Inter- and intra-molecular migration of peptide amide hydrogens during electrospray ionization

The isotopic exchange of amide hydrogens in proteins in solution strongly depends on the surrounding protein structure, thereby allowing structural studies of proteins by mass spectrometry. However, during electrospray ionization (ESI), gas phase processes may scramble or deplete the isotopic information. These processes have been investigated by on-line monitoring of the exchange of labile deuterium atoms in homopeptides with hydrogens from a solvent suitable for ESI. The relative contribution of intra- and inter-molecular exchange in the gas phase could be studied from their distinct influence on the well-characterized exchange processes in the spraying solution. The deuterium content of individual labile hydrogens was assessed from the isotopic patterns of two consecutive collision-induced dissociation fragments, as observed with a 9.4 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Results demonstrate that gas phase exchange in the high-pressure region between the capillary and the skimmer cause substantial depletion of the isotopic information of penta-phenylalanine and penta-aspartic acid. For penta-alanine and hexa-tyrosine, the amide hydrogens located close to the N-terminus are depleted from deuterium during mass analysis. Amide hydrogens located close to the C-terminus still retain the information of the isotopic state in solution, but they are redistributed by intra-molecular exchange of the amide hydrogens with the C-terminal hydroxyl group.     

Protophilic isotopic hydrogen exchange of 1-ferrocenyl-2-(nitrophenyl)ethylenes

cis-1-Ferrocenyl-2-(4-nitrophenyl)ethylene enters into the protium/deuterium exchange in basic medium at the expense of hydrogens of the phenyl ring, at ortho positions in respect of the nitro group. The homoaromatic analogue, 4-nitrostilbene, under the same conditions, undergoes isotopic exchange occurring exclusively at the vinylic CH fragment attached to the nitrophenyl group. The difference is eliminated as a result of the shift of the nitro group from position 4 into position 2 of the phenyl ring: cis-1-ferrocenyl-2-(2-nitrophenyl)ethylene enters into H⁺/D⁺ exchange in the same manner as 4-nitrostilbene. Correspondence to: Professor Z.V. Todres.     

A mass spectral investigation of water and acetic acid elimination from 1- and 2-indan derivatives

Water and acetic acid eliminations from 1- and 2-indan derivatives have been investigated. Deuterium labeling, high resolution peak matching and the metastable peak analysis capabilities of a high resolution triple analyzer (E B E) mass spectrometer were employed to examine the eliminations. These experiments showed that water was lost from 1-indanol via 1,2 and 1,3 processes. These results contrast with those obtained for 1-tetralol, which specifically eliminates water in a 1,4 process involving the benzylic hydrogens. Water elimination from 2-indanol is preceded by a slow hydroxyl-benzylic hydrogen exchange and proceeds specifically 1,2. Water losses from both 1- and 2-indanol are characterized by large kinetic energy releases. Acetic acid elimination is shown to occur specifically 1,3 from 1-acetoxyindan and 1,2 from 2-acetoxyindan.     

Determination of chemical purity and isotopic composition of natural and carbon-13-labeled arsenobetaine bromide standards by quantitative1H-NMR

In this study, we report the characterization of three arsenobetaine-certified reference materials by quantitative NMR. We have synthesized an arsenobetaine bromide high-purity standard of natural isotopic composition (ABET-1) and two carbon-13-labeled isotopic standards (BBET-1 and CBET-1). Assignments of the chemical purity and isotopic composition are not trivial in the case of arsenobetaine, and in this study we utilized quantitative¹H-NMR techniques for the determination of the mass fractions (chemical purity). The isotopic purity of all three standards was also assessed by NMR from the carbon-13 satellite signals. The standards are non-hygroscopic, high-purity (ca. 0.99 g/g), and the carbon-13 enrichment for both isotopic standards is x(¹³C)≈0.99. These standards are designed for use as primary calibrators for mass spectrometric determination of arsenobetaine in environmental samples.     

