1
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Kirschbaum C, Greis K, Torres-Boy A, Riedel J, Gewinner S, Schöllkopf W, Meijer G, Helden GV, Pagel K. Studying the Intrinsic Reactivity of Chromanes by Gas-Phase Infrared Spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1950-1958. [PMID: 38950388 PMCID: PMC11311547 DOI: 10.1021/jasms.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/03/2024]
Abstract
Tandem mass spectrometry is routinely used for the structural analysis of organic molecules, but many fragmentation reactions are not well understood. Because several potential structures can correspond to a measured mass, the assignment of product ions is ambiguous using mass spectrometry alone. Here, we combine mass spectrometry with high-resolution gas-phase infrared spectroscopy and computational chemistry tools to identify product ion structures and derive collision-induced fragmentation mechanisms of the chromane derivatives Trolox and Methyltrolox. We find that protonated Trolox and Methyltrolox fragment identically via dehydration and decarbonylation, while deprotonated ions display substantially diverging reactivities. For deprotonated Methyltrolox, we observe unusual radical fragmentation reactions and suggest a [1,2]-Wittig rearrangement involving aryl migration in the gas phase. Overall, the combined experimental and theoretical approach presented here revealed complex proton dynamics and intramolecular rearrangement reactions, which expand our understanding on structure-reactivity relationships of isolated molecules in different protonation states.
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Affiliation(s)
- Carla Kirschbaum
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Kim Greis
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | | | - Jerome Riedel
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Sandy Gewinner
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | | | - Gerard Meijer
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Kevin Pagel
- Freie
Universität Berlin, Institute of Chemistry
and Biochemistry, 14195 Berlin, Germany
- Fritz
Haber Institute of the Max Planck Society, 14195 Berlin, Germany
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2
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Greis K, Kirschbaum C, Ober K, Taccone MI, Torres-Boy A, Meijer G, Pagel K, von Helden G. Infrared Spectroscopy of Fluorenyl Cations at Cryogenic Temperatures. J Phys Chem Lett 2023; 14:11313-11317. [PMID: 38064287 PMCID: PMC10749476 DOI: 10.1021/acs.jpclett.3c02928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023]
Abstract
The notion of (anti)aromaticity is a successful concept in chemistry to explain the structure and stability of polycyclic hydrocarbons. Cyclopentadienyl and fluorenyl cations are among the most studied classical antiaromatic systems. In this work, fluorenyl cations are investigated by high-resolution gas-phase infrared spectroscopy in helium droplets. Bare fluorenyl cations are generated in the gas phase by electrospray ionization. After mass-to-charge selection, ions are captured in ultracold helium nanodroplets and probed by infrared spectroscopy using a widely tunable free-electron laser in the 600-1700 cm-1 range. The highly resolved cryogenic infrared spectra confirm, in combination with DFT computations, that all cations are present in their singlet states.
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Affiliation(s)
- Kim Greis
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Katja Ober
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martín I. Taccone
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - América
Y. Torres-Boy
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerard Meijer
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Altensteinstraße 23A, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz
Haber Institute of the Max Planck Society, Berlin, Faradayweg 4-6, 14195 Berlin, Germany
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3
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Lee J, Im D, Liu Y, Fang J, Tian X, Kim M, Zhang WB, Seo J. Distinguishing Protein Chemical Topologies Using Supercharging Ion Mobility Spectrometry-Mass Spectrometry. Angew Chem Int Ed Engl 2023; 62:e202314980. [PMID: 37937859 DOI: 10.1002/anie.202314980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/09/2023]
Abstract
A technique combining ion mobility spectrometry-mass spectrometry (IMS-MS) and supercharging electrospray ionization (ESI) has been demonstrated to differentiate protein chemical topology effectively. Incorporating as many charges as possible into proteins via supercharging ESI allows the protein chains to be largely unfolded and stretched, revealing their hidden chemical topology. Different chemical topologies result in differing geometrical sizes of the unfolded proteins due to constraints in torsional rotations in cyclic domains. By introducing new topological indices, such as the chain-length-normalized collision cross-section (CCS) and the maximum charge state (zM ) in the extensively unfolded state, we were able to successfully differentiate various protein chemical topologies, including linear chains, ring-containing topologies (lasso, tadpole, multicyclics, etc.), and mechanically interlocked rings, like catenanes.
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Affiliation(s)
- Jiyeon Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
| | - Dahye Im
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
| | - Yajie Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jing Fang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Xibao Tian
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Minsu Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
| | - Wen-Bin Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry & Physics of Ministry of Education, Center for Soft Matter Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jongcheol Seo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, 37673, Gyeonsangbuk-do (Republic of, Korea
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4
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Kirschbaum C, Young RSE, Greis K, Menzel JP, Gewinner S, Schöllkopf W, Meijer G, von Helden G, Causon T, Narreddula VR, Poad BLJ, Blanksby SJ, Pagel K. Establishing carbon-carbon double bond position and configuration in unsaturated fatty acids by gas-phase infrared spectroscopy. Chem Sci 2023; 14:2518-2527. [PMID: 36908944 PMCID: PMC9993887 DOI: 10.1039/d2sc06487a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/25/2023] [Indexed: 01/26/2023] Open
Abstract
Fatty acids are an abundant class of lipids that are characterised by wide structural variation including isomeric diversity arising from the position and configuration of functional groups. Traditional approaches to fatty acid characterisation have combined chromatography and mass spectrometry for a description of the composition of individual fatty acids while infrared (IR) spectroscopy has provided insights into the functional groups and bond configurations at the bulk level. Here we exploit universal 3-pyridylcarbinol ester derivatization of fatty acids to acquire IR spectra of individual lipids as mass-selected gas-phase ions. Intramolecular interactions between the protonated pyridine moiety and carbon-carbon double bonds present highly sensitive probes for regiochemistry and configuration through promotion of strong and predictable shifts in IR resonances. Gas-phase IR spectra obtained from unsaturated fatty acids are shown to discriminate between isomers and enable the first unambiguous structural assignment of 6Z-octadecenoic acid in human-derived cell lines. Compatibility of 3-pyridylcarbinol ester derivatization with conventional chromatography-mass spectrometry and now gas-phase IR spectroscopy paves the way for comprehensive structure elucidation of fatty acids that is sensitive to regio- and stereochemical variations and with the potential to uncover new pathways in lipid metabolism.
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Affiliation(s)
- Carla Kirschbaum
- Institut für Chemie und Biochemie, Freie Universität Berlin Altensteinstraße 23a 14195 Berlin Germany .,Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin Germany
| | - Reuben S E Young
- School of Chemistry and Physics, Queensland University of Technology Brisbane QLD 4000 Australia .,Central Analytical Research Facility, Queensland University of Technology Brisbane QLD 4000 Australia
| | - Kim Greis
- Institut für Chemie und Biochemie, Freie Universität Berlin Altensteinstraße 23a 14195 Berlin Germany .,Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin Germany
| | - Jan Philipp Menzel
- School of Chemistry and Physics, Queensland University of Technology Brisbane QLD 4000 Australia .,Centre for Materials Science, Queensland University of Technology Brisbane QLD 4000 Australia
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin Germany
| | - Tim Causon
- Institute of Analytical Chemistry, University of Natural Resources and Life Sciences Vienna 1190 Vienna Austria
| | - Venkateswara R Narreddula
- School of Chemistry and Physics, Queensland University of Technology Brisbane QLD 4000 Australia .,Centre for Materials Science, Queensland University of Technology Brisbane QLD 4000 Australia
| | - Berwyck L J Poad
- School of Chemistry and Physics, Queensland University of Technology Brisbane QLD 4000 Australia .,Central Analytical Research Facility, Queensland University of Technology Brisbane QLD 4000 Australia.,Centre for Materials Science, Queensland University of Technology Brisbane QLD 4000 Australia
| | - Stephen J Blanksby
- School of Chemistry and Physics, Queensland University of Technology Brisbane QLD 4000 Australia .,Central Analytical Research Facility, Queensland University of Technology Brisbane QLD 4000 Australia.,Centre for Materials Science, Queensland University of Technology Brisbane QLD 4000 Australia
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin Altensteinstraße 23a 14195 Berlin Germany .,Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin Germany
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5
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Zappe A, Miller RL, Struwe WB, Pagel K. State-of-the-art glycosaminoglycan characterization. MASS SPECTROMETRY REVIEWS 2022; 41:1040-1071. [PMID: 34608657 DOI: 10.1002/mas.21737] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/02/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Glycosaminoglycans (GAGs) are heterogeneous acidic polysaccharides involved in a range of biological functions. They have a significant influence on the regulation of cellular processes and the development of various diseases and infections. To fully understand the functional roles that GAGs play in mammalian systems, including disease processes, it is essential to understand their structural features. Despite having a linear structure and a repetitive disaccharide backbone, their structural analysis is challenging and requires elaborate preparative and analytical techniques. In particular, the extent to which GAGs are sulfated, as well as variation in sulfate position across the entire oligosaccharide or on individual monosaccharides, represents a major obstacle. Here, we summarize the current state-of-the-art methodologies used for GAG sample preparation and analysis, discussing in detail liquid chromatograpy and mass spectrometry-based approaches, including advanced ion activation methods, ion mobility separations and infrared action spectroscopy of mass-selected species.
