1
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Zimnicka MM. Structural studies of supramolecular complexes and assemblies by ion mobility mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:526-559. [PMID: 37260128 DOI: 10.1002/mas.21851] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/02/2023]
Abstract
Recent advances in instrumentation and development of computational strategies for ion mobility mass spectrometry (IM-MS) studies have contributed to an extensive growth in the application of this analytical technique to comprehensive structural description of supramolecular systems. Apart from the benefits of IM-MS for interrogation of intrinsic properties of noncovalent aggregates in the experimental gas-phase environment, its merits for the description of native structural aspects, under the premises of having maintained the noncovalent interactions innate upon the ionization process, have attracted even more attention and gained increasing interest in the scientific community. Thus, various types of supramolecular complexes and assemblies relevant for biological, medical, material, and environmental sciences have been characterized so far by IM-MS supported by computational chemistry. This review covers the state-of-the-art in this field and discusses experimental methods and accompanying computational approaches for assessing the reliable three-dimensional structural elucidation of supramolecular complexes and assemblies by IM-MS.
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Affiliation(s)
- Magdalena M Zimnicka
- Mass Spectrometry Group, Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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2
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Wesdemiotis C, Williams-Pavlantos KN, Keating AR, McGee AS, Bochenek C. Mass spectrometry of polymers: A tutorial review. MASS SPECTROMETRY REVIEWS 2024; 43:427-476. [PMID: 37070280 DOI: 10.1002/mas.21844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 03/03/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Ever since the inception of synthetic polymeric materials in the late 19th century, the number of studies on polymers as well as the complexity of their structures have only increased. The development and commercialization of new polymers with properties fine-tuned for specific technological, environmental, consumer, or biomedical applications requires powerful analytical techniques that permit the in-depth characterization of these materials. One such method with the ability to provide chemical composition and structure information with high sensitivity, selectivity, specificity, and speed is mass spectrometry (MS). This tutorial review presents and exemplifies the various MS techniques available for the elucidation of specific structural features in a synthetic polymer, including compositional complexity, primary structure, architecture, topology, and surface properties. Key to every MS analysis is sample conversion to gas-phase ions. This review describes the fundamentals of the most suitable ionization methods for synthetic materials and provides relevant sample preparation protocols. Most importantly, structural characterizations via one-step as well as hyphenated or multidimensional approaches are introduced and demonstrated with specific applications, including surface sensitive and imaging techniques. The aim of this tutorial review is to illustrate the capabilities of MS for the characterization of large, complex polymers and emphasize its potential as a powerful compositional and structural elucidation tool in polymer chemistry.
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Affiliation(s)
| | | | - Addie R Keating
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Andrew S McGee
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
| | - Calum Bochenek
- Department of Chemistry, The University of Akron, Akron, Ohio, USA
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3
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Williamson DL, Windsor HM, Nagy G. Isolating the Contributions from Moments of Inertia in Isotopic Shifts Measured by High-Resolution Cyclic Ion Mobility Separations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 38654703 DOI: 10.1021/jasms.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The unexpected finding that isotopomers (i.e., isotopic isomers) can be separated with high-resolution ion mobility spectrometry-mass spectrometry (IMS-MS) has raised new structural considerations affecting an ion's mobility, namely its center of mass (CoM) and moments of inertia (MoI). Unfortunately, thus far, no studies have attempted to experimentally isolate either CoM or MoI, as they are intrinsically linked by their definitions, where MoI is calculated in relation to CoM. In this study, we designed and synthesized four isotopically labeled tetrapropylammonium (TAA3) ions, each with a unique mass distribution. Three of the synthesized TAA3 ions were labeled symmetrically, thus having identical CoM but differing MoI, which we verified using density functional theory (DFT) calculations. Consequently, we were able to isolate the effect of MoI changes in high-resolution IMS-MS separations. Cyclic ion mobility spectrometry-mass spectrometry (cIMS-MS) separations of the isotopically labeled TAA3 variants revealed isotopic mobility shifts attributable solely to changes in MoI. A 60-m cIMS-MS separation demonstrated that two nominally isobaric TAA3 pseudoisotopomers could be partially resolved, showcasing potential feasibility for isotopomer separations on commercially available IMS-MS platforms. With our previously established collision cross section (CCS) calibration protocol, we also quantified the relationship between MoI and CCS. Our results represent the first demonstration of IMS-MS separations based solely on MoI differences. We believe these findings will contribute important evidence to the growing body of literature on the physical nature of isotopic shifts in IMS-MS separations and work toward more accurate CCS predictions.
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Affiliation(s)
- David L Williamson
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Haisley M Windsor
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Gabe Nagy
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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4
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Nagy K, Gellén G, Papp D, Schlosser G, Révész Á. Optimum collision energies for proteomics: The impact of ion mobility separation. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4957. [PMID: 37415399 DOI: 10.1002/jms.4957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography-mass spectrometry (LC-MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC-MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values-giving the highest identification score-for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument-located before and after the IMS cell-were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).
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Affiliation(s)
- Kinga Nagy
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gabriella Gellén
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Dávid Papp
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
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5
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Ghosh D, Rosu F, Gabelica V. Negative Electrospray Supercharging Mechanisms of Nucleic Acid Structures. Anal Chem 2022; 94:15386-15394. [DOI: 10.1021/acs.analchem.2c03187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debasmita Ghosh
- INSERM, CNRS, Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, Univ. Bordeaux, 33600Pessac, France
| | - Frédéric Rosu
- CNRS, INSERM, Institut Européen de Chimie et Biologie (IECB, UAR3033, US001), Univ. Bordeaux, 33600Pessac, France
| | - Valérie Gabelica
- INSERM, CNRS, Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, Univ. Bordeaux, 33600Pessac, France
- CNRS, INSERM, Institut Européen de Chimie et Biologie (IECB, UAR3033, US001), Univ. Bordeaux, 33600Pessac, France
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6
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Saintmont F, Hoyas S, Rosu F, Gabélica V, Brocorens P, Gerbaux P. Structural Characterization of Dendriplexes In Vacuo: A Joint Ion Mobility/Molecular Dynamics Investigation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1555-1568. [PMID: 35875874 DOI: 10.1021/jasms.2c00122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The combination between ion mobility mass spectrometry and molecular dynamics simulations is demonstrated for the first time to afford valuable information on structural changes undergone by dendriplexes containing ds-DNA and low-generation dendrimers when transferred from the solution to the gas phase. Dendriplex ions presenting 1:1 and 2:1 stoichiometries are identified using mass spectrometry experiments, and the collision cross sections (CCS) of the 1:1 ions are measured using drift time ion mobility experiments. Structural predictions using Molecular Dynamics (MD) simulations showed that gas-phase relevant structures, i.e., with a good match between the experimental and theoretical CCS, are generated when the global electrospray process is simulated, including the solvent molecule evaporation, rather than abruptly transferring the ions from the solution to the gas phase. The progressive migration of ammonium groups (either NH4+ from the buffer or protonated amines of the dendrimer) into the minor and major grooves of DNA all along the evaporation processes is shown to compact the DNA structure by electrostatic and hydrogen-bond interactions. The subsequent proton transfer from the ammonium (NH4+ or protonated amino groups) to the DNA phosphate groups allows creation of protonated phosphate/phosphate hydrogen bonds within the compact structures. MD simulations showed major structural differences between the dendriplexes in solution and in the gas phase, not only due to the loss of the solvent but also due to the proton transfers and the huge difference between the solution and gas-phase charge states.
