Thomas Wyttenbach - Academia.edu (original) (raw)
Papers by Thomas Wyttenbach
![Research paper thumbnail of Conformations of alkali ion cationized polyethers in the gas phase: polyethylene glycol and bis[(benzo-15-crown-5)-15-ylmethyl] pimelate](https://attachments.academia-assets.com/102153962/thumbnails/1.jpg)
](International Journal of Mass Spectrometry and Ion Processes, 1997
Ion chromatography/ion mobility methods are applied to two polyether systems cationized by alkali... more Ion chromatography/ion mobility methods are applied to two polyether systems cationized by alkali ions. MALDI is used to generate the ions in all cases. Polyethylene glycol (PEG) 600 is cationized by Li+ and Cs+ and compared to earlier work by von Helden et al. on Na+ cationized PEG 600. A very similar distribution is obtained in the MALDI spectrum of all three metals suggesting the true PEG 600 distribution is being observed. Each cation efficiently wraps the polymer around it, however, the detailed structure of the inner coordination sphere of ether oxygens around the metal ion is metal dependent. Both Li+ and Na+ prefer a near planar five-fold coordination sphere capped on top and bottom leading to seven-fold coordination (Li+) and eight-fold coordination (Na+). The much larger Cs+ prefers 11-fold coordination if sufficient oxygen centers are available. The second system studied is the interesting dicrown bis[(benzo-1.5~crown-5)-15ylmethyl] pimelate, or BBP. This tweezers-like molecule coordinates the metal ions primarily in folded, or sandwich, complexes where both rings are involved. Other structures that include metal coordination to one ring and a carbonyl oxygen (partially folded) and to one ring and no additional oxygens (unfolded) are observed in elevated temperature molecular dynamics simulations and are more important for small alkali ions (Li+> and essentially not important for large ions (Cs+). The AMBER 4.0 suite of programs is used for all calculations which in general are in excellent agreement with experiment. A quite detailed discussion of the folding dynamics of cationized BBP is presented.
Mol Phys, 1988
The laser excitation spectrum of the &(B)tilde;2π3/2←&(X)tilde;2π3/2 transition o... more The laser excitation spectrum of the &(B)tilde;2π3/2←&(X)tilde;2π3/2 transition of bromocyanogen cation in the 445-560 nm region is reported. On the basis of this the electronic origin of this transition is reassigned to 18 756·20(±0·01) and 18 759·79(±0·07)cm-1 for 79BrCN+ and 81BrCN+, respectively. Vibrational assignment of the spectrum leads to consistent values for ν3 (C-Br stretch) in the upper state. In addition, a double resonance technique (stimulated emission pumping) was employed to confirm the assignment for bands to the two isotopic bromine species, and enabled the ν3 frequency in the ground state to be determined. Tentative assignments are made of bands involving the Rennet-Teller split ν2 mode excited in both the upper and lower states. Rotationally resolved spectra are reported for the 0<span class="strikethrough">0/0</span>, 3<span class="strikethrough">0/1</span> and 3<span class="strikethrough">0/2</span> and 3<span class="strikethrough">0/1</span>2<span class="strikethrough">0/2</span> bands. Analysis of these bands yields values for the ground state rotational constants. The rotational parameters determined for the different vibronic levels in the upper &(B)tilde;2π3/2 electronic state suggest that some of the levels are perturbed.
International Journal of Mass Spectrometry and Ion Processes, 1997
Matrix assisted laser desorption ionization (MALDI) was used to generate sodiated parent ions of ... more Matrix assisted laser desorption ionization (MALDI) was used to generate sodiated parent ions of a number of oligosaccharides, including three tetraoses and two hexaoses. No fragmentation was observed in any of the systems. Ion mobility studies yielded gas phase cross sections which could be compared with predictions made by molecular mechanics/molecular dynamics calculations. In all three tetraoses (celiotetraose, maltotetraose and isomahotetraose) the Na + ion coordinated with all four sugar moities forming very similar structures even though the neutral structures are very different. In the two hexaose systems (ct-cyclodextrin and maltohexaose) again the Na + ion coordinated with four sugars. Molecular dynamics studies indicated that at temperatures above 300 K the Na + ion was mobile and sampled all six sugars of the hexaoses. This work is compared to other work in the literature, and differences are discussed.
International Journal of Mass Spectrometry and Ion Processes, 1990
A design for a new Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR) is presen... more A design for a new Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR) is presented. The FT-ICR consists of two differentially pumped vacuum chambers, one housing two Newport pulsed valves, the other housing a 2 in cubic ICR cell which employs an IonSpec FTMS 2000 electronics console for detection. The combination of pulsed valves and an excimer-pumped dye laser permits the formation of vibrationally state-selected ions via resonance-enhanced multiphoton ionization in the absence of relaxing collisions. Experiments are presented which demonstrate that the state-selected ions exist at near-thermal translational energies and sub-thermal rotational energies. Data are presented illustrating the capabilities of this instrument for the measurement of long-lived electronic and vibrational state radiative lifetimes, as well as the reactivity of vibrationally state-selected NO ÷ (X ~ Z ÷ ,v = 0, 1, 2, 3) with a number of neutral substrate molecules.
Faraday Discussions of the Chemical Society, 1988
ABSTRACT The application of the techniques of matrix-absorption, laser-excitation and laser-absor... more ABSTRACT The application of the techniques of matrix-absorption, laser-excitation and laser-absorption spectroscopies of mass-selected ion beams to the study of small open-shell cations at reduced temperatures is described. The spectroscopic characterization of the B 4Σ–uâ†� X 4Σ–g transition of C+2 was carried out first in a neon matrix, then at high-resolution using laser-excitation spectroscopy. Two-photon ion-absorption experiments which are being developed to characterize cations spectroscopically are demonstrated on N2O+. The instrument used is a triple-quadrupole mass spectrometer designed to select primary ions, constrain them for photon absorption and to detect fragment ions.