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Affiliation(s)
- Andreas Zappe
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Rebecca L Miller
- Department of Cellular and Molecular Medicine, Copenhagen Centre for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Kevin Pagel
- Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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6
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Greis K, Leichnitz S, Kirschbaum C, Chang CW, Lin MH, Meijer G, von Helden G, Seeberger PH, Pagel K. The Influence of the Electron Density in Acyl Protecting Groups on the Selectivity of Galactose Formation. J Am Chem Soc 2022; 144:20258-20266. [PMID: 36289569 PMCID: PMC9650713 DOI: 10.1021/jacs.2c05859] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The stereoselective formation of 1,2-cis-glycosidic
bonds is a major bottleneck in the synthesis of carbohydrates. We
here investigate how the electron density in acyl protecting groups
influences the stereoselectivity by fine-tuning the efficiency of
remote participation. Electron-rich C4-pivaloylated galactose building
blocks show an unprecedented α-selectivity. The trifluoroacetylated
counterpart with electron-withdrawing groups, on the other hand, exhibits
a lower selectivity. Cryogenic infrared spectroscopy in helium nanodroplets
and density functional theory calculations revealed the existence
of dioxolenium-type intermediates for this reaction, which suggests
that remote participation of the pivaloyl protecting group is the
origin of the high α-selectivity of the pivaloylated building
blocks. According to these findings, an α-selective galactose
building block for glycosynthesis is developed based on rational considerations
and is subsequently employed in automated glycan assembly exhibiting
complete stereoselectivity. Based on the obtained selectivities in
the glycosylation reactions and the results from infrared spectroscopy
and density functional theory, we suggest a mechanism by which these
reactions could proceed.
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Affiliation(s)
- Kim Greis
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Sabrina Leichnitz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Carla Kirschbaum
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Chun-Wei Chang
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Mei-Huei Lin
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany
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7
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Albertini S, Gruber E, Zappa F, Krasnokutski S, Laimer F, Scheier P. Chemistry and physics of dopants embedded in helium droplets. MASS SPECTROMETRY REVIEWS 2022; 41:529-567. [PMID: 33993543 DOI: 10.1002/mas.21699] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 05/18/2023]
Abstract
Helium droplets represent a cold inert matrix, free of walls with outstanding properties to grow complexes and clusters at conditions that are perfect to simulate cold and dense regions of the interstellar medium. At sub-Kelvin temperatures, barrierless reactions triggered by radicals or ions have been observed and studied by optical spectroscopy and mass spectrometry. The present review summarizes developments of experimental techniques and methods and recent results they enabled.
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Affiliation(s)
- Simon Albertini
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Elisabeth Gruber
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Fabio Zappa
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Serge Krasnokutski
- Laboratory Astrophysics Group of the MPI for Astronomy, University of Jena, Jena, Germany
| | - Felix Laimer
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
| | - Paul Scheier
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Innsbruck, Austria
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8
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Lee J, Clowers BH, Hogan CJ. Condensable Vapor Sorption by Low Charge State Protein Ions. Anal Chem 2022; 94:7050-7059. [PMID: 35500255 DOI: 10.1021/acs.analchem.2c00357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurement of the gas-phase ion mobility of proteins provides a means to quantitatively assess the relative sizes of charged proteins. However, protein ion mobility measurements are typically singular values. Here, we apply tandem mobility analysis to low charge state protein ions (+1 and +2 ions) introduced into the gas phase by nanodroplet nebulization. We first determine protein ion mobilities in dry air and subsequently examine shifts in mobilities brought about by the clustering of vapor molecules. Tandem mobility analysis yields mobility-vapor concentration curves for each protein ion, expanding the information obtained from mobility analysis. This experimental procedure and analysis is extended to bovine serum albumin, transferrin, immunoglobulin G, and apoferritin with water, 1-butanol, and nonane. All protein ions appear to adsorb vapor molecules, with mobility "diameter" shifts of up to 6-7% at conditions just below vapor saturation. We parametrize results using κ-Köhler theory, where the term κ quantifies the extent of uptake beyond Köhler model expectations. For 1-butanol and nonane, κ decreases with increasing protein ion size, while it increases with increasing protein ion size for water. For the systems probed, the extent of mobility shift for the organic vapors is unaffected by the nebulized solution pH, while shifts with water are sensitive to pH.
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Affiliation(s)
- Jihyeon Lee
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brian H Clowers
- Department of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Christopher J Hogan
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
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9
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Gagkayeva ZV, Gorshunov BP, Kachesov AY, Motovilov KA. Infrared fingerprints of water collective dynamics indicate proton transport in biological systems. Phys Rev E 2022; 105:044409. [PMID: 35590571 DOI: 10.1103/physreve.105.044409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
Recent publications on spectroscopy of water layers in water bridge structures revealed a significant enhancement of the proton mobility and the dielectric contribution of translational vibrations of water molecules in the interfacial layers compared to bulk water. Herewith, the results of long-term studies of proton dynamics in solid-state acids have shown that proton mobility increases significantly with the predominance of hydronium, but not Zundel, cations in the aqueous phase. In the present work, in the light of these data, we reanalyzed our previously published results on broadband dielectric spectroscopy of bovine heart cytochrome c, bovine serum albumin, and the extracellular matrix and filaments of Shewanella oneidensis MR-1. We revealed that, just as in water bridges, an increase in electrical conductivity in these systems correlates with an increase in the dielectric contribution of water molecular translational vibrations. In addition, the appearance of spectral signatures of the hydronium cations was observed only in those cases when the system revealed noticeable electrical conductivity due to delocalized charge carriers.
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Affiliation(s)
- Z V Gagkayeva
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - B P Gorshunov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - A Ye Kachesov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - K A Motovilov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
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10
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Zhou M, Jiao L, Xu S, Xu Y, Du M, Zhang X, Kong X. A novel method for photon unfolding spectroscopy of protein ions in the gas phase. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:043003. [PMID: 35489914 DOI: 10.1063/5.0080040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
In this study, a new experimental method for photon unfolding spectroscopy of protein ions based on a Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer was developed. The method of short-time Fourier transform has been applied here to obtain decay curves of target ions trapped in the cell of the FT ICR mass spectrometer. Based on the decay constants, the collision cross sections (CCSs) of target ions were calculated using the energetic hard-sphere model. By combining a tunable laser to the FT ICR mass spectrometer, the changes of CCSs of the target ions were recorded as a function of the wavelengths; thus, the photon isomerization spectrum was obtained. As one example, the photon isomerization spectrum of [Cyt c + 13H]13+ was recorded as the decay constants relative to the applied wavelengths of the laser in the 410-480 nm range. The spectrum shows a maximum at 426 nm, where an unfolded structure induced by a 4 s irradiation can be deduced. The strong peak at 426 nm was also observed for another ion of [Cyt c + 15H]15+, although some difference at 410 nm between the two spectra was found at the same time. This novel method can be expanded to ultraviolet or infrared region, making the experimental study of wavelength-dependent photon-induced structural variation of a variety of organic or biological molecules possible.