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Affiliation(s)
- Fabrice Saintmont
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Sébastien Hoyas
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, Institut Européen de Chimie et Biologie (IECB, UAR3033, US001), 2 rue Robert Escarpait, 33607 Pessac, France
| | - Valérie Gabélica
- Univ. Bordeaux, CNRS, INSERM, Institut Européen de Chimie et Biologie (IECB, UAR3033, US001), 2 rue Robert Escarpait, 33607 Pessac, France
- Univ. Bordeaux, INSERM, CNRS, Acides Nucléiques Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Patrick Brocorens
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
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7
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Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
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Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
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8
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Weber P, Hoyas S, Halin É, Coulembier O, De Winter J, Cornil J, Gerbaux P. On the Conformation of Anionic Peptoids in the Gas Phase. Biomacromolecules 2022; 23:1138-1147. [PMID: 35041390 DOI: 10.1021/acs.biomac.1c01442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although N-(S)-phenylethyl peptoids are known to adopt helical structures in solutions, the corresponding positively charged ions lose their helical structure during the transfer from the solution to the gas phase due to the so-called charge solvation effect. We, here, considered negatively charged peptoids to investigate by ion mobility spectrometry-mass spectrometry whether the structural changes described in the positive ionization mode can be circumvented in the negative mode by a fine-tuning of the peptoid sequence, that is, by positioning the negative charge at the positive side of the helical peptoid macrodipole. N-(S)-(1-carboxy-2-phenylethyl) (Nscp) and N-(S)-phenylethyl (Nspe) were selected as the negative charge carrier and as the helix inductor, respectively. We, here, report the results of a joint theoretical and experimental study demonstrating that the structures adopted by the NspenNscp anions remain compactly folded in the gas phase for chains containing up to 10 residues, whereas no evidence of the presence of a helical structure was obtained, even if, for selected sequences and lengths, different gas phase conformations are detected.
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Affiliation(s)
- Perrine Weber
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.,Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Sébastien Hoyas
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.,Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Émilie Halin
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Olivier Coulembier
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
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9
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Edwards AN, Tran HM, Gallagher ES. Propagating Error through Traveling-Wave Ion Mobility Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2621-2630. [PMID: 34662111 DOI: 10.1021/jasms.1c00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Native mass spectrometry (MS) is used to elucidate the stoichiometry of protein complexes and quantify binding interactions by maintaining native-like, noncovalent interactions in the gas phase. However, ionization forces proteins into specific conformations, losing the solution-phase dynamics associated with solvated protein structures. Comparison of gas-phase structures to those in solution, or to other gas-phase ion populations, has many biological implications. For one, analyzing the variety of conformations that are maintained in the gas-phase can provide insight into a protein's solution-phase energy landscape. The gas-phase conformations of proteins and complexes can be investigated using ion mobility (IM) spectrometry. Specifically, drift tube (DT)-IM utilizes uniform electric fields to propel a population of gas-phase ions through a region containing a neutral gas. By measuring the mobility (K) of gas-phase ions, users are able to calculate an average momentum transfer cross section (DTCCS), which provides structural information on the ion. Conversely, in traveling-wave ion mobility spectrometry (TWIMS), TWCCS values cannot be derived directly from an ion's mobility but must be determined following calibration. Though the required calibration adds uncertainty, it is common to report only an average and standard deviation of the calculated TWCCS, accounting for uncertainty associated with replicate measurements, which is a fraction of the overall uncertainty. Herein, we calibrate a TWIMS instrument and derive TWCCSN2 and TWCCSN2→He values for four proteins: cytochrome c, ubiquitin, apo-myoglobin, and holo-myoglobin. We show that compared to reporting only the standard deviation of TWCCS, propagating error through the calibration results in a significant increase in the number of calculated TWCCS values that agree within experimental error with literature values (DTCCS). Incorporating this additional uncertainty provides a more thorough assessment of a protein ion's gas-phase conformations, enabling the structures sampled by native IM-MS to be compared against other reported structures, both experimental and computational.
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Affiliation(s)
- Alexis N Edwards
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Hien M Tran
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, Texas 76798, United States
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Gabelica V. Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand. Acc Chem Res 2021; 54:3691-3699. [PMID: 34546031 DOI: 10.1021/acs.accounts.1c00396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of fundamental understanding and with new methodological developments. A first goal was to develop mass spectrometry approaches to detect noncovalent interactions between antitumor drugs and their DNA target. Twenty years ago, our attention turned toward specific DNA structures such as the G-quadruplex (a structure formed by guanine-rich strands). Mass spectrometry allows one to discern which molecules interact with one another by measuring the masses of the complexes, and quantify the affinities by measuring their abundance. The most important findings came from unexpected masses. For example, we showed the formation of higher- or lower-order structures by G-quadruplexes used in traditional biophysical assays. We also derived complete thermodynamic and kinetic description of G-quadruplex folding pathways by measuring cation binding, one at a time. Getting quantitative information requires accounting for nonspecific adduct formation and for the response factors of the different molecular forms. With these caveats in mind, the approach is now mature enough for routine biophysical characterization of nucleic acids. A second goal is to obtain more detailed structural information on each of the complexes separated by the mass spectrometer. One such approach is ion mobility spectrometry, and even today the challenge lies in the structural interpretation of the measurements. We showed that, although structures such as G-quadruplexes are well-preserved in the MS conditions, double helices actually get more compact in the gas phase. These major rearrangements forced us to challenge comfortable assumptions. Further work is still needed to generalize how to deduce structures in solution from ion mobility spectrometry data and, in particular, how to account for the electrospray charging mechanisms and for ion internal energy effects. These studies also called for complementary approaches to ion mobility spectrometry. Recently, we applied isotope exchange labeling mass spectrometry to characterize nucleic acid structures for the first time, and we reported the first ever circular dichroism ion spectroscopy measurement on mass-selected trapped ions. Circular dichroism plays a key role in assigning the stacking topology, and our new method now opens the door to characterizing a wide variety of chiral molecules by mass spectrometry. In summary, advanced mass spectrometry approaches to characterize gas-phase structures work well for G-quadruplexes because they are stiffened by inner cations. The next objective will be to generalize these methodologies to a wider range of nucleic acid structures.
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Affiliation(s)
- Valérie Gabelica
- Université de Bordeaux, CNRS, INSERM,
ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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11
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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12
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Vicent C, Valls A, Escorihuela J, Altava B, Luis S. Unveiling anion-induced folding in tripodal imidazolium receptors by ion-mobility mass spectrometry. Chem Commun (Camb) 2021; 57:8616-8619. [PMID: 34369516 DOI: 10.1039/d1cc02818a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The anion-induced folding of tripodal imidazolium receptors has been investigated by NMR spectroscopy, electrospray ionization ion mobility mass spectrometry and DFT calculations. Such folding can be switched by anion release upon collision induced dissociation.
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Affiliation(s)
- Cristian Vicent
- Servei Central d'Instrumentació Científica (SCIC), Universitat Jaume I, Avda. Sos Baynat s/n, 12006 Castellón, Spain.
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13
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Parchami R, Tabrizchi M. Effective collisional cross-section of small ions in the gas phase: Application to ion mobility spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9090. [PMID: 33760281 DOI: 10.1002/rcm.9090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE The observed drift times of monoatomic ions, including alkali metal ions and halide anions, are not fully consistent with their size. When the effect of mass is included through the Mason-Schamp equation, the deviation gets worse so that the trend of the experimental collisional cross-sections becomes completely opposite to what is expected. This is attributed to the stronger local electric field around smaller ions. The strong electric field in the vicinity of a small ion leads to strong ion-neutral interactions and creates a drag force against ion motion. The smaller the ions, the stronger the interaction, because of the higher charge density. METHODS In view of this, a modified equation is introduced to describe the relationship between the observed drift times or ion mobilities and the cross-sections of small ions. Here, for small ions with high charge density, the experimental collision cross-section is expressed as the effective collision cross-section, Ωeff = σi (1 + α/ri 3 ), that takes into account both intrinsic ion size, σi , and the ion-molecule interactions through a correction term of α/ri 3 , which is proportional to the charge density. RESULTS A linear fit of the drift times of alkali metal ions and halide anions to the proposed equation showed relative deviations of <8.2%. The model successfully predicted the drift time of other small diatomic ions with reasonable error. CONCLUSIONS The proposed model can be used as a simple and efficient relationship in predicting the effective cross-section of small ions.