Energetics of Stable Molecules and Reactive Intermediates, 1999
In this paper a number of methods for determining thermochemical data for gas phase ions are desc... more In this paper a number of methods for determining thermochemical data for gas phase ions are described. Of most importance are ion equilibrium measurements where emphasis is placed on the differences in our work from earlier studies. Most of the paper is devoted to novel applications. These emphasize transition metal centers, the roles ligands play in activating them, and the very subtle interplay between the nearly degenerate s and d orbitals. A case study of sequential ligation by dihydrogen of the entire first transition metal series is given. Generally the first solvation sphere closes at n = 6 but interesting exceptions are noted. High level ab initio calculations are done on each system allowing structural information and details of the bonding to be obtained. Other systems discussed include a few second row metals, the role of the Cp ligand in activating Co+ and the discussion of a novel cluster assisted σ-bond activation scheme. The paper concludes with a demonstration that the structurally important ion chromatography technique can be used to extract thermochemical information on macromolecules under favorable conditions.
Annual review of physical chemistry, 2014
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-... more The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.
The Journal of Physical Chemistry B, 2008
The aggregation of α-synuclein (α-syn), a protein implicated in Parkinson's disease (PD), is beli... more The aggregation of α-synuclein (α-syn), a protein implicated in Parkinson's disease (PD), is believed to progress through the formation of a partially folded intermediate. Using nano-electrospray ionization (ESI) mass spectrometry combined with ion mobility measurements we found evidence for a highly compact partially folded family of structures for α-syn and its disease-related A53T mutant with net charges of −6, −7 and −8. For the other early-onset PD mutant, A30P, this highly compact population was only evident when the protein had a net charge of −6. When bound to spermine near physiologic pH, all three proteins underwent a charge reduction from the favored solution charge state of −10 to a net charge of −6. This charge reduction is accompanied by a dramatic size reduction of about a factor of two (cross section of 2600Å 2 (−10 charge state) down to 1430Å 2 (−6 charge state)). We conclude that spermine increases the aggregation rate of α-syn by inducing a collapsed conformation, which then proceeds to form aggregates.
The Journal of Physical Chemistry B, 2010
A combination of ion mobility and mass spectrometry methods was used to characterize the molecula... more A combination of ion mobility and mass spectrometry methods was used to characterize the molecular shape of the protein calmodulin (CaM) and its complexes with calcium and a number of peptide ligands. CaM, a calcium-binding protein composed of 148 amino acid residues, was found by X-ray crystallography to occur both in a globular shape and in the shape of an extended dumbbell. Here, it was found, as solutions of CaM and CaM complexes were sprayed into the solvent-free environment of the mass spectrometer, that major structural features of the molecule and the stoichiometry of the units constituting a complex in solution were preserved in the desolvation process. Two types of CaM structures were observed in our experiments: a compact and an extended form of CaM with measured cross sections in near-perfect agreement with those calculated for the known globular and extended dumbbell X-ray geometries. Calcium-free solutions yielded predominantly an extended CaM conformation. Ca n 2+-CaM complexes were observed in calcium-containing solutions, n) 0-4, with the population of the compact conformation increasing relative to the elongated conformation as n increases. For n) 4, a predominantly compact globular conformation was observed. Solutions containing the peptide CaMKII 290-309 , the CaM target domain of the Ca 2+ /calmodulin-dependent protein kinase II (CaMKII) enzyme, yielded predominantly globular Ca 4 2+-CaM-CaMKII 290-309 complexes. Similar results were obtained with the 26-residue peptide melittin. For the 14-residue C-terminal melittin fragment, on the other hand, formation of both a 1:1 and a 1:2 CaM-peptide complex was detected. On the basis of the entirety of our results, we conclude that the collapse of extended (dumbbell-like) CaM structures into more compact globular structures occurs upon specific binding of four calcium ions. Furthermore, this calcium-induced structural collapse of CaM appears to be a prerequisite for formation of a particularly stable CaM-peptide complex involving peptides long enough to be engaged in interactions with both lobes of CaM.
The Journal of Physical Chemistry B, 2009
Using a mass spectrometer equipped with a drift cell, water binding energies of protonated argini... more Using a mass spectrometer equipped with a drift cell, water binding energies of protonated arginine (ArgH +) and protonated lysine (LysH +) were determined in equilibrium experiments and supplementary calculations at the B3LYP/6-311++G** level of theory. The binding energy of the first water molecule was measured to be 10.3 and 10.9 kcal/mol for ArgH + and LysH + , respectively. Water binding energies decrease with increasing degree of hydration reaching values of 6-7 kcal/mol for the fourth and fifth water molecule. Theory reproduces this trend of decreasing binding energies correctly and theoretical water binding energies agree with experiment quantitatively within 2 kcal/mol. Lowest-energy theoretical structures of ArgH + and LysH + are characterized by protonated side chains and neutral R-amino and carboxyl groups which form intramolecular hydrogen bonds to the ionic group (charge solvation or CS structures). The salt bridge (SB) structures with two cationic groups (side chain and R-amine) and one anionic group (carboxyl) are 13.1 and 9.3 kcal/mol higher in energy for ArgH + and LysH + , respectively. Theory indicated that the first water molecule binds to the ionic group of the CS structures of ArgH + and LysH +. With increasing degree of hydration intramolecular interactions are replaced one by one with water bridges with water inserted into the intramolecular hydrogen bonds. Whereas the global minima of ArgH + • (H 2 O) n and LysH + • (H 2 O) n , n < 7, were calculated to represent CS structures, 7-fold hydrated CS and SB structures, ArgH + • (H 2 O) 7 and LysH + • (H 2 O) 7 , are nearly isoenergetic (within <1 kcal/mol).