A new method for the accurate determination of the isotopic state of single amide hydrogens within peptides using Fourier transform ion cyclotron resonance mass spectrometry

A new method is presented to accurately determine the probability of having a deuterium or hydrogen atom on a specific amide position within a peptide after deuterium/hydrogen (D/H) exchange in solution. Amide hydrogen exchange has been proven to be a sensitive probe for studying protein structures and structural dynamics. At the same time, mass spectrometry in combination with physical fragmentation methods is commonly used to sequence proteins based on an amino acid residue specific mass analysis. In the present study it is demonstrated that the isotopic patterns of a series of peptide fragment ions obtained with capillary-skimmer dissociation, as observed with a 9.4 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer, can be used to calculate the isotopic state of specific amide hydrogens. This calculation is based on the experimentally observed isotopic patterns of two consecutive fragments and on the isotopic binomial distributions of the atoms in the residue constituting the difference between these two consecutive fragments. The applicability of the method is demonstrated by following the sequence-specific D/H exchange rate in solution of single amide hydrogens within some peptides.     

Photoreduction of oxoisoaporphine dyes by amines: transient-absorption and semiempirical quantum-chemical studies

Photoreduction by amines of oxoisoaporphine dyes occurs via a stepwise mechanism of electron-proton-electron transfer that leads to the metastable N-hydrogen oxoisoaporphine anion. During photoreduction that occurs from the triplet manifold of the oxoisoaporphine, a radical ion A(-)(*), a neutral-hydrogenated radical A-NH(*), and the metastable ion A-NH(-) of the oxoisoaporphine are formed. We present time-resolved spectroscopic data and quantum mechanical semiempirical PM3 and ZINDO/S results for the transient species formed during the flash photolysis of oxoisoaporphines in the presence of amines. These calculations reproduce adequately the experimental spectra of the triplet-triplet absorption near 450 nm, and that of neutral hydrogenated radical of the studied oxoisoaporphines centered at 390 nm. A transient absorption observed near 490 nm, for all of the studied systems, was explained by considering the formation of radical ion pair between the radical anion of the oxoisoaporphine, A(-)(*), and the radical cation of the amine, whose ZINDO/S calculated spectra generate the strongest transition near the experimentally observed absorption maximum at 490 nm, supporting the formation of a radical ion pair complex as the first step of the photoreduction.     

Computational evaluation of the evidence for tri-trans-[12]annulene

[reaction: see text] Automerization in tri-trans-[12]annulene (1) was investigated by DFT, MP2, and coupled-cluster methods. Using the highest level of theory employed here, CCSD(T)/cc-pVDZ//BHandHLYP/6-311+G(d,p), we located two low-energy pathways for degenerate conformational change from the lowest-energy conformer of 1 (1a): one with E(a) = 4.5 kcal/mol that interconverts the three inner trans hydrogens with the three outer trans hydrogens and one with E(a) = 2.7 kcal/mol that interconverts the three inner hydrogens with each other. These results are consistent with the experimental results of Oth and co-workers on [12]annulene 1a (Oth, J. F. M.; R?ttele, H.; Schr?der, G. Tetrahedron Lett. 1970, 61). The conformational exchange of the inner trans hydrogens with the outer ones is predicted to occur via a one-step process involving a C(2)-symmetric transition state and not via the D(3)-symmetric transition state (1b) that was postulated earlier. Conformer 1b was found to be a shallow minimum 6.7 kcal/mol above 1a with a barrier of 0.4 kcal/mol for conversion to 1a. Finally, GIAO-B3LYP/6-311+G(d,p) and BHandHLYP/6-311+G(d,p) computed (1)H NMR chemical shifts of 1a and three other low-lying isomers support Oth's original assignment of observed (1)H NMR peaks to 1a at both low and high temperature.     

The gas-phase H/D exchange mechanism of protonated amino acids

A mass spectrometry and Density Functional Theory study of gas-phase H/D exchange in protonated Ala, Cys, Ile, Leu, Met, and Val is reported. Site-specific rate constants were determined and results identify the alpha-amino group as the protonation site. Lack of exchange on the Cys thiol group is explained by the absence of strong intramolecular hydrogen bonding within the reaction complex. In aliphatic amino acids the presence of a methyl group at the beta-C atom was found to lower the site-specific H/D exchange rate for amino hydrogens. Study of the exchange mechanism showed that isotopic exchange occurs in two independent reactions: in one, only the carboxylic hydrogen is exchanged and in the other, both carboxylic and amino group hydrogens exchange. The proposed reaction mechanisms, calculated structures of various species, and a number of structural findings are consistent with experimental data.     