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Affiliation(s)
- Razieh Parchami
- Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Mahmoud Tabrizchi
- Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran
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14
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Lloyd Williams OH, Rijs NJ. Reaction Monitoring and Structural Characterisation of Coordination Driven Self-Assembled Systems by Ion Mobility-Mass Spectrometry. Front Chem 2021; 9:682743. [PMID: 34169059 PMCID: PMC8217442 DOI: 10.3389/fchem.2021.682743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/14/2021] [Indexed: 01/03/2023] Open
Abstract
Nature creates exquisite molecular assemblies, required for the molecular-level functions of life, via self-assembly. Understanding and harnessing these complex processes presents an immense opportunity for the design and fabrication of advanced functional materials. However, the significant industrial potential of self-assembly to fabricate highly functional materials is hampered by a lack of knowledge of critical reaction intermediates, mechanisms, and kinetics. As we move beyond the covalent synthetic regime, into the domain of non-covalent interactions occupied by self-assembly, harnessing and embracing complexity is a must, and non-targeted analyses of dynamic systems are becoming increasingly important. Coordination driven self-assembly is an important subtype of self-assembly that presents several wicked analytical challenges. These challenges are "wicked" due the very complexity desired confounding the analysis of products, intermediates, and pathways, therefore limiting reaction optimisation, tuning, and ultimately, utility. Ion Mobility-Mass Spectrometry solves many of the most challenging analytical problems in separating and analysing the structure of both simple and complex species formed via coordination driven self-assembly. Thus, due to the emerging importance of ion mobility mass spectrometry as an analytical technique tackling complex systems, this review highlights exciting recent applications. These include equilibrium monitoring, structural and dynamic analysis of previously analytically inaccessible complex interlinked structures and the process of self-sorting. The vast and largely untapped potential of ion mobility mass spectrometry to coordination driven self-assembly is yet to be fully realised. Therefore, we also propose where current analytical approaches can be built upon to allow for greater insight into the complexity and structural dynamics involved in self-assembly.
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Affiliation(s)
| | - Nicole J. Rijs
- School of Chemistry, UNSW Sydney, Sydney, NSW, Australia
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15
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Santos IC, Brodbelt JS. Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020). J Sep Sci 2021; 44:340-372. [PMID: 32974962 PMCID: PMC8378248 DOI: 10.1002/jssc.202000833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
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16
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Abi-Ghanem J, Rabin C, Porrini M, Rosu F, Gabelica V. Compaction of RNA Hairpins and Their Kissing Complexes in Native Electrospray Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2035-2043. [PMID: 32812759 DOI: 10.1021/jasms.0c00060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
When electrosprayed from typical native MS solution conditions, RNA hairpins and kissing complexes acquire charge states at which they get significantly more compact in the gas phase than their initial structure in solution. Here, we also show the limits of using force field molecular dynamics to interpret the structures of nucleic acid complexes in the gas phase, as the predicted CCS distributions do not fully match the experimental ones. We suggest that higher level calculation levels should be used in the future.
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Affiliation(s)
- Josephine Abi-Ghanem
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Clémence Rabin
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Massimiliano Porrini
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Frédéric Rosu
- Univ Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
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17
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Structural insights into Escherichia coli phosphopantothenoylcysteine synthetase by native ion mobility-mass spectrometry. Biochem J 2020; 476:3125-3139. [PMID: 31488574 DOI: 10.1042/bcj20190318] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/22/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022]
Abstract
CoaBC, part of the vital coenzyme A biosynthetic pathway in bacteria, has recently been validated as a promising antimicrobial target. In this work, we employed native ion mobility-mass spectrometry to gain structural insights into the phosphopantothenoylcysteine synthetase domain of E. coli CoaBC. Moreover, native mass spectrometry was validated as a screening tool to identify novel inhibitors of this enzyme, highlighting the utility and versatility of this technique both for structural biology and for drug discovery.
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18
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Saintmont F, De Winter J, Chirot F, Halin E, Dugourd P, Brocorens P, Gerbaux P. How Spherical Are Gaseous Low Charged Dendrimer Ions: A Molecular Dynamics/Ion Mobility Study? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1673-1683. [PMID: 32558569 DOI: 10.1021/jasms.0c00113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The globular shape of gaseous ions, resulting from the ionization of large molecules such as polymers and proteins, is a recurring subject that has undergone a renewed interest with the advent of ion mobility spectrometry (IMS), especially in conjunction with theoretical chemistry techniques such as Molecular Dynamics (MD). Globular conformations result from a fine balance between entropy and enthalpy considerations. For multiply charged ions isolated in the gas phase of a mass spectrometer, the Coulombic repulsion between the different charges tends to prevent the ions from adopting a compact, and folded 3D structure. In the present paper, we closely associate data from IMS experiments and MD simulations to unambiguously access the conformations of dendrimer ions in the gas phase with special attention paid to the dendrimer structure, the generation, and the charge state. By doing so, we here combine a set of structural tools able to evaluate the (non)globular shape of ions based on both experimental and theoretical results.
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Affiliation(s)
- Fabrice Saintmont
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Julien De Winter
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Fabien Chirot
- Univ Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Emilie Halin
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Philippe Dugourd
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Lyon, France
| | - Patrick Brocorens
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000 Mons, Belgium
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19
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Vimer S, Ben-Nissan G, Morgenstern D, Kumar-Deshmukh F, Polkinghorn C, Quintyn RS, Vasil’ev YV, Beckman JS, Elad N, Wysocki VH, Sharon M. Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry. ACS CENTRAL SCIENCE 2020; 6:573-588. [PMID: 32342007 PMCID: PMC7181328 DOI: 10.1021/acscentsci.0c00080] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Indexed: 05/06/2023]
Abstract
Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the Thermoplasma acidophilum archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast (Saccharomyces cerevisiae) and mammals (rat - Rattus norvegicus, rabbit - Oryctolagus cuniculus and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies.