The Journal of Physical Chemistry B, 2009
The structure of the 21-30 fragment of the amyloid β-protein (Aβ) was investigated by ion-mobilit... more The structure of the 21-30 fragment of the amyloid β-protein (Aβ) was investigated by ion-mobility mass spectrometry and replica exchange dynamics simulations. Mutations associated with familial Alzheimer's disease (E22G, E22Q, E22K, and D23N) of Aβ(21-30) were also studied, in order to understand any structural changes that might occur with these substitutions. The structure of the WT peptide shows a bend and a perpendicular turn in the backbone which is maintained by a network of D23 hydrogen bonding. Results for the mutants show that substitutions at E22 do little to alter the overall structure of the fragment. A substitution at D23 resulted in a change of structure for Aβ (21-30). A comparison of these gas-phase studies to previous solution-phase studies reveals that the peptide can fold in the absence of solvent to a structure also seen in solution, highlighting the important role of the D23 hydrogen bonding network in stabilizing the fragment's folded structure.
The Journal of Physical Chemistry A, 2009
The gas-phase structures of a series of potassiated tertiary amino acids have been systematically... more The gas-phase structures of a series of potassiated tertiary amino acids have been systematically investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, ion mobility spectrometry (IMS), and computational modeling. The examined analytes comprise a set of five linear N,N-dimethyl amino acids derived from N,N-dimethyl glycine and three cyclic N-methyl amino acids including N-methyl proline. The number of methylene groups in either the alkyl chain of the linear members or in the ring of the cyclic members of the series is gradually varied. The spectra of the cyclic potassiated molecular ions are similar and well resolved, whereas the clear signals in the respective spectra of the linear analytes increasingly overlap with longer alkyl chains. Measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311++G(2d,2p) level of theory to identify the structures present in the experimental studies. On the basis of these experiments and calculations, all potassiated molecular ions of this series adopt salt bridge structures in the gas phase, involving bidentate coordination of the potassium cation to the carboxylate moiety. The assigned salt bridge structures are predicted to be the global minima on the potential energy surfaces. IMS cross-section measurements of the potassiated systems show a monotonic increase with growing system size, suggesting that the precursor ions adopt the same type of structure and comparisons between experimental and theoretical cross sections are consistent with salt bridge structures and the IRMPD results.
Protein Science, 2006
The structural properties of the Ab42 peptide, a main constituent of the amyloid plaques formed i... more The structural properties of the Ab42 peptide, a main constituent of the amyloid plaques formed in Alzheimer's disease, were investigated through a combination of ion-mobility mass spectrometry and theoretical modeling. Replica exchange molecular dynamics simulations using a fully atomic description of the peptide and implicit water solvent were performed on the-3 charge state of the peptide, its preferred state under experimental conditions. Equilibrated structures at 300 K were clustered into three distinct families with similar structural features within a family and with significant root mean square deviations between families. An analysis of secondary structure indicates the Ab42 peptide conformations are dominated by loops and turns but show some helical structure in the C-terminal hydrophobic tail. A second calculation on Ab42 in a solvent-free environment yields compact structures turned "inside out" from the solution structures (hydrophobic parts on the outside, polar parts on the inside). Ion mobility experiments on the Ab42-3 charge state electrosprayed from solution yield a bimodal arrival time distribution. This distribution can be quantitatively fit using cross-sections from dehydrated forms of the three families of calculated solution structures and the calculated solvent-free family of structures. Implications of the calculations on the early stages of aggregation of Ab42 are discussed.
Physical Chemistry Chemical Physics, 2008
Nature Chemistry, 2009
In recent years, small protein oligomers have been implicated in the aetiology of a number of imp... more In recent years, small protein oligomers have been implicated in the aetiology of a number of important amyloid diseases, such as type 2 diabetes, Parkinson's disease and Alzheimer's disease. As a consequence, research efforts are being directed away from traditional targets, such as amyloid plaques, and towards characterization of early oligomer states. Here we present a new analysis method, ion mobility coupled with mass spectrometry, for this challenging problem, which allows determination of in vitro oligomer distributions and the qualitative structure of each of the aggregates. We applied these methods to a number of the amyloid-b protein isoforms of Ab40 and Ab42 and showed that their oligomer-size distributions are very different. Our results are consistent with previous observations that Ab40 and Ab42 self-assemble via different pathways and provide a candidate in the Ab42 dodecamer for the primary toxic species in Alzheimer's disease. M any diseases share the common trait of peptide-protein misfolding that leads to oligomerization and, eventually, formation of plaques of b-sheet structure. Prominent among these are type 2 diabetes 1 , Parkinson's disease 2 and Alzheimer's disease 3,4. Of these, Alzheimer's disease is the leading cause of late-life dementia and is the focus of this paper. An increasing body of evidence links oligomerization of a ubiquitous peptide, the amyloid-b protein, to disease causation 3-6. For this reason, elucidation of pathways of oligomer formation may be critical for the identification of therapeutic targets. Many types of oligomeric amyloid-b assemblies have been described (for a review, see Lazo et al. 7). Recently, Bitan et al. 8-10 used photoinduced cross-linking of unmodified proteins (PICUP) to reveal that the 42-residue form of amyloid-b, Ab42, formed (Ab42) 5 and (Ab42) 6 oligomers ('paranuclei') that could oligomerize to form structures of higher order. Ab40 did not form paranuclei, but instead existed as a mixture of monomers, dimers, trimers and tetramers. Chen and Glabe 11 , in contrast, used fluorescence and gel electrophoresis to determine oligomer states of amyloid-b refolded from denaturing solutions. They observed only Ab42 monomer and trimer bands, and no oligomers of Ab40. Differences such as these may exist because of the diverse experimental systems used to monitor amyloid-b self-association. Also, it has been argued that, in addition to the intrinsic potential of amyloid-b to traverse different assembly pathways, flaws in experimental design may have misled researchers in their quest to elucidate fully the amyloid-b oligomerization process 12. Hence there is significant uncertainty about amyloid-b oligomer states and their position and relevance to amyloid-b aggregation.