Probing high order structure of proteins by fast-atom bombardment mass spectrometry

During the past decade, numerous investigations have demonstrated that the rate at which amide hydrogens located at peptide linkages undergo isotopic exchange is a sensitive probe of the high order structure and dynamics of proteins. The present investigation demonstrates that microbore high-performance liquid chromatography (HPLC) continuous-flow fast-atom bombardment mass spectrometry (FABMS) can be used to accurately quantify deuterium located at peptide linkages in short segments of large proteins. This result is important because it demonstrates the feasibility of using mass spectrometry as a tool for studying the high order structure and dynamics of large proteins. Following a period of deuterium exchange-in, a protein was placed into slow-exchange conditions and fragmented into peptides with pepsin. The digest was analyzed by continuous-flow HPLC FABMS to determine the molecular weights of the peptides, from which the number of deuterons located at the peptide linkages could be deduced. The HPLC step was used both to fractionate the peptides according to their hydrophobicities and to remove through back-exchange all deuterium except that located at peptide amide linkages. This approach has been applied to α-crystallin, a lens protein composed of two gene products with monomer molecular weights of 20 kDa and an aggregate molecular weight approaching 1000 kDa. Results from this study show that some of the peptide amide hydrogens in αA-crystallin exchange very rapidly (k > 10 h^?1) while others exchange very slowly (k < 10^?3 h^?1). The ability not only to detect that a conformational change has occurred, but also to identify the specific regions within the protein where the change occurred, was demonstrated by measuring changes in the exchange rates within these regions as the deuterium exchange-in temperature was increased from 10 to 80 ° C.     

Kinetics of thermo-induced micelle-to-vesicle transitions in a catanionic surfactant system investigated by stopped-flow temperature jump

The kinetics of thermo-induced micelle-to-vesicle transitions in a catanionic surfactant system consisting of sodium dodecyl sulfate (SDS) and dodecyltriethylammonium bromide (DEAB) were investigated by the stopped-flow temperature jump technique, which can achieve T-jumps within ～2-3 ms. SDS/DEAB aqueous mixtures ([SDS]/[DEAB] = 2/1, 10 mM) undergo microstructural transitions from cylindrical micelles to vesicles when heated above 33 °C. Upon T-jumps from 20 °C to final temperatures in the range of 25-31 °C, relaxation processes associated with negative amplitudes can be ascribed to the dilution-induced structural rearrangement of cylindrical micelles and to the dissolution of non-equilibrium mixed aggregates. In the final temperature range of 33-43 °C the obtained dynamic traces can be fitted by single exponential functions, revealing one relaxation time (τ) in the range of 82-440 s, which decreases with increasing temperature. This may be ascribed to the transformation of floppy bilayer structures into precursor vesicles followed by further growth into final equilibrium vesicles via the exchange and insertion/expulsion of surfactant monomers. In the final temperature range of 45-55 °C, vesicles are predominant. Here T-jump relaxations revealed a distinctly different kinetic behavior. All dynamic traces can only be fitted with double exponential functions, yielding two relaxation times (τ(1) and τ(2)), exhibiting a considerable decrease with increasing final temperatures. The fast process (τ(1)～ 5.2-28.5 s) should be assigned to the formation of non-equilibrium precursor vesicles, and the slow process (τ(2)～ 188-694 s) should be ascribed to their further growth into final equilibrium vesicles via the fusion/fission of precursor vesicles. In contrast, the reverse vesicle-to-micelle transition process induced by a negative T-jump from elevated temperatures to 20 °C occurs quite fast and almost completes within the stopped-flow dead time (～2-3 ms).     