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Affiliation(s)
- Shay Vimer
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - David Morgenstern
- Israel
Structural Proteomics Center, Weizmann Institute
of Science, Rehovot, Israel
| | | | - Caley Polkinghorn
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
| | - Royston S. Quintyn
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Yury V. Vasil’ev
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
| | - Joseph S. Beckman
- e-MSion
Inc., 2121 NE Jack London
Drive, Corvallis, Oregon 97330, United States
- Linus
Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Nadav Elad
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot, Israel
| | - Vicki H. Wysocki
- Department
of Chemistry and Biochemistry and Resource for Native Mass Spectrometry
Guided Structural Biology, Ohio State University, Columbus, Ohio 43210, United States
| | - Michal Sharon
- Department
of Biomolecular Sciences, Weizmann Institute
of Science, Rehovot, Israel
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20
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Morsa D, Hanozin E, Eppe G, Quinton L, Gabelica V, Pauw ED. Effective Temperature and Structural Rearrangement in Trapped Ion Mobility Spectrometry. Anal Chem 2020; 92:4573-4582. [DOI: 10.1021/acs.analchem.9b05850] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Denis Morsa
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Emeline Hanozin
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Gauthier Eppe
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Loïc Quinton
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, Laboratoire Acides Nucléiques: Régulations Naturelles et Artificielles (ARNA, U1212, UMR5320), IECB, Pessac 33600, France
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, MolSys Research Unit, University of Liège, Liège 4000, Belgium
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21
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Punt PM, Stratmann LM, Sevim S, Knauer L, Strohmann C, Clever GH. Heteroleptic Coordination Environments in Metal-Mediated DNA G-Quadruplexes. Front Chem 2020; 8:26. [PMID: 32064249 PMCID: PMC7000376 DOI: 10.3389/fchem.2020.00026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/09/2020] [Indexed: 12/28/2022] Open
Abstract
The presence of metal centers with often highly conserved coordination environments is crucial for roughly half of all proteins, having structural, regulatory, or enzymatic function. To understand and mimic the function of metallo-enzymes, bioinorganic chemists pursue the challenge of synthesizing model compounds with well-defined, often heteroleptic metal sites. Recently, we reported the design of tailored homoleptic coordination environments for various transition metal cations based on unimolecular DNA G-quadruplex structures, templating the regioselective positioning of imidazole ligandosides LI. Here, we expand this modular system to more complex, heteroleptic coordination environments by combining LI with a new benzoate ligandoside LB within the same oligonucleotide. The modifications still allow the correct folding of parallel tetramolecular and antiparallel unimolecular G-quadruplexes. Interestingly, the incorporation of LB results in strong destabilization expressed in lower thermal denaturation temperatures Tm. While no transition metal cations could be bound by G-quadruplexes containing only LB, heteroleptic derivatives containing both LI and LB were found to complex CuII, NiII, and ZnII. Especially in case of CuII we found strong stabilizations of up to ΔTm = +34°C. The here shown system represents an important step toward the design of more complex coordination environments inside DNA scaffolds, promising to culminate in the preparation of functional metallo-DNAzymes.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Lukas M Stratmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Sinem Sevim
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Lena Knauer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
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22
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Simmonds AL, Lopez-Clavijo AF, Winn PJ, Russell DH, Styles IB, Cooper HJ. Structural Analysis of 14-3-3-ζ-Derived Phosphopeptides Using Electron Capture Dissociation Mass Spectrometry, Traveling Wave Ion Mobility Spectrometry, and Molecular Modeling. J Phys Chem B 2020; 124:461-469. [PMID: 31859508 DOI: 10.1021/acs.jpcb.9b08506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Previously, we have demonstrated the effect of salt bridges on the electron capture dissociation mass spectrometry behavior of synthetic model phosphopeptides and applied an ion mobility spectrometry/molecular modeling approach to rationalize the findings in terms of peptide ion structure. Here, we develop and apply the approach to a biologically derived phosphopeptide. Specifically, we have investigated variants of a 15-mer phosphopeptide VVGARRSsWRVVSSI (s denotes phosphorylated Ser) derived from Akt1 substrate 14-3-3-ζ, which contains the phosphorylation motif RRSsWR. Variants were generated by successive arginine-to-leucine substitutions within the phosphorylation motif. ECD fragmentation patterns for the eight phosphopeptide variants show greater sequence coverage with successive R → L substitutions. Peptides with two or more basic residues had regions with no sequence coverage, while full sequence coverage was observed for peptides with one or no basic residues. For three of the peptide variants, low-abundance fragments were observed between the phosphoserine and a basic residue, possibly due to the presence of multiple conformers with and without noncovalent interactions between these residues. For the five variants whose dissociation behavior suggested the presence of intramolecular noncovalent interactions, we employed ion mobility spectrometry and molecular modeling to probe the nature of these interactions. Our workflow allowed us to propose candidate structures whose noncovalent interactions were consistent with the ECD data for all of the peptides modeled. Additionally, the AMBER parameter sets created for and validated by this work are presented and made available online ( http://www.biosciences-labs.bham.ac.uk/cooper/datasets.php ).
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Affiliation(s)
| | | | | | - David H Russell
- Texas A&M University , College Station , Texas 77843 , United States
| | - Iain B Styles
- Centre of Membrane Proteins and Receptors (COMPARE) , Universities of Birmingham and Nottingham , Midlands , U.K
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23
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Hoyas S, Halin E, Lemaur V, De Winter J, Gerbaux P, Cornil J. Helicity of Peptoid Ions in the Gas Phase. Biomacromolecules 2020; 21:903-909. [DOI: 10.1021/acs.biomac.9b01567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sébastien Hoyas
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
| | - Emilie Halin
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
- Department of General, Organic Biomedical Chemistry, NMR and Molecular Imaging Laboratory, University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
| | - Julien De Winter
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons (UMONS), 23 Place du Parc, 7000 Mons, Belgium
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24
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Punt PM, Clever GH. Tailored Transition-Metal Coordination Environments in Imidazole-Modified DNA G-Quadruplexes. Chemistry 2019; 25:13987-13993. [PMID: 31468606 PMCID: PMC6899475 DOI: 10.1002/chem.201903445] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/28/2019] [Indexed: 12/18/2022]
Abstract
Two types of imidazole ligands were introduced both at the end of tetramolecular and into the loop region of unimolecular DNA G‐quadruplexes. The modified oligonucleotides were shown to complex a range of different transition‐metal cations including NiII, CuII, ZnII and CoII, as indicated by UV/Vis absorption spectroscopy and ion mobility mass spectrometry. Molecular dynamics simulations were performed to obtain structural insight into the investigated systems. Variation of ligand number and position in the loop region of unimolecular sequences derived from the human telomer region (htel) allows for a controlled design of distinct coordination environments with fine‐tuned metal affinities. It is shown that CuII, which is typically square‐planar coordinated, has a higher affinity for systems offering four ligands, whereas NiII prefers G‐quadruplexes with six ligands. Likewise, the positioning of ligands in a square‐planar versus tetrahedral fashion affects binding affinities of CuII and ZnII cations, respectively. Gaining control over ligand arrangement patterns will spur the rational development of transition‐metal‐modified DNAzymes. Furthermore, this method is suited to combine different types of ligands, for example, those typically found in metalloenzymes, inside a single DNA architecture.
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Affiliation(s)
- Philip M Punt
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
| | - Guido H Clever
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Straße 6, 44227, Dortmund, Germany
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25
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D'Atri V, Gabelica V. DNA and RNA telomeric G-quadruplexes: what topology features can be inferred from ion mobility mass spectrometry? Analyst 2019; 144:6074-6088. [PMID: 31528871 DOI: 10.1039/c9an01216h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Maintenance of the telomeres is key to chromosome integrity and cell proliferation. The G-quadruplex structures formed by telomeric DNA and RNA (TTAGGG and UUAGGG repeats, respectively) are key to this process. However, because these sequences are particularly polymorphic, solving high-resolution structures is not always possible, and there is a need for new methodologies to characterize the multiple structures coexisting in solution. In this context, we evaluated whether ion mobility spectrometry coupled to native mass spectrometry could help separate and assign the G-quadruplex topologies. We explored the circular dichroism spectra, multimer formation, cation binding, and ion mobility spectra of several 4-repeat and 8-repeat telomeric DNA and RNA sequences, both in NH4+ and in K+. In 1 mM K+ and 100 mM trimethylammonium acetate, all RNAs fold intramolecularly (no multimer). In 8-repeat sequences, the subunits are not independent: in DNA the first subunit disfavors the folding of the second one, whereas in RNA the two subunits fold cooperatively via cation-mediated stacking. Ion mobility spectrometry shows that gas-phase structures keep a memory of - but are not identical to - the solution ones. At the native charge states, the loops can rearrange in a variety of ways (unless they are constrained by pre-formed hydrogen bonds), thereby wrapping the core and masking the strand arrangements. Our study highlights that, to progress towards structural assignment from IM-MS experiments, deeper understanding of the solution-to-gas-phase rearrangement mechanisms is warranted.
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Affiliation(s)
- Valentina D'Atri
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 rue Robert Escarpit, 33600 Pessac, France.