Journal of the American Society for Mass Spectrometry, 2004
The protein ␣-synuclein, implicated in Parkinson's disease, was studied by combining nano-electro... more The protein ␣-synuclein, implicated in Parkinson's disease, was studied by combining nano-electrospray ionization (N-ESI) mass spectrometry and ion mobility. It was found that both the charge-state distribution in the mass spectra and the average protein shape deduced from ion mobility data, depend on the pH of the spray solution. Negative-ion N-ESI of pH 7 solutions yielded a broad charge-state distribution from Ϫ6 to Ϫ16, centered at Ϫ11, and ion mobility data consistent with extended protein structures. Data obtained for pH 2.5 solutions, on the other hand, showed a narrow charge-state distribution from Ϫ6 to Ϫ11, centered at Ϫ8, and ion mobilities in agreement with compact ␣-synuclein structures. The data indicated that there are two distinct families of structures: one consisting of relatively compact proteins with eight or less negative charges and one consisting of relatively extended structures with nine or more charges. The average cross section of a-synuclein at pH 2.5 is 33% smaller than for the extended protein sprayed from pH 7 solution. Significant dimer formation was observed when sprayed from pH 7 solution but no dimers were observed from the low pH solution. A plausible mechanism for aggregate formation in solution is proposed.
Journal of the American Society for Mass Spectrometry, 1999
In this article the folding dynamics and energetics for a set of poly(ethylene terephthalate) (PE... more In this article the folding dynamics and energetics for a set of poly(ethylene terephthalate) (PET) oligomers cationized by various alkali ions are studied: M ϩ PETn for n ϭ 2 to 7 and M ϭ Li, Na, and K. Experimental cross sections were determined for matrix-assisted laser desorption/ionization (MALDI) generated ions using the ion mobility based ion chromatography method. Very good agreement was obtained with cross sections generated by the amber 4.0 suite of molecular dynamics programs. For n ϭ 2 and 4 the benzene rings of the oligomers stack with the metal ion coordinated to both terminal hydroxyl oxygen atoms and several of the nearby carbonyl oxygen atoms. For n ϭ 3, two isomers are both observed and predicted by theory: an open form where the third PET monomer attaches to the dimer and extends into space and a closed form where the third PET moiety bends back and coordinates its hydroxyl oxygen with the metal ion. For Na ϩ PET3, equilibrium is observed between 100 and 180 K with an Arrhenius analysis yielding an open to closed form isomerization barrier of 1.6 kcal/mol. For this same system the two isomeric forms are frozen out at 80 K and coupling the observed isomeric distribution with an RRKM analysis indicates the closed form is more stable by 0.5 kcal/mol. For K ϩ PET3 the barrier to isomerization is too low to observe (Ͻ1.0 kcal/mol), whereas for Li ϩ PET3 a temperature independent isomer distribution is observed (80 to 55°K). Using methods developed for determining isomerization barriers in carbon clusters it was possible to obtain an open to closed form isomerization barrier of 7 Ϯ 2 kcal/mol for Li ϩ PET3. In this system, the open and closed form isomer populations were observed to be strong functions of the laser power in the MALDI source. This allowed a detailed description of the formation mechanism to be formulated and indicated alkali ion attachment to the polymer during expansion of the plume emanating from the surface. Finally, the mass spectrum of a PET oligomer sample has been shown to strongly depend on the cationizing alkali metal ion. It is qualitatively shown that M ϩ-PETn binding energies and structures are responsible.
Journal of the American Chemical Society, 1995
Crown ethers have been intensely studied since their initial characterization nearly 30 years ago... more Crown ethers have been intensely studied since their initial characterization nearly 30 years ago.' Much of the interest stems from their ability to selectively complex cations in solution2 and consequently act either as cleansing agents for unwanted or dangerous ionic contaminants3 or as possible delivery agents for transporting ionic species to specific binding sites in living tissue^.^ The prototypical systems are alkali ion
Journal of the American Chemical Society, 2008
Journal of the American Chemical Society, 2009
The first steps of hydration of the protonated aromatic amino acids phenylalanine, tryptophan, an... more The first steps of hydration of the protonated aromatic amino acids phenylalanine, tryptophan, and tyrosine were studied experimentally employing a mass spectrometer equipped with a drift cell to examine the sequential addition of individual water molecules in equilibrium experiments and theoretically by a combination of molecular mechanics and electronic structure calculations (B3LYP/6-311++G**) on the three amino acid systems including up to five water molecules. It is found that both the ammonium and carboxyl groups offer good water binding sites with binding energies of the order of 13 kcal/mol for the first water molecule. Subsequent water molecules bind less strongly, in the range of 7-11 kcal/mol for the second through fifth water molecules. The ammonium group is able to host up to three water molecules and the carboxyl group one water molecule before additional water molecules bind either to the amino acid side chain as in tyrosine or to already-bound water in a second solvation shell around the ammonium group. Reasons for the surprisingly high water affinity of the neutral carboxyl group, comparable to that of the charge-carrying ammonium group, are found to be high intrinsic hydrophilicity, favorable charge-dipole alignment, and s for the case of multiply hydrated species s favorable dipole-dipole interaction among water molecules and the lack of alternative fully exposed hydration sites.
