Robust Fluorescence Collection Module for Wide-Bore Ion Cyclotron Resonance Mass Spectrometers

Mass spectrometers are at the heart of the most powerful toolboxes available to scientists when studying molecular structure, conformation, and dynamics in controlled molecular environments. Improved molecular characterization brought about by the implementation of new orthogonal methods into mass spectrometry-enabled analyses opens deeper insight into the complex interplay of forces that underlie chemistry. Here, we detail how one can add fluorescence detection to commercial ultrahigh-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers without adverse effects to its preexisting analytical tools. This advance enables measurements based on fluorescence detection, such as Förster resonance energy transfer (FRET), to be used in conjunction with other MS/MS techniques to probe the conformation and dynamics of large biomolecules, such as proteins and their complexes, in the highly controlled environment of a Penning trap.

Gas-Phase Fluorescence of Proflavine Reveals Two Close-Lying, Brightly Emitting States

Surprising excitation-dependent, dual emission from a small organic model fluorophore is reported. Gas-phase fluorescence spectra of proflavine (a diaminoacridine) ions reveal two long-lived emitting states, with distinct bands separated by just 1700 cm^-1. The relative intensities of these two bands depend on the excitation wavelength. Time-dependent density functional theory (TD-DFT) calculations support the existence of two close-lying singlet electronic states, with excitation into S₂ predicted to be >1000-fold more likely than into S₁. These data strongly suggest that internal conversion (IC) rates are suppressed relative to solvated proflavine, and that IC is competitive with intramolecular vibrational relaxation (IVR). This work offers an in-depth assessment of the gas-phase photophysics of a simple fluorophore that could open a new pathway to understanding dual emission in fluorophores.

Hydrogen-Deuterium Exchange and Electron Capture Dissociation to Interrogate the Conformation of Gaseous Melittin Ions

There is a need in the field of biological mass spectrometry for structural tools which can report on regional, rather than solely global, structure of gaseous protein ions. Site-specific hydrogen-deuterium (H/D) exchange has shown promise in fulfilling this need, but requires additional method development to prove its utility. In this study, we use H/D exchange and electron capture dissociation (ECD) to probe the gaseous structure of two peptides which are α-helical in solution and which differ by a single point mutation. Global H/D exchange levels, ECD fragmentation profiles, and region specific H/D exchange profiles are compared between wild type (WT) melittin, which adopts a hinged helix conformation in solution, and a mutant P14A melittin which folds into a single helix in solution. High protection from H/D exchange by both peptides is consistent with retention of secondary structure in the gas phase (or refolding into some other compact structure). The P14A mutant melittin exhibits lower ECD fragmentation efficiency than WT melittin, suggesting that it contains more secondary structure in the gas phase, which may indicate that these peptides retain some memory of their solution-phase structures. Examination of the isotopic distributions of fragment ions derived from H/D exchange with subsequent ECD reveals that the C-terminus of these peptides adopts multiple conformations. The results reported here offer insight into the stability of alpha helices in the gas phase, and also highlight the value of combining gas-phase H/D exchange with electron capture dissociation to interrogate gaseous peptide conformation.

Deuterium isotope effect in fluorescence of gaseous oxazine dyes

The increased utility of fluorescence-based methods in recent years has highlighted the need for brighter, more efficient fluorophores. In order to design these fluorophores, an improved fundamental understanding is necessary of the structural components that intrinsically effect fluorescence efficiency. Here, we characterize the intrinsic effects of deuteration on fluorescence from gaseous oxazine dyes, without the influence of dye-solvent interactions, by making use of an ion trap mass spectrometer that has been altered to enable optical measurements. Comparison of emission spectra of four oxazine dyes: cresyl violet, oxazine 4, oxazine 170, and darrow red, show little change in profile upon deuteration of amine groups. However, deuteration significantly increases the efficiency of fluorescence with an increase in fluorescence lifetime and brightness by 10-23% for the gaseous dyes. This increase is less than half that of the quantum yield increase observed in deuterated solution. This indicates the large fluorescence efficiency changes for the oxazine dyes in deuterated solution result from a combination of both intrinsic effects as well as substantial contribution from altered fluorophore-solvent interactions. The intrinsic effects behind increased lifetime upon deuteration are explored using time-dependent density functional theory (TD-DFT) calculations of potential energy surfaces (PESs) for ground and low lying excited electronic states. In accord with experimental observations, calculated S1-S0 emission spectra show only minor differences between deuterated and non-deuterated forms indicating that the deuteration does not affect the radiative channel appreciably. Relaxed PES scans along the torsional motions of the amino groups reveal that the increase in lifetimes upon deuteration is likely due to quenching of different radiationless changes channels in different oxazine dyes. Calculations suggest that tunneling to access twisted intramolecular charge transfer states in S1 is critical in several of the oxazines. However, in at least one of the dyes examined, the large isotope effect is more likely due to differences in intersystem crossing rates. Overall, this combined experimental and computational investigation elucidates the photophysics of a well-known fluorescent scaffold and provides insight into how small differences can dramatically affect fluorescence outcomes.

