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Now showing items 1 - 16 of 36

  • Recommendations for reporting ion mobility Mass Spectrometry measurements

    Gabelica, Valérie   Shvartsburg, Alexandre A.   Afonso, Carlos   Barran, Perdita   Benesch, Justin L.P.   Bleiholder, Christian   Bowers, Michael T.   Bilbao, Aivett   Bush, Matthew F.   Campbell, J. Larry   Campuzano, Iain D.G.   Causon, Tim   Clowers, Brian H.   Creaser, Colin S.   De Pauw, Edwin   Far, Johann   Fernandez-Lima, Francisco   Fjeldsted, John C.   Giles, Kevin   Groessl, Michael   Hogan, Christopher J.   Hann, Stephan   Kim, Hugh I.   Kurulugama, Ruwan T.   May, Jody C.   McLean, John A.   Pagel, Kevin   Richardson, Keith   Ridgeway, Mark E.   Rosu, Frédéric   Sobott, Frank   Thalassinos, Konstantinos   Valentine, Stephen J.   Wyttenbach, Thomas  

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  • Recommendations for reporting ion mobility Mass Spectrometry measurements

    Gabelica, Valerie   Shvartsburg, Alexandre A.   Afonso, Carlos   Barran, Perdita   Benesch, Justin L. P.   Bleiholder, Christian   Bowers, Michael T.   Bilbao, Aivett   Bush, Matthew F.   Campbell, J. Larry   Campuzano, Iain D. G.   Causon, Tim   Clowers, Brian H.   Creaser, Colin S.   De Pauw, Edwin   Far, Johann   Fernandez-Lima, Francisco   Fjeldsted, John C.   Giles, Kevin   Groessl, Michael   Hogan, Christopher J., Jr.   Hann, Stephan   Kim, Hugh I.   Kurulugama, Ruwan T.   May, Jody C.   McLean, John A.   Pagel, Kevin   Richardson, Keith   Ridgeway, Mark E.   Rosu, Frederic   Sobott, Frank   Thalassinos, Konstantinos   Valentine, Stephen J.   Wyttenbach, Thomas  

    Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K-0) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. (c) 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.
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  • Ion Mobility Analysis of Molecular Dynamics

    Wyttenbach, Thomas   Pierson, Nicholas A.   Clemmer, David E.   Bowers, Michael T.  

    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 nonpolarmolecules, 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 inter-conversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but caremust be taken in the experimental protocols. The power of theoretical modeling is demonstrated.
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  • Ion mobility analysis of molecular dynamics.

    Wyttenbach, Thomas   Pierson, Nicholas A   Clemmer, David E   Bowers, Michael T  

    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. =20
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  • Conformational Stability of Syrian Hamster Prion Protein PrP(90-231)

    Grabenauer, Megan   Wyttenbach, Thomas   Sanghera, Narinder   Slade, Susan E.   Pinheiro, Teresa J. T.   Scrivens, James H.   Bowers, Michael T.  

    Many transmissible spongiform encephalopathies (TSEs) are believed to be caused by a misfolded form of the normal cellular prion protein (PrP(C)) known as PrP(Sc). While PrP(Sc) is known to be exceptionally stable and resistant to protease degradation, PrP(C) has not shown these same unusual characteristics. However, using ion mobility spectrometry mass spectrometry (IMS-MS), we found evidence for at least one very stable conformation of a truncated form of recombinant PrP(C) consisting of residues 90-231, which resists unfolding in the absence of solvent at high injection energies and at temperatures in excess of 600 K. We also report the first absolute collision cross sections measured for recombinant Syrian hamster prion protein PrP(90-231).
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  • Interactions of the Hormone Oxytocin with Divalent Metal Ions

    Wyttenbach, Thomas   Liu, Dengfeng   Bowers, Michael T.  

    The interaction of the cyclic nonapeptide oxytocin (OT) with a number of alkaline earth and divalent transition metal ions (X2+) was examined employing mass spectrometry (MS) and ion mobility spectrometry (IMS) techniques in combination with molecular dynamics (MD) and density functional theory (DFT) calculations. Under acidic conditions it was found that OT exhibits an exceptionally strong affinity for all divalent metal ions resulting in strong [OT + X](2+) peaks in the mass spectrum. Under basic conditions only Cu2+ and Ni2+-OT complexes were detected and these were singly, doubly, triply, or quadruply deprotonated. Collision-induced dissociation of the [OT - 3H + Cu](-) complex yielded exclusively C-terminal Cu2+-containing fragments (Cu(2+)fragment(3-)), suggesting that the Cu2+ ligation site includes deprotonated C-terminal backbone amide nitrogen atoms and the N-terminal amino nitrogen atom in [OT - 3H + Cu](-). MD and DFT calculations indicate a square-planar complex is consistent with these observations and with experimental collision cross sections. MID and DFT calculations also indicate either an octahedral or trigonal-bipyramidal complex between Zn2+ and OT is lowest in energy with carbonyl oxygens being the primary ligation sites. Both complexes yield cross sections in agreement with experiment. The biological impact of the structural changes induced in OT by divalent metal ion coodination is discussed.
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  • Structure of the 21-30 fragment of amyloid beta-protein

    Baumketner, Andrij   Bernstein, Summer L.   Wyttenbach, Thomas   Lazo, Noel D.   Teplow, David B.   Bowers, Michael T.  