International Journal of Mass Spectrometry and Ion Processes, 1997
Ion chromatography/ion mobility methods are applied to two polyether systems cationized by alkali... more Ion chromatography/ion mobility methods are applied to two polyether systems cationized by alkali ions. MALDI is used to generate the ions in all cases. Polyethylene glycol (PEG) 600 is cationized by Li+ and Cs+ and compared to earlier work by von Helden et al. on Na+ cationized PEG 600. A very similar distribution is obtained in the MALDI spectrum of all three metals suggesting the true PEG 600 distribution is being observed. Each cation efficiently wraps the polymer around it, however, the detailed structure of the inner coordination sphere of ether oxygens around the metal ion is metal dependent. Both Li+ and Na+ prefer a near planar five-fold coordination sphere capped on top and bottom leading to seven-fold coordination (Li+) and eight-fold coordination (Na+). The much larger Cs+ prefers 11-fold coordination if sufficient oxygen centers are available. The second system studied is the interesting dicrown bis[(benzo-1.5~crown-5)-15ylmethyl] pimelate, or BBP. This tweezers-like molecule coordinates the metal ions primarily in folded, or sandwich, complexes where both rings are involved. Other structures that include metal coordination to one ring and a carbonyl oxygen (partially folded) and to one ring and no additional oxygens (unfolded) are observed in elevated temperature molecular dynamics simulations and are more important for small alkali ions (Li+> and essentially not important for large ions (Cs+). The AMBER 4.0 suite of programs is used for all calculations which in general are in excellent agreement with experiment. A quite detailed discussion of the folding dynamics of cationized BBP is presented.
Mol Phys, 1988
The laser excitation spectrum of the &(B)tilde;2π3/2←&(X)tilde;2π3/2 transition o... more The laser excitation spectrum of the &(B)tilde;2π3/2←&(X)tilde;2π3/2 transition of bromocyanogen cation in the 445-560 nm region is reported. On the basis of this the electronic origin of this transition is reassigned to 18 756·20(±0·01) and 18 759·79(±0·07)cm-1 for 79BrCN+ and 81BrCN+, respectively. Vibrational assignment of the spectrum leads to consistent values for ν3 (C-Br stretch) in the upper state. In addition, a double resonance technique (stimulated emission pumping) was employed to confirm the assignment for bands to the two isotopic bromine species, and enabled the ν3 frequency in the ground state to be determined. Tentative assignments are made of bands involving the Rennet-Teller split ν2 mode excited in both the upper and lower states. Rotationally resolved spectra are reported for the 0<span class="strikethrough">0/0</span>, 3<span class="strikethrough">0/1</span> and 3<span class="strikethrough">0/2</span> and 3<span class="strikethrough">0/1</span>2<span class="strikethrough">0/2</span> bands. Analysis of these bands yields values for the ground state rotational constants. The rotational parameters determined for the different vibronic levels in the upper &(B)tilde;2π3/2 electronic state suggest that some of the levels are perturbed.
International Journal of Mass Spectrometry and Ion Processes, 1997
Matrix assisted laser desorption ionization (MALDI) was used to generate sodiated parent ions of ... more Matrix assisted laser desorption ionization (MALDI) was used to generate sodiated parent ions of a number of oligosaccharides, including three tetraoses and two hexaoses. No fragmentation was observed in any of the systems. Ion mobility studies yielded gas phase cross sections which could be compared with predictions made by molecular mechanics/molecular dynamics calculations. In all three tetraoses (celiotetraose, maltotetraose and isomahotetraose) the Na + ion coordinated with all four sugar moities forming very similar structures even though the neutral structures are very different. In the two hexaose systems (ct-cyclodextrin and maltohexaose) again the Na + ion coordinated with four sugars. Molecular dynamics studies indicated that at temperatures above 300 K the Na + ion was mobile and sampled all six sugars of the hexaoses. This work is compared to other work in the literature, and differences are discussed.
International Journal of Mass Spectrometry and Ion Processes, 1990
A design for a new Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR) is presen... more A design for a new Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICR) is presented. The FT-ICR consists of two differentially pumped vacuum chambers, one housing two Newport pulsed valves, the other housing a 2 in cubic ICR cell which employs an IonSpec FTMS 2000 electronics console for detection. The combination of pulsed valves and an excimer-pumped dye laser permits the formation of vibrationally state-selected ions via resonance-enhanced multiphoton ionization in the absence of relaxing collisions. Experiments are presented which demonstrate that the state-selected ions exist at near-thermal translational energies and sub-thermal rotational energies. Data are presented illustrating the capabilities of this instrument for the measurement of long-lived electronic and vibrational state radiative lifetimes, as well as the reactivity of vibrationally state-selected NO ÷ (X ~ Z ÷ ,v = 0, 1, 2, 3) with a number of neutral substrate molecules.
Faraday Discussions of the Chemical Society, 1988
ABSTRACT The application of the techniques of matrix-absorption, laser-excitation and laser-absor... more ABSTRACT The application of the techniques of matrix-absorption, laser-excitation and laser-absorption spectroscopies of mass-selected ion beams to the study of small open-shell cations at reduced temperatures is described. The spectroscopic characterization of the B 4Σ–uâ†� X 4Σ–g transition of C+2 was carried out first in a neon matrix, then at high-resolution using laser-excitation spectroscopy. Two-photon ion-absorption experiments which are being developed to characterize cations spectroscopically are demonstrated on N2O+. The instrument used is a triple-quadrupole mass spectrometer designed to select primary ions, constrain them for photon absorption and to detect fragment ions.