The effect of methylation on the intrinsic photophysical properties of simple rhodamines

Gas-phase studies of progressively methylated rhodamines display unexpected photophysical trends that are obscured in solution, revealing key solvent effects.

Protomers of DNA-binding dye fluoresce different colours: intrinsic photophysics of Hoechst 33258

A new form of DNA-binder Hoechst 33258 is stabilised upon desolvation. Altered optical properties include a distinct green fluorescence.

Idebenone and coenzyme Q10 are novel PPARα/γ ligands, with potential for treatment of fatty liver diseases

Current peroxisome proliferator-activated receptor (PPAR)-targeted drugs, such as the PPARγ-directed diabetes drug rosiglitazone, are associated with undesirable side effects due to robust agonist activity in non-target tissues. To find new PPAR ligands with fewer toxic effects, we generated transgenic zebrafish that can be screened in high throughput for new tissue-selective PPAR partial agonists. A structural analog of coenzyme Q₁₀ (idebenone) that elicits spatially restricted partial agonist activity for both PPARα and PPARγ was identified. Coenzyme Q₁₀ was also found to bind and activate both PPARs in a similar fashion, suggesting an endogenous role in relaying the states of mitochondria, peroxisomes and cellular redox to the two receptors. Testing idebenone in a mouse model of type 2 diabetes revealed the ability to reverse fatty liver development. These findings indicate new mechanisms of action for both PPARα and PPARγ, and new potential treatment options for nonalcoholic fatty liver disease (NAFLD) and steatosis.

This article has an associated First Person interview with the first author of the paper.

Summary: A zebrafish screen identifies a novel PPARα/γ ligand, idebenone, with potential for treatment of fatty liver diseases, as seen by testing it in a mouse model of type 2 diabetes.

Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation

An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen-deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes. Graphical Abstract ᅟ.

Fluorescence imaging for visualization of the ion cloud in a quadrupole ion trap mass spectrometer

Laser-induced fluorescence is used to visualize populations of gaseous ions stored in a quadrupole ion trap (QIT) mass spectrometer. Presented images include the first fluorescence image of molecular ions collected under conditions typically used in mass spectrometry experiments. Under these "normal" mass spectrometry conditions, the radial (r) and axial (z) full-width at half maxima (FWHM) of the detected ion cloud are 615 and 214 μm, respectively, corresponding to ~6% of r0 and ~3% of z0 for the QIT used. The effects on the shape and size of the ion cloud caused by varying the pressure of helium bath gas, the number of trapped ions, and the Mathieu parameter q z are visualized and discussed. When a "tickle voltage" is applied to the exit end-cap electrode, as is done in collisionally activated dissociation, a significant elongation in the axial, but not the radial, dimension of the ion cloud is apparent. Finally, using spectroscopically distinguishable fluorophores of two different m/z values, images are presented that illustrate stratification of the ion cloud; ions of lower m/z (higher qz) are located in the center of the trapping region, effectively excluding higher m/z (lower qz) ions, which form a surrounding layer. Fluorescence images such as those presented here provide a useful reference for better understanding the collective behavior of ions in radio frequency (rf) trapping devices and how phenomena such as collisions and space-charge affect ion distribution.