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Affiliation(s)
- Min Zhou
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Luyang Jiao
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Shiyin Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Yicheng Xu
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Mengying Du
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
| | - Xianyi Zhang
- School of Physics and Electronic Information, Anhui Normal University, Wuhu 241000, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-organic Chemistry, Collage of Chemistry, Nankai University, Tianjin 300071, China
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11
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Staji M, Sadeghzadeh N, Zamanlui S, Azarani M, Golchin A, Soleimani M, Ardeshirylajimi A, Khojasteh A, Hosseinzadeh S. Evaluation of dermal growth of keratinocytes derived from foreskin in co-culture condition with mesenchymal stem cells on polyurethane/gelatin/amnion scaffold. INT J POLYM MATER PO 2021. [DOI: 10.1080/00914037.2021.2018316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Masumeh Staji
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Soheila Zamanlui
- Stem Cell and Cell Therapy Research Center, Tissue Engineering and Regenerative Medicine Institute, Tehran, Central Branch, Islamic Azad University, Tehran, Iran
| | - Mojgan Azarani
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Golchin
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Masoud Soleimani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Abdolreza Ardeshirylajimi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Khojasteh
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Simzar Hosseinzadeh
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
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12
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Li TJ, Wen BY, Ma XH, Huang WT, Wu JZ, Lin XM, Zhang YJ, Li JF. Rapid and Simple Analysis of the Human Pepsin Secondary Structure Using a Portable Raman Spectrometer. Anal Chem 2021; 94:1318-1324. [PMID: 34928126 DOI: 10.1021/acs.analchem.1c04531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human pepsin is a digestive protease that plays an important role in the human digestive system. The secondary structure of human pepsin determines its bioactivity. Therefore, an in-depth understanding of human pepsin secondary structure changes is particularly important for the further improvement of the efficiency of human pepsin biological function. However, the complexity and diversity of the human pepsin secondary structure make its analysis difficult. Herein, a convenient method has been developed to quickly detect the secondary structure of human pepsin using a portable Raman spectrometer. According to the change of surface-enhanced Raman spectroscopy (SERS) signal intensity and activity of human pepsin at different pH values, we analyze the change of the human pepsin secondary structure. The results show that the content of the β-sheet gradually increased with the increase in the pH in the active range, which is in good agreement with circular dichroism (CD) measurements. The change of the secondary structure improves the sensitivity of human pepsin SERS detection. Meanwhile, human pepsin is a commonly used disease marker for the noninvasive diagnosis of gastroesophageal reflux disease (GERD); the detection limit of human pepsin we obtained is 2 μg/mL by the abovementioned method. The real clinical detection scenario is also simulated by spiking pepsin solution in saliva, and the standard recovery rate is 80.7-92.3%. These results show the great prospect of our method in studying the protein secondary structure and furthermore promote the application of SERS in clinical diagnosis.
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Affiliation(s)
- Tong-Jiang Li
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
| | - Bao-Ying Wen
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
| | - Xiao-Hui Ma
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
| | - Wan-Ting Huang
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
| | - Jin-Zhun Wu
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
| | - Xiu-Mei Lin
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
| | - Yue-Jiao Zhang
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
| | - Jian-Feng Li
- Women and Children's Hospital Affiliated to Xiamen University, School of medicine, College of Chemistry and Chemical Engineering, College of Energy, Xiamen University, Xiamen 361005, China
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13
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Dadgar Pakdel F, Mirshahi A, Zahedi P, Mohammad K, Hemmati F, Dadgar Pakdel J, Nicknam MH, Abedin Dorkoosh F. A Novel Approach for Development of Intraocular Biodegradable Ranibizumab Implant: A Solution for Stability of Protein Activity. Adv Pharm Bull 2021; 11:632-642. [PMID: 34888210 PMCID: PMC8642803 DOI: 10.34172/apb.2021.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/02/2020] [Accepted: 10/17/2020] [Indexed: 01/07/2023] Open
Abstract
Purpose: Ranibizumab is a monoclonal antibody fragment, targeting all isoforms of vascular endothelial growth factor A (VEGF-A), a protein involved in angiogenesis. It is used to treat age-related macular degeneration (AMD), retinal vein occlusion (RVO), and diabetic macular edema (DME), which are associated with blindness worldwide. However, proper treatment can decrease the loss of vision in about 90% of patients. Because of poor drug uptake in topical therapy and several adverse side effects of systemic irregularities and intravitreal injections, sustained-release drug delivery systems are more suitable for treatment. However, there are many challenges in the development of these systems due to the loss of protein activities. Methods: After drug complexation by the ion pairing method and preparation of a polymeric implant, containing the drug, the characteristics of the complexes were examined by Fourier-transform infrared spectroscopy and circular dichroism spectroscopy. The stability of antibody activity and biocompatibility of the released drug from the implant were assessed by bioassays and MTT assay, respectively. Finally, the release kinetics were investigated. Results: The bioassays showed the higher activity of the drug complex, compared to the free form, besides good biocompatibility in vitro. Also, the release data confirmed sustained and controlled release characteristics for the prepared implant. Conclusion: In this study, for the first time, we proposed a method for developing a sustained-release intraocular implant, consisting of ranibizumab by the heating method. This method allows for the industrial production of ranibizumab by extrusion and eliminates the complications related to reservoir systems.
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Affiliation(s)
- Fatemeh Dadgar Pakdel
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Mirshahi
- Department of Ophthalmology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Payam Zahedi
- Department of Polymer, School of Chemical Engineering, College of Engineering, University of Tehran, P. O. Box: 11155-4563, Tehran, Iran
| | - Kazem Mohammad
- Epidemiology and Biostatistics Department, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Hemmati
- Caspian Faculty of Engineering, College of Engineering, University of Tehran, P.O.BOX 43841-119, Gilan, Iran
| | | | - Mohammad Hossein Nicknam
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Molecular Immunology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Farid Abedin Dorkoosh
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.,Medical Biomaterial Research Centre (MBRC), Tehran University of Medical Sciences, Tehran, Iran
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14
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Mundlapati VR, Imani Z, D'mello VC, Brenner V, Gloaguen E, Baltaze JP, Robin S, Mons M, Aitken DJ. N-H⋯X interactions stabilize intra-residue C5 hydrogen bonded conformations in heterocyclic α-amino acid derivatives. Chem Sci 2021; 12:14826-14832. [PMID: 34820098 PMCID: PMC8597926 DOI: 10.1039/d1sc05014a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N–H⋯O
Created by potrace 1.16, written by Peter Selinger 2001-2019
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C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures. Exploiting the synergy between gas phase (experimental and quantum chemistry) and solution spectroscopies to decipher IR spectroscopic data, this work demonstrates that the extended C5-based conformation in 4-membered ring heterocyclic α-amino acid derivatives is significantly stabilized by the formation of an N–H⋯X H-bond. In this synergic system the strength of the C5 interaction remains constant while the N–H⋯X H-bond strength, and thereby the support provided by it, varies with the heteroatom. In 4-membered ring heterocyclic α-amino acid derivatives, extended conformations based on intraresidue C5 H-bonds can be stabilized by N–H⋯X H-bonds, making the combined C5–C6γ structures prominent in both gas phase and in weakly polar solutions.![]()
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Affiliation(s)
| | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France
| | - Viola C D'mello
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
| | | | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO 91405 Orsay France .,Université de Paris, Faculté de Pharmacie 75006 Paris France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL 91191 Gif-sur-Yvette France
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15
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Thomas DA, Taccone M, Ober K, Mucha E, Meijer G, von Helden G. Helium Nanodroplet Infrared Action Spectroscopy of the Proton-Bound Dimer of Hydrogen Sulfate and Formate: Examining Nuclear Quantum Effects. J Phys Chem A 2021; 125:9279-9287. [PMID: 34652165 PMCID: PMC8558860 DOI: 10.1021/acs.jpca.1c05705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The proton-bound dimer of hydrogen sulfate and formate is an archetypal structure for ionic hydrogen-bonding complexes that contribute to biogenic aerosol nucleation. Of central importance for the structure and properties of this complex is the location of the bridging proton connecting the two conjugate base moieties. The potential energy surface for bridging proton translocation features two local minima, with the proton localized at either the formate or hydrogen sulfate moiety. However, electronic structure methods reveal a shallow potential energy surface governing proton translocation, with a barrier on the order of the zero-point energy. This shallow potential complicates structural assignment and necessitates a consideration of nuclear quantum effects. In this work, we probe the structure of this complex and its isotopologues, utilizing infrared (IR) action spectroscopy of ions captured in helium nanodroplets. The IR spectra indicate a structure in which a proton is shared between the hydrogen sulfate and formate moieties, HSO4-···H+···-OOCH. However, because of the nuclear quantum effects and vibrational anharmonicities associated with the shallow potential for proton translocation, the extent of proton displacement from the formate moiety remains unclear, requiring further experiments or more advanced theoretical treatments for additional insight.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Martín Taccone
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Katja Ober
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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16
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Kirschbaum C, Greis K, Polewski L, Gewinner S, Schöllkopf W, Meijer G, von Helden G, Pagel K. Unveiling Glycerolipid Fragmentation by Cryogenic Infrared Spectroscopy. J Am Chem Soc 2021; 143:14827-14834. [PMID: 34473927 PMCID: PMC8447261 DOI: 10.1021/jacs.1c06944] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Mass spectrometry
is routinely employed for structure elucidation
of molecules. Structural information can be retrieved from intact
molecular ions by fragmentation; however, the interpretation of fragment
spectra is often hampered by poor understanding of the underlying
dissociation mechanisms. For example, neutral headgroup loss from
protonated glycerolipids has been postulated to proceed via an intramolecular
ring closure but the mechanism and resulting ring size have never
been experimentally confirmed. Here we use cryogenic gas-phase infrared
(IR) spectroscopy in combination with computational chemistry to unravel
the structures of fragment ions and thereby shed light on elusive
dissociation mechanisms. Using the example of glycerolipid fragmentation,
we study the formation of protonated five-membered dioxolane and six-membered
dioxane rings and show that dioxolane rings are predominant throughout
different glycerolipid classes and fragmentation channels. For comparison,
pure dioxolane and dioxane ions were generated from tailor-made dehydroxyl
derivatives inspired by natural 1,2- and 1,3-diacylglycerols and subsequently
interrogated using IR spectroscopy. Furthermore, the cyclic structure
of an intermediate fragment occurring in the phosphatidylcholine fragmentation
pathway was spectroscopically confirmed. Overall, the results contribute
substantially to the understanding of glycerolipid fragmentation and
showcase the value of vibrational ion spectroscopy to mechanistically
elucidate crucial fragmentation pathways in lipidomics.