Energetics of Stable Molecules and Reactive Intermediates, 1999
In this paper a number of methods for determining thermochemical data for gas phase ions are desc... more In this paper a number of methods for determining thermochemical data for gas phase ions are described. Of most importance are ion equilibrium measurements where emphasis is placed on the differences in our work from earlier studies. Most of the paper is devoted to novel applications. These emphasize transition metal centers, the roles ligands play in activating them, and the very subtle interplay between the nearly degenerate s and d orbitals. A case study of sequential ligation by dihydrogen of the entire first transition metal series is given. Generally the first solvation sphere closes at n = 6 but interesting exceptions are noted. High level ab initio calculations are done on each system allowing structural information and details of the bonding to be obtained. Other systems discussed include a few second row metals, the role of the Cp ligand in activating Co+ and the discussion of a novel cluster assisted σ-bond activation scheme. The paper concludes with a demonstration that the structurally important ion chromatography technique can be used to extract thermochemical information on macromolecules under favorable conditions.
Annual review of physical chemistry, 2014
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-... more The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.
The Journal of Physical Chemistry B, 2008
The aggregation of α-synuclein (α-syn), a protein implicated in Parkinson's disease (PD), is beli... more The aggregation of α-synuclein (α-syn), a protein implicated in Parkinson's disease (PD), is believed to progress through the formation of a partially folded intermediate. Using nano-electrospray ionization (ESI) mass spectrometry combined with ion mobility measurements we found evidence for a highly compact partially folded family of structures for α-syn and its disease-related A53T mutant with net charges of −6, −7 and −8. For the other early-onset PD mutant, A30P, this highly compact population was only evident when the protein had a net charge of −6. When bound to spermine near physiologic pH, all three proteins underwent a charge reduction from the favored solution charge state of −10 to a net charge of −6. This charge reduction is accompanied by a dramatic size reduction of about a factor of two (cross section of 2600Å 2 (−10 charge state) down to 1430Å 2 (−6 charge state)). We conclude that spermine increases the aggregation rate of α-syn by inducing a collapsed conformation, which then proceeds to form aggregates.
The Journal of Physical Chemistry B, 2010
A combination of ion mobility and mass spectrometry methods was used to characterize the molecula... more A combination of ion mobility and mass spectrometry methods was used to characterize the molecular shape of the protein calmodulin (CaM) and its complexes with calcium and a number of peptide ligands. CaM, a calcium-binding protein composed of 148 amino acid residues, was found by X-ray crystallography to occur both in a globular shape and in the shape of an extended dumbbell. Here, it was found, as solutions of CaM and CaM complexes were sprayed into the solvent-free environment of the mass spectrometer, that major structural features of the molecule and the stoichiometry of the units constituting a complex in solution were preserved in the desolvation process. Two types of CaM structures were observed in our experiments: a compact and an extended form of CaM with measured cross sections in near-perfect agreement with those calculated for the known globular and extended dumbbell X-ray geometries. Calcium-free solutions yielded predominantly an extended CaM conformation. Ca n 2+-CaM complexes were observed in calcium-containing solutions, n) 0-4, with the population of the compact conformation increasing relative to the elongated conformation as n increases. For n) 4, a predominantly compact globular conformation was observed. Solutions containing the peptide CaMKII 290-309 , the CaM target domain of the Ca 2+ /calmodulin-dependent protein kinase II (CaMKII) enzyme, yielded predominantly globular Ca 4 2+-CaM-CaMKII 290-309 complexes. Similar results were obtained with the 26-residue peptide melittin. For the 14-residue C-terminal melittin fragment, on the other hand, formation of both a 1:1 and a 1:2 CaM-peptide complex was detected. On the basis of the entirety of our results, we conclude that the collapse of extended (dumbbell-like) CaM structures into more compact globular structures occurs upon specific binding of four calcium ions. Furthermore, this calcium-induced structural collapse of CaM appears to be a prerequisite for formation of a particularly stable CaM-peptide complex involving peptides long enough to be engaged in interactions with both lobes of CaM.
The Journal of Physical Chemistry B, 2009
Using a mass spectrometer equipped with a drift cell, water binding energies of protonated argini... more Using a mass spectrometer equipped with a drift cell, water binding energies of protonated arginine (ArgH +) and protonated lysine (LysH +) were determined in equilibrium experiments and supplementary calculations at the B3LYP/6-311++G** level of theory. The binding energy of the first water molecule was measured to be 10.3 and 10.9 kcal/mol for ArgH + and LysH + , respectively. Water binding energies decrease with increasing degree of hydration reaching values of 6-7 kcal/mol for the fourth and fifth water molecule. Theory reproduces this trend of decreasing binding energies correctly and theoretical water binding energies agree with experiment quantitatively within 2 kcal/mol. Lowest-energy theoretical structures of ArgH + and LysH + are characterized by protonated side chains and neutral R-amino and carboxyl groups which form intramolecular hydrogen bonds to the ionic group (charge solvation or CS structures). The salt bridge (SB) structures with two cationic groups (side chain and R-amine) and one anionic group (carboxyl) are 13.1 and 9.3 kcal/mol higher in energy for ArgH + and LysH + , respectively. Theory indicated that the first water molecule binds to the ionic group of the CS structures of ArgH + and LysH +. With increasing degree of hydration intramolecular interactions are replaced one by one with water bridges with water inserted into the intramolecular hydrogen bonds. Whereas the global minima of ArgH + • (H 2 O) n and LysH + • (H 2 O) n , n < 7, were calculated to represent CS structures, 7-fold hydrated CS and SB structures, ArgH + • (H 2 O) 7 and LysH + • (H 2 O) 7 , are nearly isoenergetic (within <1 kcal/mol).