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26
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Porter JE, Chapagain P, Fernandez-Lima F. Single-stranded DNA structural diversity: TAGGGT from monomers to dimers to tetramer formation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 2:60-65. [PMID: 30506977 DOI: 10.1002/rcm.8367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
RATIONALE DNA quadruplex structures have emerged as novel drug targets due to their role in preventing abnormal gene transcription and maintaining telomere stability. Trapped Ion Mobility Spectrometry-Mass Spectrometry (TIMS-MS), combined with theoretical modeling, is a powerful tool for studying the kinetic intermediates of DNA complexes formed in solution and interrogated in the gas phase after desolvation. METHODS A TAGGGT ssDNA sequence was purchased and studied in 10 mM ammonium acetate using nanospray electrospray ionization (nESI)-TIMS-MS in positive and negative ion mode. Collisional cross section (CCS) profiles were measured using internal calibration (Tune Mix). Theoretical structures were proposed based on molecular dynamics, charge location and geometry optimization for the most intense IMS bands based on the number of TAGGGT units, adduct form and charge states. RESULTS A distribution of monomeric, dimeric and tetrameric TAGGGT structures were formed in solution and separated in the gas phase based on their mobility and m/z value (e.g., [M + 2H]+2 , [2M + 3H]+3 , [M - 2H]-2 , [2M - 3H]-3 , [4M + 4H]+4 , [4M + 3H + NH4 ]+4 , [4M + 2H + 2NH4 ]+4 and [4M + H + 3NH4 ]+4 ). The high mobility resolution of the TIMS-MS analyzer permitted the observation of multiple CCS bands per molecular ion form. Comparison with theoretical candidate structures suggests that monomeric TAGGGT species are stabilized by A-T and G+ -G interactions, with the size of the conformer influenced by the proton location. In the case of the TAGGGT quadruplex, the protonated species displayed a broad CCS distribution, while six discrete conformers were stabilized by the presence of ammonium ions (n = 1-3). CONCLUSIONS This is the first observation of multiple conformations of TAGGGT complexes (n = 1, 2 and 4) in 10 mM ammonium acetate. Candidate structures with intramolecular interactions of the form of G+ -G and traditional A-T base pairing agreed with the experimental trends. Our results demonstrate the structural diversity of TAGGGT monomers, dimers and tetramers in the gas phase beyond the previously reported solution structure, using 10 mM ammonium acetate to replicate biological conditions.
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Affiliation(s)
- Jacob E Porter
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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Khristenko N, Amato J, Livet S, Pagano B, Randazzo A, Gabelica V. Native Ion Mobility Mass Spectrometry: When Gas-Phase Ion Structures Depend on the Electrospray Charging Process. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1069-1081. [PMID: 30924079 DOI: 10.1007/s13361-019-02152-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
Ion mobility spectrometry (IMS) has become popular to characterize biomolecule folding. Numerous studies have shown that proteins that are folded in solution remain folded in the gas phase, whereas proteins that are unfolded in solution adopt more extended conformations in the gas phase. Here, we discuss how general this tenet is. We studied single-stranded DNAs (human telomeric cytosine-rich sequences with CCCTAA repeats), which fold into an intercalated motif (i-motif) structure in a pH-dependent manner, thanks to the formation of C-H+-C base pairs. As i-motif formation is favored at low ionic strength, we could investigate the ESI-IMS-MS behavior of i-motif structures at pH ~ 5.5 over a wide range of ammonium acetate concentrations (15 to 100 mM). The control experiments consisted of either the same sequence at pH ~ 7.5, wherein the sequence is unfolded, or sequence variants that cannot form i-motifs (CTCTAA repeats). The surprising results came from the control experiments. We found that the ionic strength of the solution had a greater effect on the compactness of the gas-phase structures than the solution folding state. This means that electrosprayed ions keep a memory of the charging process, which is influenced by the electrolyte concentration. We discuss these results in light of the analyte partitioning between the droplet interior and the droplet surface, which in turn influences the probability of being ionized via a charged residue-type pathway or a chain extrusion-type pathway.
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Affiliation(s)
- Nina Khristenko
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131, Naples, Italy
| | - Sandrine Livet
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, via Domenico Montesano 49, 80131, Naples, Italy
| | - Valérie Gabelica
- Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle, Université de Bordeaux, Inserm & CNRS (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
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28
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Myers CA, D'Esposito RJ, Fabris D, Ranganathan SV, Chen AA. CoSIMS: An Optimized Trajectory-Based Collision Simulator for Ion Mobility Spectrometry. J Phys Chem B 2019; 123:4347-4357. [PMID: 31042389 DOI: 10.1021/acs.jpcb.9b01018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A new, multithreaded, trajectory method based software platform, CoSIMS, is revealed and compared to reference MOBCAL collision cross sections (CCS). CoSIMS employs various molecular mechanics algorithms to lessen the computational resources required to simulate thousands of buffer gas-ion collisions, including the neglect of London dispersion interactions at long distances and the removal of trajectories that insignificantly contribute to the total CCS via an ellipsoidal projection approximation. The showcased program is used to calculate the collision cross sections of carbon fullerenes, proteins, and DNA strands of various lengths, sizes, and molecular weights, and these are compared against the CCSs calculated by MOBCAL. Through this analysis, it is shown that the application of the aforementioned algorithms enables both faster and more reasonable CCS calculations than MOBCAL for highly elongated molecules such as nucleic acids; for all other molecules, CoSIMS is able to reproduce the CCSs generated by MOBCAL's trajectory method within a few percent. Overall, CoSIMS is able to calculate nearly identical CCSs as MOBCAL in nearly 2 orders of magnitude less CPU time due to the various numerical methods implemented into the software, even when run on a single CPU core.
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Affiliation(s)
- Christopher A Myers
- Department of Physics , University at Albany (SUNY) , Albany , New York 12222 , United States
| | - Rebecca J D'Esposito
- Department of Chemistry , University at Albany (SUNY) , Albany , New York 12222 , United States
| | - Daniele Fabris
- Department of Chemistry , University at Albany (SUNY) , Albany , New York 12222 , United States.,The RNA Institute , University at Albany (SUNY) , Albany , New York 12222 , United States.,Department of Biological Sciences , University at Albany (SUNY) , Albany , New York 12222 , United States
| | | | - Alan A Chen
- Department of Chemistry , University at Albany (SUNY) , Albany , New York 12222 , United States.,The RNA Institute , University at Albany (SUNY) , Albany , New York 12222 , United States
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Bayat P, Gatineau D, Lesage D, Marhabaie S, Martinez A, Cole RB. Investigation of activation energies for dissociation of host-guest complexes in the gas phase using low-energy collision induced dissociation. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:437-448. [PMID: 30801903 DOI: 10.1002/jms.4345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/01/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
A low-energy collision induced dissociation (CID) (low-energy CID) approach that can determine both activation energy and activation entropy has been used to evaluate gas-phase binding energies of host-guest (H-G) complexes of a heteroditopic hemicryptophane cage host (Zn (II)@1) with a series of biologically relevant guests. In order to use this approach, preliminary calibration of the effective temperature of ions undergoing resonance excitation is required. This was accomplished by employing blackbody infrared radiative dissociation (BIRD) which allows direct measurement of activation parameters. Activation energies and pre-exponential factors were evaluated for more than 10 H-G complexes via the use of low-energy CID. The relatively long residence time of the ions inside the linear ion trap (maximum of 60 s) allowed the study of dissociations with rates below 1 s-1 . This possibility, along with the large size of the investigated ions, ensures the fulfilment of rapid energy exchange (REX) conditions and, as a consequence, accurate application of the Arrhenius equation. Compared with the BIRD technique, low-energy CID allows access to higher effective temperatures, thereby permitting one to probe more endothermic decomposition pathways. Based on the measured activation parameters, guests bearing a phosphate (-OPO3 2- ) functional group were found to bind more strongly with the encapsulating cage than those having a sulfonate (-SO3 - ) group; however, the latter ones make stronger bonds than those with a carboxylate (-CO2 - ) group. In addition, it was observed that the presence of trimethylammonium (-N(CH3 )3 + ) or phenyl groups in the guest's structure improves the strength of H-G interactions. The use of this technique is very straightforward, and it does not require any instrumental modifications. Thus, it can be applied to other H-G chemistry studies where comparison of bond dissociation energies is of paramount importance.