Intramolecular migration of amide hydrogens in protonated peptides upon collisional activation

Presently different opinions exist as to the degree of scrambling of amide hydrogens in gaseous protonated peptides and proteins upon collisional activation in tandem mass spectrometry experiments. This unsettled controversy is not trivial, since only a very low degree of scrambling is tolerable if collision-induced dissociation (CID) should provide reliable site-specific information from (1)H/(2)H exchange experiments. We have explored a series of unique, regioselectively deuterium-labeled peptides as model systems to probe for intramolecular amide hydrogen migration under low-energy collisional activation in an orthogonal quadrupole time-of-flight electrospray ionization (Q-TOF ESI) mass spectrometer. These peptides contain a C-terminal receptor-binding sequence and an N-terminal nonbinding region. When the peptides form a receptor complex, the amide hydrogens of the interacting sequences are protected against exchange with the solvent, while the amide hydrogens of the nonbinding sequences exchange rapidly with the solvent. We have utilized such long-lived complexes to generate peptides labeled with deuterium in either the binding or nonbinding region, and the expected regioselectivity of this labeling was confirmed after pepsin proteolysis. CID of such deuterated peptides, [M + 2H](2+), yielded fragment ions (b- and y-ions) having a deuterium content that resemble the theoretical values calculated for 100% scrambling. Thus, complete randomization of all hydrogen atoms attached to nitrogen and oxygen occurs in the gaseous peptide ion prior to its dissociation.     

Enhanced gas-phase hydrogen-deuterium exchange of oligonucleotide and protein ions stored in an external multipole ion reservoir

Rapid gas-phase hydrogen-deuterium (H-D) exchange from D(2)O and ND(3) into oligonucleotide and protein ions was achieved during storage in a hexapole ion reservoir. Deuterated gas is introduced through a capillary line that discharges directly into the low-pressure region of the reservoir. Following exchange, the degree of H-D exchange is determined using Fourier transform ion cyclotron resonance mass spectrometry. Gas-phase H-D exchange experiments can be conducted more than 100 times faster than observed using conventional in-cell exchange protocols that require lower gas pressures and additional pump-down periods. The short experimental times facilitate the quantitation of the number of labile hydrogens for less reactive proteins and structured oligonucleotides. For ubiquitin, we observe approximately 65 H-D exchanges after 20 s. Exchange rates of > 250 hydrogens s(-1) are observed for oligonucleotide ions when D(2)O or ND(3) is admitted directly into the external ion reservoir owing to the high local pressure in the hexapole. Partially deuterated oligonucleotide ions have been fragmented in the reservoir using infrared multiphoton dissociation (IRMPD). The resulting fragment ions show that exchange predominates at charged sites on the 5'- and 3'-ends of the oligonucleotide, whereas exchange is slower in the core. This hardware configuration is independent of the mass detector and should be compatible with other mass spectrometric platforms including quadrupole ion trap and time-of-flight mass spectrometers.     

Energetics and structural elucidation of mechanisms for gas phase H/D exchange of protonated peptides

Hydrogen/deuterium exchange reactions involving protonated triglycine and deuterated ammonia (ND(3)) have been examined in the gas phase using a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Ab initio and density functional theory (DFT) calculations have been carried out to model the exchanges and to obtain energetics and vibrational frequencies for molecules involved in the proposed exchange mechanisms. Structural optimization and frequency calculations have been performed at the B3LYP level of theory with the 6-311+G(d,p) basis set. Transition states have been calculated at the same level of theory and basis set as above using the QST2 and QST3 methods. Single-point energy calculations have been performed at the MP2/6-311+G(d,p) level. Six labile sites of protonated triglycine were found to undergo H/D exchange. Of these six labile hydrogens, two are amide, three are ammonium, and one is carboxyl. Detailed mechanisms for each of these transfers are proposed. Qualitative onium ion and tautomer mechanisms for the exchanges of ammonium and amide hydrogens, respectively, using semiempirical calculations were suggested in previous studies by Beauchamp et al. As shown by the current ab initio and DFT calculations completed during this study, the mechanisms proposed in that study are notionally correct; however, the tautomer mechanisms are shown here to be the result of the fact that a second stable isomer of protonated triglycine exists in which the amide1 carbonyl oxygen is protonated. The exchange of the carboxyl hydrogen is found to proceed via a transition state resembling an ammonium ion interacting with a carboxylate moiety via two hydrogen bonds. The current work thus provides significant mechanistic and structural detail for a considerably more in-depth understanding of the processes involved in gas phase H/D exchange of peptides.     