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Affiliation(s)
- Carla Kirschbaum
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Kim Greis
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Lukasz Polewski
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | | | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, 14195 Berlin, Germany.,Fritz-Haber-Institut der Max-Planck-Gesellschaft, 14195 Berlin, Germany
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17
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Polewski L, Springer A, Pagel K, Schalley CA. Gas-Phase Structural Analysis of Supramolecular Assemblies. Acc Chem Res 2021; 54:2445-2456. [PMID: 33900743 DOI: 10.1021/acs.accounts.1c00080] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ion mobility spectrometry and gas-phase IR action spectroscopy are two structure-sensitive mass-spectrometric methods becoming more popular recently. While ion mobility spectrometry provides collision cross sections as a size and shape dependent parameter of an ion of interest, gas-phase spectroscopy identifies functional groups and is capable of distinguishing different isomers. Both methods have recently found application for the investigation of supramolecular assemblies. We here highlight several aspects.Starting with the characterization of switching states in azobenzene photoswitches as well as redox-switchable lasso-type pseudorotaxanes, structures of isomers can be distinguished and mechanistic details analyzed. Ion mobility mass spectrometry in combination with gas-phase H/D-exchange reactions unravels subtle structural details as described for the chiral recognition of crown ether amino acid complexes. Gas-phase IR spectroscopy allows identification of details of the binding patterns in dimeric amino acid clusters as well as the serine octamer. This research can be extended into the analysis of peptide assemblies that are of medical relevance, for example, in Alzheimer's disease, and into a general hydrophobicity scale for natural as well as synthetic amino acids. The development of ultracold gas-phase spectroscopy that for example makes use of ions trapped in liquid helium droplets provides access to very well resolved spectra. The combination of ion mobility separation of ions with subsequent spectroscopic analysis even permits separation of different isomers and studying them separately with respect to their structure. This represents a great advantage of these gas-phase methods over solution experiments, in which the supramolecular complexes under study typically equilibrate and thus prevent a separate investigation of different isomers. At the end of this overview, we will discuss larger and more complex supramolecules, among them giant halogen-bonded cages and complex intertwined topologies such as molecular knots and Solomon links.
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Affiliation(s)
- Lukasz Polewski
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
| | - Andreas Springer
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie, Freie Universität Berlin, Arnimallee 20-22, 14195 Berlin, Germany
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18
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Hanozin E, Mignolet B, Martens J, Berden G, Sluysmans D, Duwez AS, Stoddart JF, Eppe G, Oomens J, De Pauw E, Morsa D. Radical-Pairing Interactions in a Molecular Switch Evidenced by Ion Mobility Spectrometry and Infrared Ion Spectroscopy. Angew Chem Int Ed Engl 2021; 60:10049-10055. [PMID: 33561311 PMCID: PMC8251753 DOI: 10.1002/anie.202014728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/07/2021] [Indexed: 12/11/2022]
Abstract
The digital revolution sets a milestone in the progressive miniaturization of working devices and in the underlying advent of molecular machines. Foldamers involving mechanically entangled components with modular secondary structures are among the most promising designs for molecular switch‐based applications. Characterizing the nature and dynamics of their intramolecular network following the application of a stimulus is the key to their performance. Here, we use non‐dissociative electron transfer as a reductive stimulus in the gas phase and probe the consecutive co‐conformational transitions of a donor‐acceptor oligorotaxane foldamer using electrospray mass spectrometry interfaced with ion mobility and infrared ion spectroscopy. A comparison of collision cross section distributions for analogous closed‐shell and radical molecular ions sheds light on their respective formation energetics, while variations in their respective infrared absorption bands evidence changes in intramolecular organization as the foldamer becomes more compact. These differences are compatible with the advent of radical‐pairing interactions.
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Affiliation(s)
- Emeline Hanozin
- Mass Spectrometry Laboratory, UR MolSys, University of Liège, 4000, Liège, Belgium
| | - Benoit Mignolet
- Theoretical Physical Chemistry, UR MolSys, University of Liège, 4000, Liège, Belgium
| | - Jonathan Martens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525, ED, Nijmegen, The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525, ED, Nijmegen, The Netherlands
| | - Damien Sluysmans
- NanoChemistry and Molecular Systems, UR MolSys, University of Liège, 4000, Liège, Belgium
| | - Anne-Sophie Duwez
- NanoChemistry and Molecular Systems, UR MolSys, University of Liège, 4000, Liège, Belgium
| | - J Fraser Stoddart
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA.,Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou, 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, 311215, China.,School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, UR MolSys, University of Liège, 4000, Liège, Belgium
| | - Jos Oomens
- Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525, ED, Nijmegen, The Netherlands.,van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 908, 1098XH, Amsterdam, The Netherlands
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, UR MolSys, University of Liège, 4000, Liège, Belgium
| | - Denis Morsa
- Mass Spectrometry Laboratory, UR MolSys, University of Liège, 4000, Liège, Belgium.,Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7, 6525, ED, Nijmegen, The Netherlands
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19
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Hanozin E, Mignolet B, Martens J, Berden G, Sluysmans D, Duwez A, Stoddart JF, Eppe G, Oomens J, De Pauw E, Morsa D. Radical‐Pairing Interactions in a Molecular Switch Evidenced by Ion Mobility Spectrometry and Infrared Ion Spectroscopy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Emeline Hanozin
- Mass Spectrometry Laboratory UR MolSys University of Liège 4000 Liège Belgium
| | - Benoit Mignolet
- Theoretical Physical Chemistry UR MolSys University of Liège 4000 Liège Belgium
| | - Jonathan Martens
- Institute for Molecules and Materials FELIX Laboratory Radboud University Toernooiveld 7 6525 ED Nijmegen The Netherlands
| | - Giel Berden
- Institute for Molecules and Materials FELIX Laboratory Radboud University Toernooiveld 7 6525 ED Nijmegen The Netherlands
| | - Damien Sluysmans
- NanoChemistry and Molecular Systems UR MolSys University of Liège 4000 Liège Belgium
| | - Anne‐Sophie Duwez
- NanoChemistry and Molecular Systems UR MolSys University of Liège 4000 Liège Belgium
| | - J. Fraser Stoddart
- Department of Chemistry Northwestern University Evanston IL 60208 USA
- Stoddart Institute of Molecular Science Department of Chemistry Zhejiang University Hangzhou 310027 China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center Hangzhou 311215 China
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
| | - Gauthier Eppe
- Mass Spectrometry Laboratory UR MolSys University of Liège 4000 Liège Belgium
| | - Jos Oomens
- Institute for Molecules and Materials FELIX Laboratory Radboud University Toernooiveld 7 6525 ED Nijmegen The Netherlands
- van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 908 1098XH Amsterdam The Netherlands
| | - Edwin De Pauw
- Mass Spectrometry Laboratory UR MolSys University of Liège 4000 Liège Belgium
| | - Denis Morsa
- Mass Spectrometry Laboratory UR MolSys University of Liège 4000 Liège Belgium
- Institute for Molecules and Materials FELIX Laboratory Radboud University Toernooiveld 7 6525 ED Nijmegen The Netherlands
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20
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Zhou M, Lantz C, Brown KA, Ge Y, Paša-Tolić L, Loo JA, Lermyte F. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem Sci 2020; 11:12918-12936. [PMID: 34094482 PMCID: PMC8163214 DOI: 10.1039/d0sc04392c] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
In biology, it can be argued that if the genome contains the script for a cell's life cycle, then the proteome constitutes an ensemble cast of actors that brings these instructions to life. Their interactions with each other, co-factors, ligands, substrates, and so on, are key to understanding nearly any biological process. Mass spectrometry is well established as the method of choice to determine protein primary structure and location of post-translational modifications. In recent years, top-down fragmentation of intact proteins has been increasingly combined with ionisation of noncovalent assemblies under non-denaturing conditions, i.e., native mass spectrometry. Sequence, post-translational modifications, ligand/metal binding, protein folding, and complex stoichiometry can thus all be probed directly. Here, we review recent developments in this new and exciting field of research. While this work is written primarily from a mass spectrometry perspective, it is targeted to all bioanalytical scientists who are interested in applying these methods to their own biochemistry and chemical biology research.