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Affiliation(s)
- Parisa Bayat
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, IPCM, 75252, Paris, France
| | - David Gatineau
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, IPCM, 75252, Paris, France
- Univ. Grenoble Alpes and CNRS, DCM (UMR 5250) BP 53, 38041, Grenoble Cedex 9, France
| | - Denis Lesage
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, IPCM, 75252, Paris, France
| | - Sina Marhabaie
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Alexandre Martinez
- Aix Marseille Université, UMR CNRS 7313-iSm2, Equipe Chirosciences, Av. Escadrille Normandie-Niemen, 13397, Marseille, France
| | - Richard B Cole
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, IPCM, 75252, Paris, France
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30
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Duez Q, Liénard R, Moins S, Lemaur V, Coulembier O, Cornil J, Gerbaux P, De Winter J. One Step Further in the Characterization of Synthetic Polymers by Ion Mobility Mass Spectrometry: Evaluating the Contribution of End-groups. Polymers (Basel) 2019; 11:E688. [PMID: 30995722 PMCID: PMC6523221 DOI: 10.3390/polym11040688] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/20/2022] Open
Abstract
Several families of polymers possessing various end-groups are characterized by ion mobility mass spectrometry (IMMS). A significant contribution of the end-groups to the ion collision cross section (CCS) is observed, although their role is neglected in current fitting models described in literature. Comparing polymers prepared from different synthetic procedures might thus, be misleading with the current theoretical treatments. We show that this issue is alleviated by comparing the CCS of various polymer ions (polyesters and polyethers) as a function of the number of atoms in the macroion instead of the usual representation involving the degree of polymerization. Finally, we extract the atom number density from the spectra which gives us the possibility to evaluate the compaction of polymer ions, and by extension to discern isomeric polymers.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Romain Liénard
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Sébastien Moins
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Olivier Coulembier
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.
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Punt PM, Clever GH. Imidazole-modified G-quadruplex DNA as metal-triggered peroxidase. Chem Sci 2019; 10:2513-2518. [PMID: 30931097 PMCID: PMC6399679 DOI: 10.1039/c8sc05020a] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 12/31/2018] [Indexed: 12/30/2022] Open
Abstract
Four imidazoles, serving as metalloprotein-inspired ligands for complexing a range of transition metal cations, were incorporated into tetramolecular G-quadruplex DNA structures. Modified quadruplexes were found to complex Cu(ii), Ni(ii), Zn(ii) and Co(ii) in a 1 : 1 ratio with unprecedented strong thermal stabilizations of up to ΔT 1/2 = +51 °C. Furthermore, addition of Cu(ii) was found to lead to extraordinarily fast G-quadruplex association rates with k on values being ∼100 times higher compared to unmodified G-quadruplexes. This is ascribed to a template effect of Cu(ii), preorganizing the four single strands via coordination, followed by rapid formation of hydrogen-bonded G-quartets. Native electrospray ionization mass spectrometry (ESI), coupled with trapped ion-mobility spectrometry (timsTOF), supports the proposed 1 : 1 G-quadruplex-metal complexes and could further disclose their ability to bind the iron-porphyrin complex hemin in a 1 : 1 stoichiometry. DNA sequence design allowed us to equip this G-quadruplex-hemin complex, known to function as a horseradish peroxidase mimic, with a metal-dependent trigger. A competitive screen of transition metals revealed a high selectivity for Cu(ii), even in mixtures of several divalent metal cations. Once formed, the Cu(ii)-carrying DNAzyme was shown to be preserved in the presence of EDTA, attributed to its remarkable kinetic stability. Stimuli-responsive G-quadruplexes promise application in DNAzymes with switchable activity, adaptive sensors and dynamic DNA origami constructs.
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Affiliation(s)
- Philip M Punt
- TU Dortmund University , Faculty for Chemistry and Chemical Biology , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Guido H Clever
- TU Dortmund University , Faculty for Chemistry and Chemical Biology , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
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32
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Ben-Nissan G, Vimer S, Tarnavsky M, Sharon M. Structural mass spectrometry approaches to study the 20S proteasome. Methods Enzymol 2019; 619:179-223. [DOI: 10.1016/bs.mie.2018.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Ben-Nissan G, Vimer S, Warszawski S, Katz A, Yona M, Unger T, Peleg Y, Morgenstern D, Cohen-Dvashi H, Diskin R, Fleishman SJ, Sharon M. Rapid characterization of secreted recombinant proteins by native mass spectrometry. Commun Biol 2018; 1:213. [PMID: 30534605 PMCID: PMC6277423 DOI: 10.1038/s42003-018-0231-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Characterization of overexpressed proteins is essential for assessing their quality, and providing input for iterative redesign and optimization. This process is typically carried out following purification procedures that require pronounced cost of time and labor. Therefore, quality assessment of recombinant proteins with no prior purification offers a major advantage. Here, we report a native mass spectrometry method that enables characterization of overproduced proteins directly from culture media. Properties such as solubility, molecular weight, folding, assembly state, overall structure, post-translational modifications and binding to relevant biomolecules are immediately revealed. We show the applicability of the method for in-depth characterization of secreted recombinant proteins from eukaryotic systems such as yeast, insect, and human cells. This method, which can be readily extended to high-throughput analysis, considerably shortens the time gap between protein production and characterization, and is particularly suitable for characterizing engineered and mutated proteins, and optimizing yield and quality of overexpressed proteins.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Aliza Katz
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Meital Yona
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yoav Peleg
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - David Morgenstern
- The De Botton protein Profiling Institute of the Nancy and Stephen Grand Israel national Center for Personalized Medicine, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Hadas Cohen-Dvashi
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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Interaction of rRNA with mRNA and tRNA in Translating Mammalian Ribosome: Functional Implications in Health and Disease. Biomolecules 2018; 8:biom8040100. [PMID: 30261607 PMCID: PMC6316650 DOI: 10.3390/biom8040100] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/31/2018] [Accepted: 09/13/2018] [Indexed: 01/01/2023] Open
Abstract
RNA-RNA interaction slowly emerges as a critical component for the smooth functioning of gene expression processes, in particular in translation where the central actor is an RNA powered molecular machine. Overall, ribosome dynamic results from sequential interactions between three main RNA species: ribosomal, transfer and messenger RNA (rRNA, tRNA and mRNA). In recent decades, special attention has been paid to the physical principles governing codon-anticodon pairing, whereas individual RNA positioning mostly relies on ribosomal RNA framework. Here, we provide a brief overview on the actual knowledge of RNA infrastructure throughout the process of translation in mammalian cells: where and how do these physical contacts occur? What are their potential roles and functions? Are they involved in disease development? What will be the main challenges ahead?
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Lippens JL, Ranganathan SV, D'Esposito RJ, Fabris D. Modular calibrant sets for the structural analysis of nucleic acids by ion mobility spectrometry mass spectrometry. Analyst 2018; 141:4084-99. [PMID: 27152369 DOI: 10.1039/c6an00453a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study explored the use of modular nucleic acid (NA) standards to generate calibration curves capable of translating primary ion mobility readouts into corresponding collision cross section (CCS) data. Putative calibrants consisted of single- (ss) and double-stranded (ds) oligo-deoxynucleotides reaching up to ∼40 kDa in size (i.e., 64 bp) and ∼5700 Å(2) in CCS. To ensure self-consistency among reference CCS values, computational data obtained in house were preferred to any experimental or computational data from disparate sources. Such values were obtained by molecular dynamics (MD) simulations and either the exact hard sphere scattering (EHSS) or the projection superposition approximation (PSA) methods, and then plotted against the corresponding experimental values to generate separate calibration curves. Their performance was evaluated on the basis of their correlation coefficients and ability to provide values that matched the CCS of selected test samples mimicking typical unknowns. The results indicated that the predictive power benefited from the exclusion of higher charged species that were more susceptible to the destabilizing effects of Coulombic repulsion. The results revealed discrepancies between EHSS and PSA data that were ascribable to the different approximations used to describe the ion mobility process. Within the boundaries defined by these approximations and the challenges of modeling NA structure in a solvent-free environment, the calibrant sets enabled the experimental determination of CCS with excellent reproducibility (precision) and error (accuracy), which will support the analysis of progressively larger NA samples of biological significance.
