular size and 3D structures. Recent advances in hydrogen/deuterium-exchange mass spectrometry (HDX-MS) have provided a means to assess higher-order structure of protein therapeutics in solution. In this review, the principles and procedures of HDX-MS for protein therapeutics characterization are presented, focusing on specific applications of epitope mapping for protein–protein interactions and higher-order structure comparison studies for conformational dynamics of protein therapeutics. Figure

HDX of protein backbone amide hydrogen     

Evidence for site‐specific intra‐ionic hydrogen/deuterium exchange in the low‐energy collision‐induced dissociation product ion spectra of protonated small molecules generated by electrospray ionisation

The experimental investigation of site‐specific intra‐ionic hydrogen/deuterium (H/D) exchange in the low‐energy collision‐induced dissociation (CID) product ion spectra of protonated small molecules generated by electrospray ionisation (ESI) is presented. The observation of intra‐ionic H/D exchange in such ions under low‐energy CID conditions has hitherto been rarely reported. The data suggest that the intra‐ionic H/D exchange takes place in a site‐specific manner between the ionising deuteron, localised at either a tertiary amine or a tertiary amine‐N‐oxide, and a γ‐hydrogen relative to the nitrogen atom. Nuclear magnetic resonance (NMR) spectroscopy measurements showed that no H/D exchange takes place in solution, indicating that the reaction occurs in the gas phase. The compounds analysed in this study suggested that electron‐withdrawing groups bonded to the carbon atom bearing the γ‐hydrogen can preclude exchange. The effect of the electron‐withdrawing group appears dependent upon its electronegativity, with lower χ value groups still allowing exchange to take place. However, the limited dataset available in this study prevented robust conclusions being drawn regarding the effect of the electron‐withdrawing group. The observation of site‐specific intra‐ionic H/D exchange has application in the area of structural elucidation, where it could be used to introduce an isotopic label into the carbon skeleton of a molecule containing specific structural features. This could increase the throughput, and minimise the cost, of such studies due to the obviation of the need to produce a deuterium‐labelled analogue by synthetic means. Copyright © 2010 John Wiley & Sons, Ltd.