Ligand migration in the gaseous insulin-CB7 complex--a cautionary tale about the use of ECD-MS for ligand binding site determination

Knowledge of the structure of protein-ligand complexes can aid in understanding their roles within complex biological processes. Here we use electrospray ionization (ESI) coupled to a Fourier transform ion cyclotron resonance mass spectrometer to investigate the noncovalent binding of the macrocycle cucurbit[7]uril (CB7) to bovine insulin. Recent condensed-phase experiments (Chinai et al., J. Am. Chem. Soc. 133:8810-8813, 2011) indicate that CB7 binds selectively to the N-terminal phenylalanine of the insulin B-chain. Competition experiments employing ESI mass spectrometry to assess complex formation between CB7 and wild type insulin B-chain vs. a mutant B-chain, confirm that the N-terminal phenylalanine plays in important role in solution-phase binding. However, analysis of fragment ions produced by electron capture dissociation (ECD) of CB7 complexed to intact insulin and to the insulin B-chain suggests a different picture. The apparent gas-phase binding site, as identified by the ECD, lies further along the insulin B-chain. Together, these studies thus indicate that the CB7 ligand migrates in the ESI mass spectrometry analysis. Migration is likely aided by the presence of additional interactions between CB7 and the insulin B-chain, which are not observed in the crystal structure. While this conformational difference may result simply from the removal of solvent and addition of excess protons by the ESI, we propose that the migration may be enhanced by charge reduction during the ECD process itself because ion-dipole interactions are key to CB7 binding. The results of this study caution against using ECD-MS as a stand-alone structural probe for the determination of solution-phase binding sites.

Binding Energies of Proton-Bound Dimers of Imidazole and n-Acetylalanine Methyl Ester Obtained by Blackbody Infrared Radiative Dissociation

The dissociation kinetics of protonated n-acetyl-L-alanine methyl ester dimer (AcAlaME(d)), imidazole dimer, and their cross dimer were measured using blackbody infrared radiative dissociation (BIRD). Master equation modeling of these data was used to extract threshold dissociation energies (E(o)) for the dimers. Values of 1.18 +/- 0.06, 1.11 +/- 0.04, and 1.12 +/- 0.08 eV were obtained for AcAlaME(d), imidazole dimer, and the cross dimer, respectively. Assuming that the reverse activation barrier for dissociation of the ion-molecule complex is negligible, the value of E(o) can be compared to the dissociation enthalpy (DeltaH(d) degrees ) from HPMS data. The E(o) values obtained for the imidazole dimer and the cross dimer are in agreement with HPMS values; the value for AcAlaME(d) is somewhat lower. Radiative rate constants used in the master equation modeling were determined using transition dipole moments calculated at the semiempirical (AM1) level for all dimers and compared to ab initio (RHF/3-21G*) calculations where possible. To reproduce the experimentally measured dissociation rates using master equation modeling, it was necessary to multiply semiempirical transition dipole moments by a factor between 2 and 3. Values for transition dipole moments from the ab initio calculations could be used for two of the dimers but appear to be too low for AcAlaME(d). These results demonstrate that BIRD, in combination with master equation modeling, can be used to determine threshold dissociation energies for intermediate size ions that are in neither the truncated Boltzmann nor the rapid energy exchange limit.

Energetics from slow infrared multiphoton dissociation of biomolecules

Photodissociation kinetics of the protonated pentapeptide leucine enkephalin measured using a cw CO(2) laser and a Fourier-transform mass spectrometer are reported. A short induction period, corresponding to the time required to raise the internal energy of the ion population to a (dissociating) steady state, is observed. After this induction period, the dissociation data are accurately fit by first-order kinetics. A plot of the log of the unimolecular dissociation rate constant, k(uni), as a function of the log of laser power is linear at low laser powers (<9 W, k(uni) <0.05 s(-1)), but tapers off at high laser power (9-33 W, k(uni) = 0.05-7 s(-1)). The entire measured dissociation curve can be accurately fit by an exponential function plus a constant. The experiment is simulated using a master equation formalism. In the model, the laser radiation is described as an energetically flat-topped distribution which is spatially uniform. This description is consistent with experimental results which indicate that ion motion within the cell averages out spatial inhomogeneities in the laser light. The model has several adjustable parameters. The effect of varying these parameters on the calculated kinetics and power dependence curves is discussed. A procedure for determining a limited range of threshold dissociation energy, E(o), which fits both the measured induction period and power dependence curves, is presented. Using this procedure, E(o) of leucine enkephalin is determined to be 1.12-1.46 eV. This result is consistent with, although less precise than, values measured previously using blackbody infrared radiative dissociation. Although the blackbody dissociation results were used as a starting point to search for fits of the master equation model to experiment, these results demonstrate that it is, in principle, possible to determine a limited range of E(o) from slow infrared multiphoton dissociation data alone.