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Affiliation(s)
| | | | | | - Daniele Fabris
- University at Albany, Albany, New York, USA. and SUNY, Albany, The RNA Institute, 1400 Washington Avenue, Albany, New York, USA
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36
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Marchand A, Rosu F, Zenobi R, Gabelica V. Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry. J Am Chem Soc 2018; 140:12553-12565. [PMID: 30183275 DOI: 10.1021/jacs.8b07302] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Designing ligands targeting G-quadruplex nucleic acid structures and affecting cellular processes is complicated because there are multiple target sequences and some are polymorphic. Further, structure alone does not reveal the driving forces for ligand binding. To know why a ligand binds, the thermodynamics of binding must be characterized. Electrospray mass spectrometry enables one to detect and quantify each specific stoichiometry (number of strands, cations, and ligands) and thus to simultaneously determine the equilibrium constants for each complex. Using a temperature-controlled nanoelectrospray source, we determined the temperature dependence of the equilibrium constants, and thus the enthalpic and entropic contributions to the formation of each stoichiometry. Enthalpy drives the formation of each quartet-K+-quartet unit, whereas entropy drives the formation of quartet-K+-triplet units. Consequently, slip-stranded structures can become more abundant as the temperature increases. In the presence of ligands (Phen-DC3, TrisQ, TMPyP4, Cu-ttpy), we observed that, even when only a 1:1 (ligand/quadruplex) complex is observed at room temperature, new states are populated at intermediate temperatures, including 2:1 complexes. In most cases, ligand-G4-quadruplex binding is entropically driven, and we discuss that this may have resulted from biases when ranking ligand potency using melting experiments. Other thermodynamic profiles could be linked to topology changes in terms of number of G-quartets (reflected in the number of specific K+ ions in the complex). The thermodynamics of ligand binding to each form, one ligand at a time, provides unprecedented detail on the interplay between ligand binding and topology changes in terms of number of G-quartets.
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Affiliation(s)
- Adrien Marchand
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Frédéric Rosu
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Valérie Gabelica
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
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Lai R, Dodds ED, Li H. Molecular dynamics simulation of ion mobility in gases. J Chem Phys 2018; 148:064109. [PMID: 29448783 DOI: 10.1063/1.4998955] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A force field molecular dynamics method is developed to directly simulate ion drift in buffer gases driven by an electric field. The ion mobility and collision cross sections (CCSs) with relevance to ion mobility spectrometry can be obtained from the simulated drift velocity in high-density buffer gases (pressure ∼50 bars) and high electric fields (∼107 V/m). Compared to trajectory methods, the advantage of the molecular dynamics method is that it can simultaneously sample the internal dynamic motions of the ion and the ion-gas collisions. For ions with less than 100 atoms, the simulated collision cross section values can be converged to within ±1%-2% by running a 100 ns simulation for 5-19 h using one computer core. By using a set of element-based Lennard-Jones parameters that are not tuned for different atomic types in different molecules, the simulated collision cross sections for 15 small molecular ions (number of atoms ranging from 17 to 85, mass ranging from 74.1 to 609.4 g/mol) are consistent with experimental values: the mean unsigned error is 2.6 Å2 for He buffer gas and 4.4 Å2 for N2 buffer gas. The sensitivity of the simulated CCS values to random diffusion, drift velocity, electric field strength, temperature, and buffer gas density is examined.
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Affiliation(s)
- Rui Lai
- Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Eric D Dodds
- Department of Chemistry and Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Hui Li
- Department of Chemistry, Nebraska Center for Materials and Nanoscience, and Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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38
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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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39
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Zanotto L, Heerdt G, Souza PCT, Araujo G, Skaf MS. High performance collision cross section calculation-HPCCS. J Comput Chem 2018; 39:1675-1681. [PMID: 29498071 DOI: 10.1002/jcc.25199] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 12/13/2022]
Abstract
Since the commercial introduction of Ion Mobility coupled with Mass Spectrometry (IM-MS) devices in 2003, a large number of research laboratories have embraced the technique. IM-MS is a fairly rapid experiment used as a molecular separation tool and to obtain structural information. The interpretation of IM-MS data is still challenging and relies heavily on theoretical calculations of the molecule's collision cross section (CCS) against a buffer gas. Here, a new software (HPCCS) is presented, which performs CCS calculations using high perfomance computing techniques. Based on the trajectory method, HPCCS can accurately calculate CCS for a great variety of molecules, ranging from small organic molecules to large protein complexes, using helium or nitrogen as buffer gas with considerable gains in computer time compared to publicly available codes under the same level of theory. HPCCS is available as free software under the Academic Use License at https://github.com/cepid-cces/hpccs. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Leandro Zanotto
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, São Paulo, 13083-852, Brazil
| | - Gabriel Heerdt
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, São Paulo, 13083-852, Brazil
| | - Paulo C T Souza
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, São Paulo, 13083-852, Brazil.,Faculty of Mathematics and Natural Sciences, University of Groningen, Groningen, 9747, AG, The Netherlands
| | - Guido Araujo
- Institute of Computing and Center for Computational Engineering & Sciences, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Munir S Skaf
- Institute of Chemistry and Center for Computational Engineering & Sciences, University of Campinas, Campinas, São Paulo, 13083-852, Brazil
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40
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Mollerup CB, Mardal M, Dalsgaard PW, Linnet K, Barron LP. Prediction of collision cross section and retention time for broad scope screening in gradient reversed-phase liquid chromatography-ion mobility-high resolution accurate mass spectrometry. J Chromatogr A 2018; 1542:82-88. [DOI: 10.1016/j.chroma.2018.02.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/06/2018] [Accepted: 02/14/2018] [Indexed: 12/15/2022]
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41
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Lespes N, Pair E, Maganga C, Bretier M, Tognetti V, Joubert L, Levacher V, Hubert-Roux M, Afonso C, Loutelier-Bourhis C, Brière JF. A Unique (3+2) Annulation Reaction between Meldrum's Acid and Nitrones: Mechanistic Insight by ESI-IMS-MS and DFT Studies. Chemistry 2018; 24:4086-4093. [PMID: 29297600 DOI: 10.1002/chem.201705714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Indexed: 11/10/2022]
Abstract
The fragile intermediates of the domino process leading to an isoxazolidin-5-one, triggered by unique reactivity between Meldrum's acid and an N-benzyl nitrone in the presence of a Brønsted base, were determined thanks to the softness and accuracy of electrospray ionization mass spectrometry coupled to ion mobility spectrometry (ESI-IMS-MS). The combined DFT study shed light on the overall organocatalytic sequence that starts with a stepwise (3+2) annulation reaction that is followed by a decarboxylative protonation sequence encompassing a stereoselective pathway issue.
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Affiliation(s)
- Nicolas Lespes
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Etienne Pair
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Clisy Maganga
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Marie Bretier
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Vincent Tognetti
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Laurent Joubert
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Vincent Levacher
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Marie Hubert-Roux
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
| | - Carlos Afonso
- Normandie Univ, INSA Rouen, UNIROUEN, CNRS, COBRA, 76000, Rouen, France
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42
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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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43
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Re S, Watabe S, Nishima W, Muneyuki E, Yamaguchi Y, MacKerell AD, Sugita Y. Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase. Sci Rep 2018; 8:1644. [PMID: 29374210 PMCID: PMC5786100 DOI: 10.1038/s41598-018-20012-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/10/2018] [Indexed: 12/18/2022] Open
Abstract
Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational differences, but the relationship between CCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gas-phase N-glycans under the electrospray ionization condition using molecular dynamics simulations with enhanced sampling. We show that the separation of CCSs between isomers reflects folding features of N-glycans, which are determined both by chemical compositions and protonation states. Providing a physicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also to estimate CCSs of complex glycans.
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Affiliation(s)
- Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shigehisa Watabe
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Wataru Nishima
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Eiro Muneyuki
- Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, 21201, USA
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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44
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Lee JW, Lee HHL, Davidson KL, Bush MF, Kim HI. Structural characterization of small molecular ions by ion mobility mass spectrometry in nitrogen drift gas: improving the accuracy of trajectory method calculations. Analyst 2018; 143:1786-1796. [DOI: 10.1039/c8an00270c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An accurate theoretical collision cross section calculation method in nitrogen was developed for reliable structural ion mobility mass spectrometry.