    Folding and self-assembly of the 42-residue amyloid beta-protein (A beta) are linked to Alzheimer's disease (AD). The 21-30 region of A beta, A beta(21-30), is resistant to proteolysis and is believed to nucleate the folding of full-length A beta. The conformational space accessible to the A beta(21-30) peptide is investigated by using replica exchange molecular dynamics simulations in explicit solvent. Conformations belonging to the global free energy minimum (the "native'' state) from simulation are in good agreement with reported NMR structures. These conformations possess a bend motif spanning the central residues V24-K28. This bend is stabilized by a network of hydrogen bonds involving the side chain of residue D23 and the amide hydrogens of adjacent residues G25, S26, N27, and K28, as well as by a salt bridge formed between side chains of K28 and E22. The non-native states of this peptide are compact and retain a native-like bend topology. The persistence of structure in the denatured state may account for the resistance of this peptide to protease degradation and aggregation, even at elevated temperatures.
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  • Hydration of mononucleotides

    Liu, Dengfeng   Wyttenbach, Thomas   Bowers, Michael T.  

    The sequential addition of water molecules to protonated and deprotonated forms of the four mononucleotides dAMP, dCMP, dGMP, and dTMP was studied experimentally by equilibrium measurements using an electrospray mass spectrometer equipped with a drift cell and theoretically by computational methods including molecular modeling and density functional theory calculations. Experiments were carried out in positive and negative ion mode, and calculations included the protonated and deprotonated forms of the four nucleotides. For deprotonated anionic nucleotides the experimental enthalpies of hydration (Delta H degrees(n)) were found to be similar for all four systems and varied between -10.1 and -11.5 kcal mol(-1) for the first water molecule (n = 1) and -8.3 and -9.6 kcal mol(-1) for additional water molecules (n = 2-4). Theory indicated that the first water molecule binds to the charge-carrying phosphate group. Simulations of deprotonated mononucleotides with four water molecules yielded a large number of structures with similar energies. In some of the structures all four water molecules cluster around the phosphate group, and in other structures the four water molecules each hydrate a different functional group of the nucleotide. These include the phosphate group, the deoxyribose hydroxyl group, and various functional groups on the nucleobases. Experimental Delta H degrees(1) values for the protonated cationic mononucleotides ranged from -10.5 to -13.5 kcal mol(-1) with more negative values (<=-12 kcal mol(-1)) for dCMP, dGMP, and dTMP and the least negative value for dAMP. For n) 2-4 the Delta H degrees(n) values varied from -6.9 to -9.7 kcal/mol and were similar in value to the deprotonated nucleotides except for dAMP. Theory on the protonated nucleotides indicated that the first water molecule binds to the charge-carrying group for dCMP, dGMP, and dTMP. For protonated dAMP, on the other hand, the charge-carrying N3 group is well self-solvated by the phosphate group and not readily available for a hydrogen bond with the water molecule. The insight gained on nucleotide stabilization by individual water molecules is used to discuss the competition between hydration of individual nucleotides and Watson-Crick base pairing.
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  • Intermolecular Interactions in Biomolecular Systems Examined by Mass Spectrometry

    Wyttenbach, Thomas   Bowers, Michael T.  

    With the development of electrospray and matrix-assisted laser desorption ionization, mass spectrometry (IMS) evolved into a powerful tool in the field of biochemistry. Whereas MS is primarily analytical in nature, an increasing number of MS research groups employ the method to address fundamental biochemical questions. Probing the interaction of noncovalendy bound molecules in the mass spectrometer is one of the most interesting MS-based experiments possible today, with the potential of making a significant contribution to the basic understanding of the structure and function of biochemical complexes. Here we review a number of current research efforts employing primarily MS techniques to investigate intermolecular interactions in biochemical systems. Examples chosen include the interaction of biomolecules with solvent molecules; interactions between nucleic-acid molecules, in particular, interactions in duplex and quadruplex structures; and interactions between proteins involved in neurodegenerative diseases. Finally we conclude by presenting a few examples of very large biomolecular assemblies in the mega-Dalton range analyzed by MS.
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  • Design of a new electrospray ion mobility mass spectrometer

    Wyttenbach, Thomas   Kemper, Paul R.   Bowers, Michael T.  