Structure of cationized arginine (arg.m, m = h, li, na, k, rb, and cs) in the gas phase: further evidence for zwitterionic arginine

The gas-phase structures of cationized arginine, Arg.M(+), M = Li, Na, K, Rb, and Cs, were studied both by hybrid method density functional theory calculations and experimentally using low-energy collisionally activated and thermal radiative dissociation. Calculations at the B3LYP/LACVP++** level of theory show that the salt-bridge structures in which the arginine is a zwitterion (protonated side chain, deprotonated C-terminus) become more stable than the charge-solvated structures with increasing metal ion size. The difference in energy between the most stable charge-solvated structure and salt-bridge structure of Arg.M(+) increases from -0.7 kcal/mol for Arg.Li(+) to +3.3 kcal/mol for Arg.Cs(+). The stabilities of the salt-bridge and charge-solvated structures reverse between M = Li and Na. These calculations are in good agreement with the results of dissociation experiments. The low-energy dissociation pathways depend on the cation size. Arginine complexed with small cations (Li and Na) loses H(2)O, while arginine complexed with larger cations (K, Rb, and Cs) loses NH(3). Loss of H(2)O must come from a charge-solvated ion, whereas the loss of NH(3) can come from the protonated side chain of a salt-bridge structure. The results of dissociation experiments using several cationized arginine derivatives are consistent with the existence of these two distinct structures. In particular, arginine methyl esters, which cannot form salt bridges, dissociate by loss of methanol, analogous to loss of H(2)O from Arg.M(+); no loss of NH(3) is observed. Although dissociation experiments probe gas-phase structure indirectly, the observed fragmentation pathways are in good agreement with the calculated lowest energy isomers. The combination of the results from experiment and theory provides strong evidence that the structure of arginine-alkali metal ion complexes in the gas phase changes from a charge-solvated structure to a salt-bridge structure as the size of the metal ion increases.

Gas-phase fluorescence excitation and emission spectroscopy of three xanthene dyes (rhodamine 575, rhodamine 590 and rhodamine 6G) in a quadrupole ion trap mass spectrometer

The gas-phase fluorescence excitation, emission and photodissociation characteristics of three xanthene dyes (rhodamine 575, rhodamine 590, and rhodamine 6G) have been investigated in a quadrupole ion trap mass spectrometer. Measured gas-phase excitation and dispersed emission spectra are compared with solution-phase spectra and computations. The excitation and emission maxima for all three protonated dyes lie at higher energy in the gas phase than in solution. The measured Stokes shifts are significantly smaller for the isolated gaseous ions than the solvated ions. Laser power-dependence measurements indicate that absorption of multiple photons is required for photodissociation. Redshifts and broadening of the dispersed fluorescence spectra at high excitation laser power provide evidence of gradual heating of the ion population, pointing to a mechanism of sequential multiple-photon activation through absorption/emission cycling. The relative brightness in the gas phase follows the order R575(1.00) < R590(1.15) < R6G(1.29). Fluorescence emission from several mass-selected product ions has been measured.

Efavirenz binding site in HIV-1 reverse transcriptase monomers

Efavirenz (EFV) is a potent nonnucleoside reverse transcriptase inhibitor (NNRTI) used in the treatment of AIDS. NNRTIs bind in a hydrophobic pocket located in the p66 subunit of reverse transcriptase (RT), which is not present in crystal structures of RT without an inhibitor. Recent studies showed that monomeric forms of the p66 and p51 subunits bind efavirenz with micromolar affinity. The effect of efavirenz on the solution conformations of p66 and p51 monomers was studied by hydrogen-deuterium exchange mass spectrometry (HXMS) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). HXMS data reveal that five peptides, four of which contain efavirenz contact residues seen in the crystal structure of the RT-EFV complex, exhibit a reduced level of exchange in monomer-EFV complexes. Moreover, peptide 232-246 undergoes slow cooperative unfolding-refolding in the bound monomers, but at a rate much slower than that observed in the p66 subunit of the RT heterodimer [Seckler, J. M., Howard, K. J., Barkley, M. D., and Wintrode, P. L. (2009) Biochemistry 48, 7646-7655]. These results suggest that the efavirenz binding site on p66 and p51 monomers is similar to the NNRTI binding pocket in the p66 subunit of RT. Nanoelectrospray ionization FT-ICR mass spectra indicate that the intact monomers each have (at least) two different conformations. In the presence of efavirenz, the mass spectra change significantly and suggest that p51 adopts a single, more compact conformation, whereas p66 undergoes facile, electrospray-induced cleavage. The population shift is consistent with a selected-fit binding mechanism.