Polar Aprotic Modifiers for Chromatographic Separation and Back-Exchange Reduction for Protein Hydrogen/Deuterium Exchange Monitored by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Hydrogen/deuterium exchange monitored by mass spectrometry is an important non-perturbing tool to study protein structure and protein–protein interactions. However, water in the reversed-phase liquid chromatography mobile phase leads to back-exchange of D for H during chromatographic separation of proteolytic peptides following H/D exchange, resulting in incorrect identification of fast-exchanging hydrogens as unexchanged hydrogens. Previously, fast high-performance liquid chromatography (HPLC) and supercritical fluid chromatography have been shown to decrease back-exchange. Here, we show that replacement of up to 40% of the water in the LC mobile phase by the modifiers, dimethylformamide (DMF) and N-methylpyrrolidone (NMP) (i.e., polar organic modifiers that lack rapid exchanging hydrogens), significantly reduces back-exchange. On-line LC micro-ESI FT-ICR MS resolves overlapped proteolytic peptide isotopic distributions, allowing for quantitative determination of the extent of back-exchange. The DMF modified solvent composition also improves chromatographic separation while reducing back-exchange relative to conventional solvent.     

Hydrogen exchange rates in proteins from water (1)H transverse magnetic relaxation

Access to the fast exchange kinetics of labile protein hydrogens in solution is provided by exchange broadening of the water 1H NMR line. We analyzed the chemical shift modulation contribution of labile hydrogens in bovine pancreatic trypsin inhibitor (BPTI) to the transverse 1H spin relaxation rate, R2, of the bulk solvent. Both the experimental pH dependence and the CPMG dispersion of R2 could be quantitatively accounted for on the basis of known chemical shifts, exchange rates, and ionization constants for BPTI. This analysis provided, for the first time, the hydrogen exchange rate constants for Lys and Arg side chains in a protein and pointed to an internal catalysis of the N-terminal amino protons in BPTI by a salt bridge. The method can be used for mapping the hydrogen exchange rates in protein solutions and biomaterials, which may be important for the control of relaxation-weighted contrast in biological MRI.     

Cycloaddition reactions of 1-lithio-1,3-dienes with aromatic nitriles affording multiply substituted pyridines, pyrroles, and linear butadienylimines

Fully or partially substituted 1-iodo- or 1-bromo-1,3-dienes could be readily lithiated using t-BuLi or n-BuLi to afford their corresponding 1-lithio-1,3-diene derivatives in quantitative yields. When these in situ generated lithium reagents were treated with organonitriles, depending on the substitution patterns of the butadienyl skeletons, substituted pyridines, pyrroles, and/or linear butadienyl imines were formed in good to excellent yields via N-lithioketimine intermediates. In the cases of 1,2,3,4-tetrasubstituted and 2,3-disubstituted 1-lithio-1,3-dienes, pyridine derivatives or linear butadienyl imines were generally formed depending on the reaction temperatures. When 1,2,3,4-tetrasubstituted 4-halo-1-lithio-1,3-dienes and 1,2-disubstituted 1-lithio-1,3-dienes were treated with organonitriles, pyrrole derivatives or linear butadienyl imines were obtained. Competition between 5-exo and 6-endo cyclization was found to be responsible for the formation of either pyrroles or pyridines. Selective elimination of RLi from the lithiated cyclic N-containing intermediates was observed. The order of elimination was found to be LiCl > Me3SiLi > LiH.     

Carbon-14 kinetic isotope effect in the decarbonylation of lactic acid[1-14C]

The carbon-14 kinetic isotope effect for the decarbonylation of lactic acid[1-¹⁴C] in sulfuric acid has been measured in the temperature interval of 20–90°C. The experimental values of (k_12C/k_14C) are compared with the theoretical¹⁴C kinetic isotope effect calculated assuming that one carbon-oxygen stretching vibration is lost in the rate-determining step. The discrepancy between experimentally observed temperature dependence of the¹⁴C kinetic isotope effect and the theoretical one is explained by the possible side reactions which change the apparent degrees of decarbonylation and isotopic composition of CH₃CHOHCOOH[1-¹⁴C] used in experiments aiming at the determination of carbon-14 kinetic isotope effect in the decarbonylation process itself.     