    The design of a new ion mobility mass spectrometer is presented. The design features an electrospray ion source; an ion funnel to transmit ions efficiently from the source to the mobility cell and to accumulate ions in the pulsed ion mode; a mobility cell, and a quadrupole mass analyzer. Each part of the instrument is described in detail. Preliminary results obtained with the new instrument are presented to demonstrate its capabilities. Equilibrium experiments showed that the ΔG°(300 K) values for the addition of the first water molecule to the doubly protonated peptides bradykinin, angiotensin II, and LHRH are in the range from −3.5 to −2.5 kcal/mol. The corresponding values for the singly protonated ions are >−0.5 kcal/mol for angiotensin II and LHRH, but equal to −2.6 kcal/mol for bradykinin. The stronger bonding in bradykinin may be due to the presence of a salt bridge structure. Ion arrival time distributions showed that singly protonated peptides can form aggregates of the form (nM + nH)n+. The mobilities of these ions indicated that they are near spherical. Heating the drift cell to 450 K caused dissociation of the (2M + 2H)2+ ion into two (M + H)+ units on the 1 ms experimental time scale. A theoretical fit to the experimental data yielded rate constants and a barrier for dissociation of 30 ± 2 kcal/mol for bradykinin and 39 ± 3 kcal/mol for LHRH.
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  • Host/guest conformations of biological systems: valinomycin/alkali ions

    Wyttenbach, Thomas   Batka Jr, Joseph J.   Gidden, Jennifer   Bowers, Michael T.  

    Collision cross sections of gas phase valinomycin–alkali ion complexes were measured in helium using the ion mobility based ion chromatography technique. For the lithiated and sodiated species a value of 267 Å2 was measured whereas the cross sections for the potassiated, rubidiated, and cesiated complexes were larger 272, 277, and 279 Å2, respectively. The systematic increase with ion size indicates that the backbone folding of the cyclic valinomycin molecule is dependent on the choice of alkali ion. This result is in good agreement with theoretical cross sections of model structures obtained by molecular mechanics simulations. The model structures demonstrate that the valinomycin host completely encapsulates the alkali ion with five or six of the polar carbonyl groups in the first solvation sphere of the alkali ion. The polar core of the complex is shielded by the aliphatic valinomycin side chains, which were found to be predominant on the complex surface. The lithium ion is solvated by a fivefold carbonyl coordination sphere with at least four of the five carbonyls belonging to valine units. The sodiated species exhibits a five- to sixfold carbonyl coordination with highly excited O…Na+ vibrations at 300 K. In the potassiated and cesiated complexes the alkali ion is coordinated by six valine carbonyl groups in a near octahedral arrangement causing the valinomycin backbone to fold in a quasi-S6 symmetric fashion. These results demonstrate that the overall size and shape of the complex is not quite the same for different alkali ions, in contrast to conclusions made from solution salt extraction experiments and assumptions made in previous molecular mechanics calculations. However, our results were found to be in good agreement with earlier spectroscopic studies carried out on alkali salt valinomycin crystals and solutions thereof in organic solvents. Relative alkali ion–valinomycin binding energies extracted from the molecular mechanics data were able to qualitatively explain the experimentally observed preference of valinomycin for hosting potassium over lithium and sodium.
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  • Systematic Study of the Structures of Potassiated Tertiary Amino Acids: Salt Bridge Structures Dominate

    Drayss, Miriam K.   Blunk, Dirk   Oomens, Jos   Gao, Bing   Wyttenbach, Thomas   Bowers, Michael T.   Schaefer, Mathias  

    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 file 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.
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  • Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid beta-protein

    Krone, Mary Griffin   Baumketner, Andrij   Bernstein, Summer L.   Wyttenbach, Thomas   Lazo, Noel D.   Teplow, David B.   Bowers, Michael T.   Shea, Joan-Emma  

    The effect of single amino acid substitutions associated with the Italian (E22K), Arctic (E22G), Dutch (E22Q) and Iowa (D23N) familial forms of Alzheimer's disease and cerebral amyloid angiopathy on the structure of the 21-30 fragment of the Alzheimer amyloid beta-protein (A beta) is investigated by replica-exchange molecular dynamics simulations. The 21-30 segment has been shown in our earlier work to adopt a bend structure in solution that may serve as the folding nucleation site for A beta. Our simulations reveal that the 24-28 bend motif is retained in all E22 mutants, suggesting that mutations involving residue E22 may not affect the structure of the folding nucleation site of A beta. Enhanced aggregation in A beta with familial Alzheimer's disease substitutions may result from the depletion of the E22-K28 salt bridge, which destabilizes the bend structure. Alternately, the E22 mutations may affect longer-range interactions outside the 21-30 segment that can impact the aggregation of A beta. Substituting at residue D23, on the other hand, leads to the formation of a turn rather than a bend motif, implying that in contrast to E22 mutants, the D23N mutant may affect monomer A beta folding and subsequent aggregation. Our simulations suggest that the mechanisms by which E22 and D23 mutations affect the folding and aggregation of A beta are fundamentally different. (C) 2008 Elsevier Ltd. All rights reserved.
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  • Effect of the Long-Range Potential on Ion Mobility Measurements

    Wyttenbach, Thomas   Helden, Gert von   Batka Jr, Joseph J.   Carlat, Douglas   Bowers, Michael T.  