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Affiliation(s)
- Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Carter Lantz
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Kyle A Brown
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison Madison WI 53706 USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Madison WI 53706 USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory Richland WA 99354 USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, Department of Biological Chemistry, University of California-Los Angeles Los Angeles CA 90095 USA
| | - Frederik Lermyte
- Department of Chemistry, Institute of Chemistry and Biochemistry, Technical University of Darmstadt 64287 Darmstadt Germany
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège 4000 Liège Belgium
- School of Engineering, University of Warwick Coventry CV4 7AL UK
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21
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Greis K, Mucha E, Lettow M, Thomas DA, Kirschbaum C, Moon S, Pardo‐Vargas A, von Helden G, Meijer G, Gilmore K, Seeberger PH, Pagel K. The Impact of Leaving Group Anomericity on the Structure of Glycosyl Cations of Protected Galactosides. Chemphyschem 2020; 21:1905-1907. [PMID: 32652759 PMCID: PMC7540451 DOI: 10.1002/cphc.202000473] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/09/2020] [Indexed: 12/31/2022]
Abstract
It has been reported that fragments produced by glycosidic bond breakage in mass spectrometry-based experiments can retain a memory of their anomeric configuration, which has major implications for glycan sequencing. Herein, we use cryogenic vibrational spectroscopy and ion mobility-mass spectrometry to study the structure of B-type fragments of protected galactosides. Cationic fragments were generated from glycosyl donors carrying trichloroacetimidate or thioethyl leaving groups of different anomeric configuration. The obtained infrared signatures indicate that the investigated fragments exhibit an identical structure, which suggests that there is no anomeric memory in B-type ions of fully protected monosaccharides.
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Affiliation(s)
- Kim Greis
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Eike Mucha
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Maike Lettow
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Daniel A. Thomas
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Carla Kirschbaum
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Sooyeon Moon
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Alonso Pardo‐Vargas
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Gert von Helden
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Gerard Meijer
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
| | - Kerry Gilmore
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Peter H. Seeberger
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Max Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Kevin Pagel
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Department of Molecular PhysicsFritz Haber Institute of the Max Planck SocietyFaradayweg 4–614195BerlinGermany
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22
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Thomas DA, Chang R, Mucha E, Lettow M, Greis K, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Probing the conformational landscape and thermochemistry of DNA dinucleotide anions via helium nanodroplet infrared action spectroscopy. Phys Chem Chem Phys 2020; 22:18400-18413. [PMID: 32797142 DOI: 10.1039/d0cp02482a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isolation of biomolecules in vacuum facilitates characterization of the intramolecular interactions that determine three-dimensional structure, but experimental quantification of conformer thermochemistry remains challenging. Infrared spectroscopy of molecules trapped in helium nanodroplets is a promising methodology for the measurement of thermochemical parameters. When molecules are captured in a helium nanodroplet, the rate of cooling to an equilibrium temperature of ca. 0.4 K is generally faster than the rate of isomerization, resulting in "shock-freezing" that kinetically traps molecules in local conformational minima. This unique property enables the study of temperature-dependent conformational equilibria via infrared spectroscopy at 0.4 K, thereby avoiding the deleterious effects of spectral broadening at higher temperatures. Herein, we demonstrate the first application of this approach to ionic species by coupling electrospray ionization mass spectrometry (ESI-MS) with helium nanodroplet infrared action spectroscopy to probe the structure and thermochemistry of deprotonated DNA dinucleotides. Dinucleotide anions were generated by ESI, confined in an ion trap at temperatures between 90 and 350 K, and entrained in traversing helium nanodroplets. The infrared action spectra of the entrained ions show a strong dependence on pre-pickup ion temperature, consistent with the preservation of conformer population upon cooling to 0.4 K. Non-negative matrix factorization was utilized to identify component conformer infrared spectra and determine temperature-dependent conformer populations. Relative enthalpies and entropies of conformers were subsequently obtained from a van't Hoff analysis. IR spectra and conformer thermochemistry are compared to results from ion mobility spectrometry (IMS) and electronic structure methods. The implementation of ESI-MS as a source of dopant molecules expands the diversity of molecules accessible for thermochemical measurements, enabling the study of larger, non-volatile species.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany.
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Marianski M, Mucha E, Greis K, Moon S, Pardo A, Kirschbaum C, Thomas DA, Meijer G, von Helden G, Gilmore K, Seeberger PH, Pagel K. Remote Participation during Glycosylation Reactions of Galactose Building Blocks: Direct Evidence from Cryogenic Vibrational Spectroscopy. Angew Chem Int Ed Engl 2020; 59:6166-6171. [PMID: 31944510 PMCID: PMC7187407 DOI: 10.1002/anie.201916245] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Indexed: 12/19/2022]
Abstract
The stereoselective formation of 1,2-cis-glycosidic bonds is challenging. However, 1,2-cis-selectivity can be induced by remote participation of C4 or C6 ester groups. Reactions involving remote participation are believed to proceed via a key ionic intermediate, the glycosyl cation. Although mechanistic pathways were postulated many years ago, the structure of the reaction intermediates remained elusive owing to their short-lived nature. Herein, we unravel the structure of glycosyl cations involved in remote participation reactions via cryogenic vibrational spectroscopy and first principles theory. Acetyl groups at C4 ensure α-selective galactosylations by forming a covalent bond to the anomeric carbon in dioxolenium-type ions. Unexpectedly, also benzyl ether protecting groups can engage in remote participation and promote the stereoselective formation of 1,2-cis-glycosidic bonds.