Blackbody infrared radiative dissociation of bradykinin and its analogues: energetics, dynamics, and evidence for salt-bridge structures in the gas phase

Blackbody infrared radiative dissociation (BIRD) spectra of singly and doubly protonated bradykinin and its analogues are measured in a Fourier-transform mass spectrometer. Rate constants for dissociation are measured as a function of temperature with reaction delays up to 600 s. From these data, Arrhenius activation parameters in the zero-pressure limit are obtained. The activation parameters and dissociation products for the singly protonated ions are highly sensitive to small changes in ion structure. The Arrhenius activation energy (E(a)) and pre-exponential (or frequency factor, A) of the singly protonated ions investigated here range from 0.6 to 1.4 eV and 10(5) to 10(12) s(-1), respectively. For bradykinin and its analogues differing by modification of the residues between the two arginine groups on either end of the molecule, the singly and doubly protonated ions have average activation energies of 1.2 and 0.8 eV, respectively, and average A values of 10(8) and 10(12) s(-1), respectively, i.e., the presence of a second charge reduces the activation energy by 0.4 eV and decreases the A value by a factor of 10(4). This demonstrates that the presence of a second charge can dramatically influence the dissociation dynamics of these ions. The doubly protonated methyl ester of bradykinin has an E(a) of 0.82 eV, comparable to the value of 0.84 eV for bradykinin itself. However, this value is 0.21 +/- 0.08 eV greater than that of singly protonated methyl ester of bradykinin, indicating that the Coulomb repulsion is not the most significant factor in the activation energy of this ion. Both singly and doubly protonated Lys-bradykinin ions have higher activation energies than the corresponding bradykinin ions indicating that the addition of a basic residue stabilizes these ions with respect to dissociation. Methylation of the carboxylic acid group of the C-terminus reduces the E(a) of bradykinin from 1.3 to 0.6 eV and the A factor from 1012 to 105 s(-1). This modification also dramatically changes the dissociation products. Similar results are observed for [Ala(6)]-bradykinin and its methyl ester. These results, in combination with others presented here, provide experimental evidence that the most stable form of singly protonated bradykinin is a salt-bridge structure.

Binding energies of protonated betaine complexes: a probe of zwitterion structure in the gas phase

The dissociation kinetics of proton-bound dimers of betaine with molecules of comparable gas-phase basicity were investigated using blackbody infrared radiative dissociation (BIRD). Threshold dissociation energies were obtained from these data using master equation modeling. For bases that have comparable or higher gas-phase basicity, the binding energy of the protonated base.betaine complex is approximately 1.4 eV. For molecules that are approximately 2 kcal/mol or more less basic, the dissociation energy of the complexes is approximately 1.2 eV. The higher binding energy of the former is attributed to an ion-zwitterion structure which has a much larger ion-dipole interaction. The lower binding energy for molecules that are approximately 2 kcal/mol or more less basic indicates that an ion-molecule structure is more favored. Semiempirical calculations at both the AM1 and PM3 levels indicate the most stable ion-molecule structure is one in which the base interacts with the charged quaternary ammonium end of betaine. These results indicate that the measurement of binding energies of neutral molecules to biological ions could provide a useful probe for the presence of zwitterions and salt bridges in the gas phase. From the BIRD data, the gas-phase basicity of betaine obtained from the kinetic method is found to be 239.2 +/- 1.0 kcal/mol. This value is in excellent agreement with the value of 239.3 kcal/mol (298 K) from ab initio calculations at the MP2/6-31+g** level. The measured value is slightly higher than those reported previously. This difference is attributed to entropy effects. The lower ion internal energy and longer time frame of BIRD experiments should provide values closer to those at standard temperature.