The Journal of Physical Chemistry B, 2009
The structure of the 21-30 fragment of the amyloid β-protein (Aβ) was investigated by ion-mobilit... more The structure of the 21-30 fragment of the amyloid β-protein (Aβ) was investigated by ion-mobility mass spectrometry and replica exchange dynamics simulations. Mutations associated with familial Alzheimer's disease (E22G, E22Q, E22K, and D23N) of Aβ(21-30) were also studied, in order to understand any structural changes that might occur with these substitutions. The structure of the WT peptide shows a bend and a perpendicular turn in the backbone which is maintained by a network of D23 hydrogen bonding. Results for the mutants show that substitutions at E22 do little to alter the overall structure of the fragment. A substitution at D23 resulted in a change of structure for Aβ (21-30). A comparison of these gas-phase studies to previous solution-phase studies reveals that the peptide can fold in the absence of solvent to a structure also seen in solution, highlighting the important role of the D23 hydrogen bonding network in stabilizing the fragment's folded structure.
The Journal of Physical Chemistry A, 2009
The gas-phase structures of a series of potassiated tertiary amino acids have been systematically... more The gas-phase structures of a series of potassiated tertiary amino acids have been systematically investigated using infrared multiple photon dissociation (IRMPD) spectroscopy utilizing light generated by a free electron laser, ion mobility spectrometry (IMS), and computational modeling. The examined analytes comprise a set of five linear N,N-dimethyl amino acids derived from N,N-dimethyl glycine and three cyclic N-methyl amino acids including N-methyl proline. The number of methylene groups in either the alkyl chain of the linear members or in the ring of the cyclic members of the series is gradually varied. The spectra of the cyclic potassiated molecular ions are similar and well resolved, whereas the clear signals in the respective spectra of the linear analytes increasingly overlap with longer alkyl chains. Measured IRMPD spectra are compared to spectra calculated at the B3LYP/6-311++G(2d,2p) level of theory to identify the structures present in the experimental studies. On the basis of these experiments and calculations, all potassiated molecular ions of this series adopt salt bridge structures in the gas phase, involving bidentate coordination of the potassium cation to the carboxylate moiety. The assigned salt bridge structures are predicted to be the global minima on the potential energy surfaces. IMS cross-section measurements of the potassiated systems show a monotonic increase with growing system size, suggesting that the precursor ions adopt the same type of structure and comparisons between experimental and theoretical cross sections are consistent with salt bridge structures and the IRMPD results.
Protein Science, 2006
The structural properties of the Ab42 peptide, a main constituent of the amyloid plaques formed i... more The structural properties of the Ab42 peptide, a main constituent of the amyloid plaques formed in Alzheimer's disease, were investigated through a combination of ion-mobility mass spectrometry and theoretical modeling. Replica exchange molecular dynamics simulations using a fully atomic description of the peptide and implicit water solvent were performed on the-3 charge state of the peptide, its preferred state under experimental conditions. Equilibrated structures at 300 K were clustered into three distinct families with similar structural features within a family and with significant root mean square deviations between families. An analysis of secondary structure indicates the Ab42 peptide conformations are dominated by loops and turns but show some helical structure in the C-terminal hydrophobic tail. A second calculation on Ab42 in a solvent-free environment yields compact structures turned "inside out" from the solution structures (hydrophobic parts on the outside, polar parts on the inside). Ion mobility experiments on the Ab42-3 charge state electrosprayed from solution yield a bimodal arrival time distribution. This distribution can be quantitatively fit using cross-sections from dehydrated forms of the three families of calculated solution structures and the calculated solvent-free family of structures. Implications of the calculations on the early stages of aggregation of Ab42 are discussed.
Physical Chemistry Chemical Physics, 2008
Nature Chemistry, 2009
In recent years, small protein oligomers have been implicated in the aetiology of a number of imp... more In recent years, small protein oligomers have been implicated in the aetiology of a number of important amyloid diseases, such as type 2 diabetes, Parkinson's disease and Alzheimer's disease. As a consequence, research efforts are being directed away from traditional targets, such as amyloid plaques, and towards characterization of early oligomer states. Here we present a new analysis method, ion mobility coupled with mass spectrometry, for this challenging problem, which allows determination of in vitro oligomer distributions and the qualitative structure of each of the aggregates. We applied these methods to a number of the amyloid-b protein isoforms of Ab40 and Ab42 and showed that their oligomer-size distributions are very different. Our results are consistent with previous observations that Ab40 and Ab42 self-assemble via different pathways and provide a candidate in the Ab42 dodecamer for the primary toxic species in Alzheimer's disease. M any diseases share the common trait of peptide-protein misfolding that leads to oligomerization and, eventually, formation of plaques of b-sheet structure. Prominent among these are type 2 diabetes 1 , Parkinson's disease 2 and Alzheimer's disease 3,4. Of these, Alzheimer's disease is the leading cause of late-life dementia and is the focus of this paper. An increasing body of evidence links oligomerization of a ubiquitous peptide, the amyloid-b protein, to disease causation 3-6. For this reason, elucidation of pathways of oligomer formation may be critical for the identification of therapeutic targets. Many types of oligomeric amyloid-b assemblies have been described (for a review, see Lazo et al. 7). Recently, Bitan et al. 8-10 used photoinduced cross-linking of unmodified proteins (PICUP) to reveal that the 42-residue form of amyloid-b, Ab42, formed (Ab42) 5 and (Ab42) 6 oligomers ('paranuclei') that could oligomerize to form structures of higher order. Ab40 did not form paranuclei, but instead existed as a mixture of monomers, dimers, trimers and tetramers. Chen and Glabe 11 , in contrast, used fluorescence and gel electrophoresis to determine oligomer states of amyloid-b refolded from denaturing solutions. They observed only Ab42 monomer and trimer bands, and no oligomers of Ab40. Differences such as these may exist because of the diverse experimental systems used to monitor amyloid-b self-association. Also, it has been argued that, in addition to the intrinsic potential of amyloid-b to traverse different assembly pathways, flaws in experimental design may have misled researchers in their quest to elucidate fully the amyloid-b oligomerization process 12. Hence there is significant uncertainty about amyloid-b oligomer states and their position and relevance to amyloid-b aggregation.