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry and BiochemistryHunter College695 Park Ave10065New YorkNYUSA
- The Ph.D. Program in ChemistryThe Graduate Center of the City University of New York365 5th AveNew YorkNY10016USA
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Kim Greis
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Sooyeon Moon
- Max-Planck-Institut für Kolloid und GrenzflächenforschungAm Mühlenberg 114476PotsdamGermany
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Alonso Pardo
- Max-Planck-Institut für Kolloid und GrenzflächenforschungAm Mühlenberg 114476PotsdamGermany
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Carla Kirschbaum
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Kerry Gilmore
- Max-Planck-Institut für Kolloid und GrenzflächenforschungAm Mühlenberg 114476PotsdamGermany
| | - Peter H. Seeberger
- Max-Planck-Institut für Kolloid und GrenzflächenforschungAm Mühlenberg 114476PotsdamGermany
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
- Institut für Chemie und BiochemieFreie Universität BerlinTakustrasse 314195BerlinGermany
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Marianski M, Mucha E, Greis K, Moon S, Pardo A, Kirschbaum C, Thomas DA, Meijer G, Helden G, Gilmore K, Seeberger PH, Pagel K. Fernpartizipation in Glykosylierungen von Galaktose‐Bausteinen: Direktnachweis durch kryogene Schwingungsspektroskopie. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916245] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mateusz Marianski
- Department of Chemistry and BiochemistryHunter College 695 Park Ave 10065 New York NY USA
- The Ph.D. Program in ChemistryThe Graduate Center of the City University of New York 365 5th Ave New York NY 10016 USA
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Kim Greis
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
- Institut für Chemie und BiochemieFreie Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Sooyeon Moon
- Max-Planck-Institut für Kolloid und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
- Institut für Chemie und BiochemieFreie Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Alonso Pardo
- Max-Planck-Institut für Kolloid und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
- Institut für Chemie und BiochemieFreie Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Carla Kirschbaum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
- Institut für Chemie und BiochemieFreie Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Gert Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Kerry Gilmore
- Max-Planck-Institut für Kolloid und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
| | - Peter H. Seeberger
- Max-Planck-Institut für Kolloid und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
- Institut für Chemie und BiochemieFreie Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
- Institut für Chemie und BiochemieFreie Universität Berlin Takustraße 3 14195 Berlin Deutschland
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Bakels S, Porskamp SBA, Rijs AM. Formation of Neutral Peptide Aggregates as Studied by Mass‐Selective IR Action Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sjors Bakels
- Radboud UniversityInstitute for Molecules and MaterialsFELIX Laboratory Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Sebastiaan B. A. Porskamp
- Radboud UniversityInstitute for Molecules and MaterialsFELIX Laboratory Toernooiveld 7c 6525 ED Nijmegen The Netherlands
| | - Anouk M. Rijs
- Radboud UniversityInstitute for Molecules and MaterialsFELIX Laboratory Toernooiveld 7c 6525 ED Nijmegen The Netherlands
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Bakels S, Porskamp SBA, Rijs AM. Formation of Neutral Peptide Aggregates as Studied by Mass-Selective IR Action Spectroscopy. Angew Chem Int Ed Engl 2019; 58:10537-10541. [PMID: 31125499 PMCID: PMC6772166 DOI: 10.1002/anie.201902644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Indexed: 01/28/2023]
Abstract
The spontaneous aggregation of proteins and peptides is widely studied owing to its relation to neurodegenerative diseases. To understand the underlying principles of peptide aggregation, elucidation of structure and structural changes upon their formation is key. This level of detail can be obtained by studying the peptide self-assembly in the gas phase. Structural characterization of aggregates is mainly done on charged species, as adding charges is an intrinsic part of the technique to bring molecules into the gas phase. Studying neutral peptide aggregates will complement the existing picture. These studies are restricted to dimers due to experimental limitations. Herein, we present advances in laser desorption molecular beam spectroscopy to form neutral peptide aggregates consisting of up to 14 monomeric peptides in the gas phase. The combination of this technique with IR-UV spectroscopy allowed us to select each aggregate by size and subsequently characterize its structure.
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Affiliation(s)
- Sjors Bakels
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 7c6525EDNijmegenThe Netherlands
| | - Sebastiaan B. A. Porskamp
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 7c6525EDNijmegenThe Netherlands
| | - Anouk M. Rijs
- Radboud UniversityInstitute for Molecules and MaterialsFELIX LaboratoryToernooiveld 7c6525EDNijmegenThe Netherlands
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Thomas DA, Mucha E, Lettow M, Meijer G, Rossi M, von Helden G. Characterization of a trans-trans Carbonic Acid-Fluoride Complex by Infrared Action Spectroscopy in Helium Nanodroplets. J Am Chem Soc 2019; 141:5815-5823. [PMID: 30883095 PMCID: PMC6727381 DOI: 10.1021/jacs.8b13542] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The high Lewis basicity
and small ionic radius of fluoride promote
the formation of strong ionic hydrogen bonds in the complexation of
fluoride with protic molecules. Herein, we report that carbonic acid,
a thermodynamically disfavored species that is challenging to investigate
experimentally, forms a complex with fluoride in the gas phase. Intriguingly,
this complex is highly stable and is observed in abundance upon nanoelectrospray
ionization of an aqueous sodium fluoride solution in the presence
of gas-phase carbon dioxide. We characterize the structure and properties
of the carbonic acid–fluoride complex, F–(H2CO3), and its deuterated isotopologue, F–(D2CO3), by helium nanodroplet
infrared action spectroscopy in the photon energy range of 390–2800
cm–1. The complex adopts a C2v symmetry structure with the carbonic acid
in a planar trans–trans conformation and both OH groups forming
ionic hydrogen bonds with the fluoride. Substantial vibrational anharmonic
effects are observed in the infrared spectra, most notably a strong
blue shift of the symmetric hydrogen stretching fundamental relative
to predictions from the harmonic approximation or vibrational second-order
perturbation theory. Ab initio thermostated ring-polymer molecular
dynamics simulations indicate that this blue shift originates from
strong coupling between the hydrogen stretching and bending vibrations,
resulting in an effective weakening of the OH···F– ionic hydrogen bonds.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
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28
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Fischer J, Fuchs S, Slenczka A, Karra M, Friedrich B. Microsolvation of porphine molecules in superfluid helium nanodroplets as revealed by optical line shape at the electronic origin. J Chem Phys 2018; 149:244306. [PMID: 30599728 DOI: 10.1063/1.5052615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate the line shape at the electronic origin of single porphine molecules doped into superfluid helium droplets as a function of the droplet size. Helium droplets comprised of less than 105 atoms are generated from an expansion of gaseous helium, while droplets with more than 105 atoms originate from liquid helium. In contrast to our recent study on phthalocyanine, porphine is found to exhibit a solvent shift to the blue with respect to the gas-phase resonance frequency as well as a multiplet splitting. A comparison of the helium-induced features of phthalocyanine and porphine with those obtained in similar studies on tetracene and pentacene reveals that these occur chiefly as two kinds of excitations distinguished by their linewidths and their dependence on the droplet size. Moreover, at quasi-bulk conditions achieved with droplets in excess of 106 helium atoms, none of these four dopant species yields an optical spectrum that can be assigned to a plausible rotational band structure.
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Affiliation(s)
- J Fischer
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053 Regensburg, Germany
| | - S Fuchs
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053 Regensburg, Germany
| | - A Slenczka
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93053 Regensburg, Germany
| | - M Karra
- Fritz-Haber-Insitut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - B Friedrich
- Fritz-Haber-Insitut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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29
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Unravelling the structure of glycosyl cations via cold-ion infrared spectroscopy. Nat Commun 2018; 9:4174. [PMID: 30301896 PMCID: PMC6177480 DOI: 10.1038/s41467-018-06764-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/25/2018] [Indexed: 12/17/2022] Open
Abstract
Glycosyl cations are the key intermediates during the glycosylation reaction that covalently links building blocks during the synthetic assembly of carbohydrates. The exact structure of these ions remained elusive due to their transient and short-lived nature. Structural insights into the intermediate would improve our understanding of the reaction mechanism of glycosidic bond formation. Here, we report an in-depth structural analysis of glycosyl cations using a combination of cold-ion infrared spectroscopy and first-principles theory. Participating C2 protective groups form indeed a covalent bond with the anomeric carbon that leads to C1-bridged acetoxonium-type structures. The resulting bicyclic structure strongly distorts the ring, which leads to a unique conformation for each individual monosaccharide. This gain in mechanistic understanding fundamentally impacts glycosynthesis and will allow to tailor building blocks and reaction conditions in the future.