    The temperature dependence of ion mobilities in helium was studied by using the ion chromatography method to investigate the effect of long-range terms in the ion-buffer gas interaction. Experimental cross sections thus determined increased significantly as the temperature was lowered from 300 to 80 K for all ions investigated, which were fullerene C+60, cationized PEG polymers, cationized crown ethers, and protonated and sodiated oligoglycines. The temperature dependence of the collision cross sections was successfully modeled by employing simple atom-atom interaction potentials including a repulsive R−12 term and the attractive long-range R−6 and R−4 terms, R being the distance between the colliding particles.
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  • Salt Bridge Structures in the Absence of Solvent? The Case for the Oligoglycines

    Wyttenbach, Thomas   Bushnell, John E.   Bowers, Michael T.  

    Protonated and sodiated oligoglycines, Gly(n) (n = 1-6), were generated in the gas phase using matrix-assisted laser desorption ionization and their structure probed by measuring collision cross sections in helium. It was found that the sodiated oligoglycines have larger cross sections than the protonated forms and that the difference between the cross sections of the two forms increases with increasing oligoglycine size (n = 2-5) reaching a value of >11% for pentaglycine. This observation indicated that the protonated forms are more compact and spherical than the sodiated species. Theoretical studies including ab initio MP2, density functional theory, and molecular mechanics calculations indicated that protonated oligoglycines assume almost spherical shapes. The same was true for sodiated forms if it was assumed that the sodium ion was bound to a zwitterion oligoglycine structure via a salt bridge system. However, structures obtained when the sodium ion was solvated by nonzwitterionic oligoglycines were fairly extended with strongly oblate shapes. Cross sections calculated for these latter structures agreed well with the experimental data of the sodiated species, while cross sections calculated for the spherical shapes agreed well with the experimental data of the protonated forms. Relative energies obtained from calculations (B3LYP/6-311++G**) on Gly(n)Na(+) (n = 1-4) indicated that the salt bridge forms are less stable than the charge solvation forms by 3, 14, 8, and 8 kcal/mol for n 1, 2, 3, and 4, respectively. Both theory and experiment indicated that sodiated oligoglycines do not form salt bridge structures in the gas phase.
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  • Gas-Phase Conformation of Biological Molecules:? Bradykinin

    Wyttenbach, Thomas   von Helden, Gert   Bowers, Michael T.  

    Several cationized forms of bradykinin (BK) were generated in the gas phase using matrix assisted laser desorption ionization (MALDI). Accurate collision cross sections were obtained using the ion chromatography method. The species studied include (B%K + H)(+), (BK + Na)(+), and (BK -H + 2Na)(+) It was found that all three species had very similar cross sections of 245 +/- 3 Angstrom(2), and these cross sections were independent of temperature from 300 to 600 K. It could be concluded from these data that BK wraps itself around the charge center(s) in a globular shape whose time average size changes little up to 600 K. The arrival time distributions of all three systems were narrow, only slightly broader than expected for a single species indicating cationized BK exists in only a few low-energy conformers at low temperature. A detailed analysis of the data was done using molecular mechanics/dynamics of the AMBER 4.0 suite of programs. The calculations were in excellent agreement with experiment in that scatter plots indicated cross sections of 100 member structural sets of (BK + H)(+), (BK + Na)(+), and (BK -H + 2Na)(+) were very similar. Further, very extensive dynamics studies over the range 200 to 600 K indicated the lowest energy conformers exhibited cross sections independent of temperature in agreement with experiment and supported the indication that only a few conformers are involved. The absolute magnitudes of the AMBER generated 0 K structures were similar to 10%smaller than experiment. The discrepancy decreased to similar to 5%when the systems were thermally averaged at 300 K. Selected0 K conformers of (BK + H)+ were calculated using AM1 and PM3 from AMBER starting structures. It was found that the 0 K cross sections increased by similar to 5%over the AMBER structures providing better agreement with experiment. The extensive conformer sets generated in the scatter plots were analyzed to see which parts of BK preferred to bind to the charge sites. As expected the binding was global, but each isomer or system had different preferred binding sites. We looked for a preference of BK forming a beta-turn in the Ser(6)-Pro(7)-Phe(8)-Arg(9) sequence since such a feature had been proposed in solution NMR studies. We found little evidence for beta-turns in our 500 conformers of variously cationized BK in the gas phase.
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