Fragmentation of protonated dipeptides containing arginine. Effect of activation method

The fragmentation reactions of the protonated dipeptides Gly-Arg and Arg-Gly have been studied using collision-induced dissociation (CID) in a quadrupole ion trap, by in-source CID in a single-quadrupole mass spectrometer and by CID in the quadrupole cell of a QqTOF mass spectrometer. In agreement with earlier quadrupole ion trap studies (Farrugia, J. M.; O'Hair, R. A. J., Int. J. Mass Spectrom., 2003, 222, 229), the CID mass spectra obtained with the ion trap for the MH(+) ions and major fragment ions are very similar for the two isomers indicating rearrangement to a common structure before fragmentation. In contrast, in-source CID of the MH(+) ions and QqTOF CID of the MH(+), [MH - NH(3)](+) and [MH <23 HN = C(NH(2))(2)](+) ions provide distinctly different spectra for the isomeric dipeptides, indicating that rearrangement to a common structure has not occurred to a significant extent under these conditions even near the threshold for fragmentation in the QqTOF instrument. Clearly, under normal operating conditions significantly different fragmentation behavior is observed in the ion trap and beam-type experiments. This different behavior probably can be attributed to the shorter observation times and concomitant higher excitation energies in the in-source and QqTOF experiments compared to the long observation times and lower excitation energies relevant to the ion trap experiments. Based largely on elemental compositions derived from accurate mass measurements in QqTOF studies fragmentation schemes are proposed for the MH(+), [MH - NH(3)](+), and [MH - (HN = C(NH(2))(2))](+) ions.

Infrared Spectroscopy of Cationized Lysine and ε-N-methyllysine in the Gas Phase: Effects of Alkali-Metal Ion Size and Proton Affinity on Zwitterion Stability

The gas-phase structures of protonated and alkali-metal-cationized lysine (Lys) and epsilon-N-methyllysine (Lys(Me)) are investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, in conjunction with ab initio calculations. IRMPD spectra of Lys.Li(+) and Lys.Na(+) are similar, but the spectrum for Lys.K(+) is different, indicating that the structure of lysine in these complexes depends on the metal ion size. The carbonyl stretch of a carboxylic acid group is clearly observed in each of these spectra, indicating that lysine is nonzwitterionic in these complexes. A detailed comparison of these spectra to those calculated for candidate low-energy structures indicates that the bonding motif for the metal ion changes from tricoordinated for Li and Na to dicoordinated for K, clearly revealing the increased importance of hydrogen-bonding relative to metal ion solvation with increasing metal ion size. Spectra for Lys(Me).M(+) show that Lys(Me), an analogue of lysine whose side chain contains a secondary amine, is nonzwitterionic with Li and zwitterionic with K and both forms are present for Na. The proton affinity of Lys(Me) is 16 kJ/mol higher than that of Lys; the higher proton affinity of a secondary amine can result in its preferential protonation and stabilization of the zwitterionic form.

Carbohydrate Amino Acids: The Intrinsic Conformational Preference for a β-Turn-Type Structure in a Carbopeptoid Building Block

Infrared ion-dip spectroscopy coupled with DFT and ab initio calculations are used to establish the intrinsic conformational preference of the basic structural unit of a peptide mimic, a cis-tetrahydrofuran-based "carbopeptoid" (amide-sugar-amide), isolated at low temperature in the gas phase. The carbopeptoid units form a beta-turn-type structure, stabilized by an intramolecular NH --> O=C hydrogen bond across the sugar ring, thus forming a 10-membered, C10 turn. Despite the clear preference for C10 beta-turn structures in the basic unit, however, the presence of multiple hydrogen-bond donating and accepting groups also generates a rich conformational landscape, and alternative structures may be populated in related molecules. Calculations on an extended, carbopeptoid dimer unit, which includes an alternating amide-sugar-amide-sugar-amide chain, identify conformers exhibiting alternative hydrogen-bonding arrangements that are somewhat more stable than the lowest-energy double beta-turn forming conformer.

Building Up Key Segments of N-Glycans in the Gas Phase: Intrinsic Structural Preferences of the α(1,3) and α(1,6) Dimannosides

The intrinsic conformer specific vibrational spectra of two important subunits of the core pentasaccharide of N-linked glycans, the alpha(1,3) and alpha(1,6) dimannosides, have been recorded in the gas phase. Coupling these measurements with a computational exploration of their conformational landscapes has enabled their conformational assignment and has identified characteristic vibrational signatures associated with particular conformational families-including those that do or do not display inter-ring hydrogen bonding across the glycosidic linkage. In addition, the IR spectra of the monosaccharide moieties provide benchmarks, through which the conformational assignments can be refined. This introduces a general concept of modularity and secondary structure in oligosaccharides--essential for the success of similar studies on larger oligosaccharides in the future.