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30
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Thomas DA, Marianski M, Mucha E, Meijer G, Johnson MA, von Helden G. Ground‐State Structure of the Proton‐Bound Formate Dimer by Cold‐Ion Infrared Action Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201805436] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mark A. Johnson
- Sterling Chemistry Laboratory Yale University 225 Prospect Street New Haven CT 06520 USA
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
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31
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Thomas DA, Marianski M, Mucha E, Meijer G, Johnson MA, von Helden G. Ground‐State Structure of the Proton‐Bound Formate Dimer by Cold‐Ion Infrared Action Spectroscopy. Angew Chem Int Ed Engl 2018; 57:10615-10619. [DOI: 10.1002/anie.201805436] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
| | - Mark A. Johnson
- Sterling Chemistry Laboratory Yale University 225 Prospect Street New Haven CT 06520 USA
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Germany
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32
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Konermann L, Metwally H, McAllister RG, Popa V. How to run molecular dynamics simulations on electrospray droplets and gas phase proteins: Basic guidelines and selected applications. Methods 2018; 144:104-112. [DOI: 10.1016/j.ymeth.2018.04.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 12/13/2022] Open
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Canzani D, Laszlo KJ, Bush MF. Ion Mobility of Proteins in Nitrogen Gas: Effects of Charge State, Charge Distribution, and Structure. J Phys Chem A 2018; 122:5625-5634. [DOI: 10.1021/acs.jpca.8b04474] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Daniele Canzani
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Kenneth J. Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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34
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Mucha E, Lettow M, Marianski M, Thomas DA, Struwe WB, Harvey DJ, Meijer G, Seeberger PH, von Helden G, Pagel K. Fucose-Migration in intakten protonierten Glykan-Ionen - ein universelles Phänomen in der Massenspektrometrie. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201801418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie, der; Freien Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie, der; Freien Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Daniel A. Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Weston B. Struwe
- Oxford Glycobiology Institute; Department of Biochemistry; University of Oxford; Großbritannien
| | - David J. Harvey
- Target Discovery Institute; Nuffield Department of Medicine; University of Oxford; Großbritannien
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Peter H. Seeberger
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Potsdam Deutschland
- Institut für Chemie und Biochemie; der Freien Universität Berlin; Deutschland
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie, der; Freien Universität Berlin; Takustraße 3 14195 Berlin Deutschland
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35
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Mucha E, Lettow M, Marianski M, Thomas DA, Struwe WB, Harvey DJ, Meijer G, Seeberger PH, von Helden G, Pagel K. Fucose Migration in Intact Protonated Glycan Ions: A Universal Phenomenon in Mass Spectrometry. Angew Chem Int Ed Engl 2018; 57:7440-7443. [PMID: 29688603 DOI: 10.1002/anie.201801418] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/23/2018] [Indexed: 11/10/2022]
Abstract
Fucose is an essential deoxysugar that is found in a wide range of biologically relevant glycans and glycoconjugates. A recurring problem in mass spectrometric analyses of fucosylated glycans is the intramolecular migration of fucose units, which can lead to erroneous sequence assignments. This migration reaction is typically assigned to activation during collision-induced dissociation (CID) in tandem mass spectrometry (MS). In this work, we utilized cold-ion spectroscopy and show for the first time that fucose migration is not limited to fragments obtained in tandem MS and can also be observed in intact glycan ions. This observation suggests a possible low-energy barrier for this transfer reaction and generalizes fucose migration to an issue that may universally occur in any type of mass spectrometry experiment.
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Affiliation(s)
- Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Maike Lettow
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Weston B Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Peter H Seeberger
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.,Institut für Chemie und Biochemie, der Freien Universität Berlin, Takustraße 3, 14195, Berlin, Germany
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36
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Thomas DA, Mucha E, Gewinner S, Schöllkopf W, Meijer G, von Helden G. Vibrational Spectroscopy of Fluoroformate, FCO 2-, Trapped in Helium Nanodroplets. J Phys Chem Lett 2018; 9:2305-2310. [PMID: 29669208 DOI: 10.1021/acs.jpclett.8b00664] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fluoroformate, also known as carbonofluoridate, is an intriguing molecule readily formed by the reductive derivatization of carbon dioxide. In spite of its well-known stability, a detailed structural characterization of the isolated anion has yet to be reported. Presented in this work is the vibrational spectrum of fluoroformate obtained by infrared action spectroscopy of ions trapped in helium nanodroplets, the first application of this technique to a molecular anion. The experimental method yields narrow spectral lines, providing experimental constraints on the structure that can be accurately reproduced using high-level ab initio methods. In addition, two notable Fermi resonances between a fundamental and combination band are observed. The electrostatic potential map of fluoroformate reveals substantial charge density on fluorine as well as on the oxygen atoms, suggesting multiple sites for interaction with hydrogen bond donors and electrophiles, which may in turn lead to intriguing solvation structures and reaction pathways.
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Affiliation(s)
- Daniel A Thomas
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gerard Meijer
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft , Faradayweg 4-6 , 14195 Berlin , Germany
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37
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Sanders JD, Grinfeld D, Aizikov K, Makarov A, Holden DD, Brodbelt JS. Determination of Collision Cross-Sections of Protein Ions in an Orbitrap Mass Analyzer. Anal Chem 2018; 90:5896-5902. [DOI: 10.1021/acs.analchem.8b00724] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- James D. Sanders
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | | | | | | | - Dustin D. Holden
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry University of Texas at Austin Austin, Texas 78712, United States
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38
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Metwally H, Konermann L. Crown Ether Effects on the Location of Charge Carriers in Electrospray Droplets: Implications for the Mechanism of Protein Charging and Supercharging. Anal Chem 2018; 90:4126-4134. [DOI: 10.1021/acs.analchem.8b00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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39
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Crisma M, Formaggio F, Alemán C, Torras J, Ramakrishnan C, Kalmankar N, Balaram P, Toniolo C. The fully‐extended conformation in peptides and proteins. Pept Sci (Hoboken) 2018. [DOI: 10.1002/bip.23100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
- Department of ChemistryUniversity of PadovaPadova35131 Italy
| | - Carlos Alemán
- Departament d'Enginyeria QuímicaEEBE, Universitat Politècnica de CatalunyaBarcelona08019 Spain
- Barcelona Research Center in Multiscale Science and EngineeringUniversitat Politècnica de CatalunyaBarcelona08019 Spain
| | - Joan Torras
- Departament d'Enginyeria QuímicaEEBE, Universitat Politècnica de CatalunyaBarcelona08019 Spain
- Barcelona Research Center in Multiscale Science and EngineeringUniversitat Politècnica de CatalunyaBarcelona08019 Spain
| | | | - Neha Kalmankar
- National Centre for Biological Sciences (TIFR), GKVK CampusBangalore560065 India
| | | | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNRPadova35131 Italy
- Department of ChemistryUniversity of PadovaPadova35131 Italy
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40
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Jašíková L, Roithová J. Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules. Chemistry 2018; 24:3374-3390. [PMID: 29314303 DOI: 10.1002/chem.201705692] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Indexed: 01/07/2023]
Abstract
Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules.
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Affiliation(s)
- Lucie Jašíková
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 43, Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 2030, Prague 2, 128 43, Czech Republic
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41
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Fundamentals of ion mobility spectrometry. Curr Opin Chem Biol 2018; 42:51-59. [DOI: 10.1016/j.cbpa.2017.10.022] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 12/13/2022]
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42
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Hoffmann W, Marianski M, Warnke S, Seo J, Baldauf C, von Helden G, Pagel K. Assessing the stability of alanine-based helices by conformer-selective IR spectroscopy. Phys Chem Chem Phys 2018; 18:19950-4. [PMID: 27398722 DOI: 10.1039/c6cp03827a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyalanine based peptides that carry a lysine at the C-terminus ([Ac-AlanLys + H](+)) are known to form α-helices in the gas phase. Three factors contribute to the stability of these helices: (i) the interaction between the helix macro dipole and the charge, (ii) the capping of dangling C[double bond, length as m-dash]O groups by lysine and (iii) the cooperative hydrogen bond network. In previous studies, the influence of the interaction between the helix dipole and the charge as well as the impact of the capping was studied intensively. Here, we complement these findings by systematically assessing the third parameter, the H-bond network. In order to selectively remove one H-bond along the backbone, we use amide-to-ester substitutions. The resulting depsi peptides were analyzed by ion-mobility and m/z-selective infrared spectroscopy as well as theoretical calculations. Our results indicate that peptides which contain only one ester bond still maintain the helical conformation. We conclude that the interaction between the charge and the helix macro-dipole is most crucial for the formation of the α-helical conformation and a single backbone H-bond has only little influence on the overall stability.