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Affiliation(s)
- Jong Wha Lee
- Center for Analytical Chemistry
- Division of Chemical and Medical Metrology
- Korea Research Institute of Standards and Science (KRISS)
- Daejeon 34113
- Republic of Korea
| | - Hyun Hee L. Lee
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
| | | | | | - Hugh I. Kim
- Department of Chemistry
- Korea University
- Seoul 02841
- Republic of Korea
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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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Marchand A, Livet S, Rosu F, Gabelica V. Drift Tube Ion Mobility: How to Reconstruct Collision Cross Section Distributions from Arrival Time Distributions? Anal Chem 2017; 89:12674-12681. [DOI: 10.1021/acs.analchem.7b01736] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Adrien Marchand
- INSERM, CNRS, Université
Bordeaux, Laboratoire Acides Nucléiques Régulations
Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Sandrine Livet
- INSERM, CNRS, Université
Bordeaux, Laboratoire Acides Nucléiques Régulations
Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Frédéric Rosu
- CNRS, INSERM, Université
Bordeaux, Institut Européen de Chimie et Biologie (IECB, UMS3033,
US001), 2 rue Robert Escarpit, 33607 Pessac, France
| | - Valérie Gabelica
- INSERM, CNRS, Université
Bordeaux, Laboratoire Acides Nucléiques Régulations
Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
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47
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Duez Q, Chirot F, Liénard R, Josse T, Choi C, Coulembier O, Dugourd P, Cornil J, Gerbaux P, De Winter J. Polymers for Traveling Wave Ion Mobility Spectrometry Calibration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2483-2491. [PMID: 28762031 DOI: 10.1007/s13361-017-1762-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/30/2017] [Accepted: 07/09/2017] [Indexed: 06/07/2023]
Abstract
One of the main issues when using traveling wave ion mobility spectrometry (TWIMS) for the determination of collisional cross-section (CCS) concerns the need for a robust calibration procedure built from referent ions of known CCS. Here, we implement synthetic polymer ions as CCS calibrants in positive ion mode. Based on their intrinsic polydispersities, polymers offer in a single sample the opportunity to generate, upon electrospray ionization, numerous ions covering a broad mass range and a large CCS window for different charge states at a time. In addition, the key advantage of polymer ions as CCS calibrants lies in the robustness of their gas-phase structure with respect to the instrumental conditions, making them less prone to collisional-induced unfolding (CIU) than protein ions. In this paper, we present a CCS calibration procedure using sodium cationized polylactide and polyethylene glycol, PLA and PEG, as calibrants with reference CCS determined on a home-made drift tube. Our calibration procedure is further validated by testing the polymer calibration to determine CCS of numerous different ions for which CCS are reported in the literature. Graphical Abstract ᅟ.
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Affiliation(s)
- Quentin Duez
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Fabien Chirot
- Université Lyon, Université Claude Bernard Lyon 1, ENS de Lyon, CNRS, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Romain Liénard
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - Thomas Josse
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - ChangMin Choi
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Olivier Coulembier
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMons, 23 Place du Parc, 7000, Mons, Belgium
| | - Philippe Dugourd
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622, Lyon, France
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), University of Mons (UMons), Place du Parc, 23, Mons, 7000, Belgium.
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48
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Chan DSH, Kavanagh ME, McLean KJ, Munro AW, Matak-Vinković D, Coyne AG, Abell C. Effect of DMSO on Protein Structure and Interactions Assessed by Collision-Induced Dissociation and Unfolding. Anal Chem 2017; 89:9976-9983. [DOI: 10.1021/acs.analchem.7b02329] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Daniel S.-H. Chan
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Madeline E. Kavanagh
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Kirsty J. McLean
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Andrew. W. Munro
- Centre
for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM),
Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Dijana Matak-Vinković
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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49
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Vangaveti S, D’Esposito RJ, Lippens JL, Fabris D, Ranganathan SV. A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry. Phys Chem Chem Phys 2017; 19:14937-14946. [PMID: 28374022 PMCID: PMC6958515 DOI: 10.1039/c7cp00717e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) is a rapidly emerging tool for the investigation of nucleic acid structure and dynamics. IMS-MS determinations can provide valuable information regarding alternative topologies, folding intermediates, and conformational heterogeneities, which are not readily accessible to other analytical techniques. The leading strategies for data interpretation rely on computational and experimental approaches to correctly assign experimental observations to putative structures. A very effective strategy involves the application of molecular dynamics (MD) simulations to predict the structure of the analyte molecule, calculate its collision cross section (CCS), and then compare this computational value with the corresponding experimental data. While this approach works well for small nucleic acid species, analyzing larger nucleic acids of biological interest is hampered by the computational cost associated with capturing their extensive structure and dynamics in all-atom detail. In this report, we describe the implementation of a coarse graining (CG) approach to reduce the cost of the computational methods employed in the data interpretation workflow. Our framework employs a five-bead model to accurately represent each nucleotide in the nucleic acid structure. The beads are appropriately parameterized to enable the direct calculation of CCS values from CG models, thus affording the ability to pursue the analysis of larger, highly dynamic constructs. The validity of this approach was successfully confirmed by the excellent correlation between the CCS values obtained in parallel by all-atom and CG workflows.
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Affiliation(s)
| | | | - J. L. Lippens
- Discovery Analytical Sciences, Amgen, Thousand Oaks, CA
| | - D. Fabris
- The RNA Institute, University at Albany, NY
- Department of Chemistry, University at Albany, NY
- Department of Biological Sciences, University at Albany, NY
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50
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Porrini M, Rosu F, Rabin C, Darré L, Gómez H, Orozco M, Gabelica V. Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry. ACS CENTRAL SCIENCE 2017; 3:454-461. [PMID: 28573208 PMCID: PMC5445532 DOI: 10.1021/acscentsci.7b00084] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Indexed: 05/25/2023]
Abstract
We report on the fate of nucleic acids conformation in the gas phase as sampled using native mass spectrometry coupled to ion mobility spectrometry. On the basis of several successful reports for proteins and their complexes, the technique has become popular in structural biology, and the conformation survival becomes more and more taken for granted. Surprisingly, we found that DNA and RNA duplexes, at the electrospray charge states naturally obtained from native solution conditions (≥100 mM aqueous NH4OAc), are significantly more compact in the gas phase compared to the canonical solution structures. The compaction is observed for all duplex sizes (gas-phase structures are more compact than canonical B-helices by ∼20% for 12-bp, and by up to ∼30% for 36-bp duplexes), and for DNA and RNA alike. Molecular modeling (density functional calculations on small helices, semiempirical calculations on up to 12-bp, and molecular dynamics on up to 36-bp duplexes) demonstrates that the compaction is due to phosphate group self-solvation prevailing over Coulomb repulsion. Molecular dynamics simulations starting from solution structures do not reproduce the experimental compaction. To be experimentally relevant, molecular dynamics sampling should reflect the progressive structural rearrangements occurring during desolvation. For nucleic acid duplexes, the compaction observed for low charge states results from novel phosphate-phosphate hydrogen bonds formed across both grooves at the very late stages of electrospray.
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Affiliation(s)
- Massimiliano Porrini
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Frédéric Rosu
- CNRS,
INSERM, Université de Bordeaux, Institut
Européen de Chimie et Biologie (IECB, UMS3033, US001), 2 rue Robert Escarpit, 33607 Pessac, France
| | - Clémence Rabin
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Leonardo Darré
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
| | - Hansel Gómez
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
| | - Modesto Orozco
- The
Barcelona Institute of Science and Technology, Institute for Research in Biomedicine (IRB) Barcelona, Baldiri Reixac 10, 08028 Barcelona, Spain
- Joint
BSC-CRG-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona, Spain
- Department
of Biochemistry and Biomedicine, University
of Barcelona, Avda Diagonal
647, 08028 Barcelona, Spain
| | - Valérie Gabelica
- INSERM,
CNRS, Université de Bordeaux, Acides
Nucléiques Régulations Naturelle et Artificielle (ARNA,
U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
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