Hydrogen Bonding and Cooperativity in Isolated and Hydrated Sugars: Mannose, Galactose, Glucose, and Lactose

The conformation of phenyl-substituted monosaccharides (mannose, galactose, and glucose) and their singly hydrated complexes has been investigated in the gas phase by means of a combination of mass selected, conformer specific ultraviolet and infrared double resonance hole burning spectroscopy experiments, and ab initio quantum chemistry calculations. In each case, the water molecule inserts into the carbohydrate at a position where it can replace a weak intramolecular interaction by two stronger intermolecular hydrogen bonds. The insertion can produce significant changes in the conformational preferences of the carbohydrates, and there is a clear preference for structures where cooperative effects enhance the stability of the monosaccharide conformers to which the water molecule chooses to bind. The conclusions drawn from the study of monosaccharide-water complexes are extended to the disaccharide lactose and discussed in the light of the underlying mechanisms that may be involved in the binding of carbohydrate assemblies to proteins and the involvement, or not, of key structural water molecules.

Adding water to sugar: A spectroscopic and computational study of α- and β-phenylxyloside in the gas phase

The gas phase structures of phenyl alpha- and beta-d-xylopyranoside (alpha- and beta-pXyl) and their mono-hydrates have been investigated using a combination of resonant two-photon ionization (R2PI), ultra-violet hole-burning and resonant infrared ion dip spectroscopy, coupled with density functional theory (DFT) and ab initio computation. The hole-burning experiments indicate the population of a single conformer only, in each of the two anomers. Their experimental and calculated infrared spectra are both consistent with a conformational assignment corresponding to the computed global minimum configuration. All three OH groups are oriented towards the oxygen atom (O1) on the anomeric carbon atom to form an all trans(ttt) counter-clockwise chain of hydrogen bonds. The mono-hydrates, alpha- and beta-pXyl(H(2)O) each populate two distinct structures in the molecular beam environment, with the water molecule inserted between OH4 and OH3 or between OH3 and OH2 in alpha-pXyl(H2O), and between OH2 and O1 in either of two alternative orientations, in beta-pXyl(H2O). In all of the mono-hydrated xyloside complexes, the water molecule inserts into the weakest link of the sugar molecules' hydrogen-bonded chain of hydroxy groups, creating a single extended chain, strengthened by co-operativity. The all-trans configuration of the xylose moiety is retained and the mono-hydrate structures correspond to those calculated to lie at the lowest relative energies.

Probing the Glycosidic Linkage: UV and IR Ion-Dip Spectroscopy of a Lactoside

The beta(1-->4) glycosidic linkage found in lactose is a prevalent structural motif in many carbohydrates and glycoconjugates. Using UV and IR ion-dip spectroscopies to probe benzyl lactoside isolated in the gas phase, we find that the disaccharide unit adopts only a single, rigid structure. Its fully resolved infrared ion-dip spectrum is in excellent agreement with that of the global minimum structure computed ab initio. This has glycosidic torsion angles of phi(H) (H1-C1-O-C4') approximately 180 degrees and psi(H) (C1-O-C4'-H4') approximately 0 degrees which correspond to a rotation of approximately 150 degrees about the glycosidic bond compared to the accepted solution-phase conformation. We discuss the biological implications of this discovery and the generality of the strategies employed in making it.

Characterization of a novel gastropod toxin (6-bromo-2-mercaptotryptamine) that inhibits shaker K channel activity

A novel potassium channel antagonist has been purified from the defensive mucus secreted by Calliostoma canaliculatum, a marine snail found in the temperate coastal waters of the western Pacific. The toxin is expelled from the hypobranchial gland as part of a defensive response and is contained within a viscous matrix that minimizes dilution and degradation. The active compound was isolated by multistage microbore HPLC separations followed by bioactivity assays. Nuclear magnetic resonance, combined with electrospray ionization Fourier-transform ion cyclotron resonance and electrospray ionization ion trap mass spectrometry indicate that the active component is a heretofore unknown indole-derivative, a disulfide-linked dimer of 6-bromo-2-mercaptotryptamine (BrMT). Exudates from the hypobranchial glands of various marine mollusks have been sources for dye compounds such as 6-6 dibromoindigo, the ancient dye Tyrian purple. BrMT represents the first correlation of a hypobranchial gland exudate with a molecular response. Voltage clamp experiments with a number of K channel subtypes indicate that BrMT inhibits certain voltage-gated K channels of the Kv1 subfamily.