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Affiliation(s)
- Waldemar Hoffmann
- Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany. and Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Mateusz Marianski
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany. and Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
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43
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Chandler SA, Benesch JL. Mass spectrometry beyond the native state. Curr Opin Chem Biol 2017; 42:130-137. [PMID: 29288996 DOI: 10.1016/j.cbpa.2017.11.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022]
Abstract
Native mass spectrometry allows the study of proteins by probing in vacuum the interactions they form in solution. It is a uniquely useful approach for structural biology and biophysics due to the high resolution of separation it affords, allowing the concomitant interrogation of multiple protein components with high mass accuracy. At its most basic, native mass spectrometry reports the mass of intact proteins and the assemblies they form in solution. However, the opportunities for more detailed characterisation are extensive, enabled by the exquisite control of ion motion that is possible in vacuum. Here we describe recent developments in mass spectrometry approaches to the structural interrogation of proteins both in, and beyond, their native state.
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Affiliation(s)
- Shane A Chandler
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Justin Lp Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
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44
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Yang Y, Liao G, Kong X. Charge-state Resolved Infrared Multiple Photon Dissociation (IRMPD) Spectroscopy of Ubiquitin Ions in the Gas Phase. Sci Rep 2017; 7:16592. [PMID: 29185478 PMCID: PMC5707388 DOI: 10.1038/s41598-017-16831-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/16/2017] [Indexed: 11/25/2022] Open
Abstract
In this study, we obtained for the first time the direct infrared multiple photon dissociation (IRMPD) spectra of ubiquitin ions in the range 2700-3750 cm-1. Ubiquitin ions with different charge states showed absorption in the two regions of 2940-3000 cm-1 and 3280-3400 cm-1. The increase of the charge state of ubiquitin ions broadened the absorption peak on the high-frequency side in the second region, indicating some hydrogen bonds were weakened due to Coulomb interaction. It is also found that the relative intensity of the absorption peak in the first region compared to the absorption peak in the second region increased with increasing charge state, making the IRMPD spectra charge-state resolved. Although it is usually reasonable to suggest the origin of the absorption in the range 2940-3000 cm-1 as the C-H bond stretching modes, the results show significantly reduced absorption after the deuteration of all labile hydrogen atoms. A possible explanation for this is that the coupling coefficients between the C-H vibrational mode and other selective modes decreased greatly after the deuteration, reducing the rate of energy redistribution and probability of consecutive IR absorption.
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Affiliation(s)
- Yijie Yang
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Guanhua Liao
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xianglei Kong
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China.
- Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin, 300071, China.
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45
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D'Atri V, Causon T, Hernandez-Alba O, Mutabazi A, Veuthey JL, Cianferani S, Guillarme D. Adding a new separation dimension to MS and LC-MS: What is the utility of ion mobility spectrometry? J Sep Sci 2017; 41:20-67. [PMID: 29024509 DOI: 10.1002/jssc.201700919] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/19/2017] [Accepted: 09/19/2017] [Indexed: 12/12/2022]
Abstract
Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).
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Affiliation(s)
- Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Tim Causon
- Division of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences (BOKU Vienna), Vienna, Austria
| | - Oscar Hernandez-Alba
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Aline Mutabazi
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Jean-Luc Veuthey
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Sarah Cianferani
- BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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46
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Manz C, Pagel K. Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy. Curr Opin Chem Biol 2017; 42:16-24. [PMID: 29107930 DOI: 10.1016/j.cbpa.2017.10.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/13/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
Abstract
Due to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to overcome this limitation is to implement ion mobility spectrometry (IMS) as an additional gas-phase separation dimension. This review highlights recent developments in which IM-MS was used as a tool for comprehensive glycan analysis or as rapid screening method for glycan feature analysis. Furthermore, we summarize a series of very recent investigations in which gas-phase spectroscopy is applied to study glycans and discuss the potential of the hyphenation between IM-MS and infrared (IR) spectroscopy as a future tool for glycomics and glycoproteomics.
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Affiliation(s)
- Christian Manz
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany; Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany.
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47
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Warnke S, Hoffmann W, Seo J, De Genst E, von Helden G, Pagel K. From Compact to String-The Role of Secondary and Tertiary Structure in Charge-Induced Unzipping of Gas-Phase Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:638-646. [PMID: 27921259 DOI: 10.1007/s13361-016-1551-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/22/2016] [Accepted: 11/01/2016] [Indexed: 06/06/2023]
Abstract
In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues. Graphical Abstract ᅟ.
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Affiliation(s)
- Stephan Warnke
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Waldemar Hoffmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Jongcheol Seo
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Erwin De Genst
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Gert von Helden
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany.
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195, Berlin, Germany.
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48
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Do TD, Comi TJ, Dunham SJB, Rubakhin SS, Sweedler JV. Single Cell Profiling Using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation. Anal Chem 2017; 89:3078-3086. [PMID: 28194949 DOI: 10.1021/acs.analchem.6b04819] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A high-throughput single cell profiling method has been developed for matrix-enhanced-secondary ion mass spectrometry (ME-SIMS) to investigate the lipid profiles of neuronal cells. Populations of cells are dispersed onto the substrate, their locations determined using optical microscopy, and the cell locations used to guide the acquisition of SIMS spectra from the cells. Up to 2,000 cells can be assayed in one experiment at a rate of 6 s per cell. Multiple saturated and unsaturated phosphatidylcholines (PCs) and their fragments are detected and verified with tandem mass spectrometry from individual cells when ionic liquids are employed as a matrix. Optically guided single cell profiling with ME-SIMS is suitable for a range of cell sizes, from Aplysia californica neurons larger than 75 μm to 7-μm rat cerebellar neurons. ME-SIMS analysis followed by t-distributed stochastic neighbor embedding of peaks in the lipid molecular mass range (m/z 700-850) distinguishes several cell types from the rat central nervous system, largely based on the relative proportions of four dominant lipids, PC(32:0), PC(34:1), PC(36:1), and PC(38:5). Furthermore, subpopulations within each cell type are tentatively classified consistent with their endogenous lipid ratios. The results illustrate the efficacy of a new approach to classify single cell populations and subpopulations using SIMS profiling of lipid and metabolite contents. These methods are broadly applicable for high throughput single cell chemical analyses.
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Affiliation(s)
- Thanh D Do
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Troy J Comi
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Sage J B Dunham
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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49
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A prevalent intraresidue hydrogen bond stabilizes proteins. Nat Chem Biol 2016; 12:1084-1088. [PMID: 27748749 PMCID: PMC5110370 DOI: 10.1038/nchembio.2206] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/10/2016] [Indexed: 11/08/2022]
Abstract
Current limitations in de novo protein structure prediction and design suggest an incomplete understanding of the interactions that govern protein folding. Here we demonstrate that previously unappreciated hydrogen bonds occur within proteins between the amide proton and carbonyl oxygen of the same residue. Quantum calculations, infrared spectroscopy, and nuclear magnetic resonance spectroscopy show that these interactions share hallmark features of canonical hydrogen bonds. Biophysical analyses demonstrate that selective attenuation or enhancement of these C5 hydrogen bonds affects the stability of synthetic β-sheets. These interactions are common, affecting approximately 5% of all residues and 94% of proteins, and their cumulative impact provides several kcal/mol of conformational stability to a typical protein. C5 hydrogen bonds stabilize, especially, the flat β-sheets of the amyloid state, which is linked with Alzheimer’s disease and other neurodegenerative disorders. Inclusion of these interactions in computational force fields would improve models of protein folding, function, and dysfunction.
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50
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Seo J, Hoffmann W, Warnke S, Bowers MT, Pagel K, von Helden G. Die Erhaltung nativer Proteinstrukturen unter Ausschluss von Lösungsmittel: eine Untersuchung mit Hilfe der Kombination von Ionenmobilität mit Spektroskopie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jongcheol Seo
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Waldemar Hoffmann
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Stephan Warnke
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry University of California Santa Barbara Santa Barbara CA 93106 USA
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie der Freien Universität Berlin Takustraße 3 14195 Berlin Deutschland
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4–6 14195 Berlin Deutschland
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