Journal of the American Society for Mass Spectrometry, 2004
The protein ␣-synuclein, implicated in Parkinson's disease, was studied by combining nano-electro... more The protein ␣-synuclein, implicated in Parkinson's disease, was studied by combining nano-electrospray ionization (N-ESI) mass spectrometry and ion mobility. It was found that both the charge-state distribution in the mass spectra and the average protein shape deduced from ion mobility data, depend on the pH of the spray solution. Negative-ion N-ESI of pH 7 solutions yielded a broad charge-state distribution from Ϫ6 to Ϫ16, centered at Ϫ11, and ion mobility data consistent with extended protein structures. Data obtained for pH 2.5 solutions, on the other hand, showed a narrow charge-state distribution from Ϫ6 to Ϫ11, centered at Ϫ8, and ion mobilities in agreement with compact ␣-synuclein structures. The data indicated that there are two distinct families of structures: one consisting of relatively compact proteins with eight or less negative charges and one consisting of relatively extended structures with nine or more charges. The average cross section of a-synuclein at pH 2.5 is 33% smaller than for the extended protein sprayed from pH 7 solution. Significant dimer formation was observed when sprayed from pH 7 solution but no dimers were observed from the low pH solution. A plausible mechanism for aggregate formation in solution is proposed.
Journal of the American Society for Mass Spectrometry, 1999
In this article the folding dynamics and energetics for a set of poly(ethylene terephthalate) (PE... more In this article the folding dynamics and energetics for a set of poly(ethylene terephthalate) (PET) oligomers cationized by various alkali ions are studied: M ϩ PETn for n ϭ 2 to 7 and M ϭ Li, Na, and K. Experimental cross sections were determined for matrix-assisted laser desorption/ionization (MALDI) generated ions using the ion mobility based ion chromatography method. Very good agreement was obtained with cross sections generated by the amber 4.0 suite of molecular dynamics programs. For n ϭ 2 and 4 the benzene rings of the oligomers stack with the metal ion coordinated to both terminal hydroxyl oxygen atoms and several of the nearby carbonyl oxygen atoms. For n ϭ 3, two isomers are both observed and predicted by theory: an open form where the third PET monomer attaches to the dimer and extends into space and a closed form where the third PET moiety bends back and coordinates its hydroxyl oxygen with the metal ion. For Na ϩ PET3, equilibrium is observed between 100 and 180 K with an Arrhenius analysis yielding an open to closed form isomerization barrier of 1.6 kcal/mol. For this same system the two isomeric forms are frozen out at 80 K and coupling the observed isomeric distribution with an RRKM analysis indicates the closed form is more stable by 0.5 kcal/mol. For K ϩ PET3 the barrier to isomerization is too low to observe (Ͻ1.0 kcal/mol), whereas for Li ϩ PET3 a temperature independent isomer distribution is observed (80 to 55°K). Using methods developed for determining isomerization barriers in carbon clusters it was possible to obtain an open to closed form isomerization barrier of 7 Ϯ 2 kcal/mol for Li ϩ PET3. In this system, the open and closed form isomer populations were observed to be strong functions of the laser power in the MALDI source. This allowed a detailed description of the formation mechanism to be formulated and indicated alkali ion attachment to the polymer during expansion of the plume emanating from the surface. Finally, the mass spectrum of a PET oligomer sample has been shown to strongly depend on the cationizing alkali metal ion. It is qualitatively shown that M ϩ-PETn binding energies and structures are responsible.
Journal of the American Chemical Society, 1995
Crown ethers have been intensely studied since their initial characterization nearly 30 years ago... more Crown ethers have been intensely studied since their initial characterization nearly 30 years ago.' Much of the interest stems from their ability to selectively complex cations in solution2 and consequently act either as cleansing agents for unwanted or dangerous ionic contaminants3 or as possible delivery agents for transporting ionic species to specific binding sites in living tissue^.^ The prototypical systems are alkali ion
Journal of the American Chemical Society, 2008
Journal of the American Chemical Society, 2009
The first steps of hydration of the protonated aromatic amino acids phenylalanine, tryptophan, an... more The first steps of hydration of the protonated aromatic amino acids phenylalanine, tryptophan, and tyrosine were studied experimentally employing a mass spectrometer equipped with a drift cell to examine the sequential addition of individual water molecules in equilibrium experiments and theoretically by a combination of molecular mechanics and electronic structure calculations (B3LYP/6-311++G**) on the three amino acid systems including up to five water molecules. It is found that both the ammonium and carboxyl groups offer good water binding sites with binding energies of the order of 13 kcal/mol for the first water molecule. Subsequent water molecules bind less strongly, in the range of 7-11 kcal/mol for the second through fifth water molecules. The ammonium group is able to host up to three water molecules and the carboxyl group one water molecule before additional water molecules bind either to the amino acid side chain as in tyrosine or to already-bound water in a second solvation shell around the ammonium group. Reasons for the surprisingly high water affinity of the neutral carboxyl group, comparable to that of the charge-carrying ammonium group, are found to be high intrinsic hydrophilicity, favorable charge-dipole alignment, and s for the case of multiply hydrated species s favorable dipole-dipole interaction among water molecules and the lack of alternative fully exposed hydration sites.