Gas phase RNA and DNA ions 2. Conformational dependence of the gas-phase H/D exchange of nucleotide-5′-monophosphates

The conformational dependence of the gas-phase hydrogen/deuterium (H/D) exchange of nucleotide-5-monophosphate anions with the H/D exchange reagent D2S is reported here. The electrospray-generated [M-H]- anions of adenosine-5'-monophosphate, adenosine-5'-carboxylic acid, ribitol-5-phosphate, and 2-deoxy-ribitol-5-phosphate were reacted with D2S in the gas phase. Their reactivity (adenosine-5'-monophosphate exchanged 2 of 5 labile hydrogens, adenosine-5'-carboxylic acid exchanged 1 of 4, ribitol-5-phosphate exchanged 2 of 3, and 2-deoxy-ribitol-5-phosphate exchanged 1 of 2) suggests that the hydroxyl group in the 2 position of the ribose sugar and the amino hydrogen on the nucleobase do not exchange readily with D2S. Semiempirical molecular orbital calculations suggest that the labile hydrogens in these positions are thermodynamically facile to exchange but as a conformation inaccessible to the presumed phosphate anion, consistent with a mechanism in which the phosphate anion complexes with the exchange reagent and assists H/D exchange at a neighboring site.     

Photoactivated h/d exchange in tyrosine: involvement of a radical anion intermediate

The aromatic hydrogen nuclei of tyrosine are photochemically labile and exchange with deuterons in neutral D(2)O solution. The site meta to the ring hydroxyl substituent is preferentially deuterated, exhibiting a meta/ortho deuteration rate of approximately 4:1. In contrast with acid-catalyzed H/D exchange and with nearly all of the reported photoactivated H/D exchange studies, the UV-induced H/D exchange of tyrosine is optimal at pH 9 and is effectively quenched at acid pH. Photochemical H/D exchange is strongly stimulated by the alpha-amino group (the aromatic hydrogens of p-cresol are far less subject to exchange) and by imidazole or phosphate buffers. On the basis of the results obtained here and on the previously identified cyclohexadienyl radical (Bussandri, A.; van Willigen, H. J. Phys. Chem. A 2002, 106, 1524-1532), we conclude that the exchange reaction involves a radical intermediate and results from two distinct roles of tyrosine: (1) as a phototransducer of light energy into solvated electrons (e(aq)(-)), and (2) as an acceptor of an electron to create a radical anion intermediate which is rapidly protonated, yielding a neutral cyclohexadienyl radical. Regeneration of the tyrosine can occur via a bimolecular redox reaction of the cyclohexadienyl and phenoxyl radicals to yield a carbocation/phenoxide pair, followed by deprotonation of the carbocation. The oxidation step is pH dependent, requiring the deprotonated form of the cyclohexadienyl radical. The H/D exchange thus results from a cyclic one-electron (Birch) reduction/protonation/reoxidation (by phenoxyl radical)/deprotonation cycle. Consistent with these mechanistic conclusions, the aromatic hydrogens of tyrosine O-methyl ether are photochemically inert, but become labile in the presence of tyrosine at high pH. The deuteration rate of O-methyl tyrosine is lower than that of tyrosine and shows a preference for the ortho positions. This difference is proposed to result from a variation in the oxidation step, characterized by a preferential oxidation of a cyclohexadienyl resonance structure with the unpaired electron localized on the oxygen substituent.     

Reaction of 4-methyl, 4-phenyl, and 4-hydrogen substituted 1-lithio-1,3-butadienes with aldehydes: preparation of multiply substituted cyclopentadienes

Reaction of aldehydes with 1-lithio-1,3-butadiene reagents possessing a methyl substituent, a phenyl substituent or a hydrogen at position 4 of the butadienyl skeletons was studied. Polysubstituted cyclopentadiene derivatives were obtained in high yields upon hydrolysis using strong acidic solution. Reaction mechanism study revealed that these cyclopentadienes were formed via an acid-promoted cyclization of conjugated dienols. Thus, stereodefined all-cis substituted dienols or a wide diversity of substituted cyclopentadienes can be obtained from the same 1-lithio-1,3-butadiene reagent and aldehyde by adjusting the hydrolysis conditions.