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Girgis M, Petruncio G, Russo P, Peyton S, Paige M, Campos D, Sanda M. Analysis of N- and O-linked site-specific glycosylation by ion mobility mass spectrometry: State of the art and future directions. Proteomics 2024; 24:e2300281. [PMID: 38171879 DOI: 10.1002/pmic.202300281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/22/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]
Abstract
Glycosylation, the major post-translational modification of proteins, significantly increases the diversity of proteoforms. Glycans are involved in a variety of pivotal structural and functional roles of proteins, and changes in glycosylation are profoundly connected to the progression of numerous diseases. Mass spectrometry (MS) has emerged as the gold standard for glycan and glycopeptide analysis because of its high sensitivity and the wealth of fragmentation information that can be obtained. Various separation techniques have been employed to resolve glycan and glycopeptide isomers at the front end of the MS. However, differentiating structures of isobaric and isomeric glycopeptides constitutes a challenge in MS-based characterization. Many reports described the use of various ion mobility-mass spectrometry (IM-MS) techniques for glycomic analyses. Nevertheless, very few studies have focused on N- and O-linked site-specific glycopeptidomic analysis. Unlike glycomics, glycoproteomics presents a multitude of inherent challenges in microheterogeneity, which are further exacerbated by the lack of dedicated bioinformatics tools. In this review, we cover recent advances made towards the growing field of site-specific glycosylation analysis using IM-MS with a specific emphasis on the MS techniques and capabilities in resolving isomeric peptidoglycan structures. Furthermore, we discuss commonly used software that supports IM-MS data analysis of glycopeptides.
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Affiliation(s)
- Michael Girgis
- Department of Bioengineering, College of Engineering & Computing, George Mason University, Fairfax, Virginia, USA
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
| | - Gregory Petruncio
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
- Department of Chemistry & Biochemistry, College of Science, George Mason University, Fairfax, Virginia, USA
| | - Paul Russo
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Steven Peyton
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
| | - Mikell Paige
- Center for Molecular Engineering, George Mason University, Manassas, Virginia, USA
- Department of Chemistry & Biochemistry, College of Science, George Mason University, Fairfax, Virginia, USA
| | - Diana Campos
- Max-Planck-Institut fuer Herz- und Lungenforschung, Bad Nauheim, Germany
| | - Miloslav Sanda
- Max-Planck-Institut fuer Herz- und Lungenforschung, Bad Nauheim, Germany
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2
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Kohoutek KM, Harrington PDB. Electrospray Ionization Ion Mobility Mass Spectrometry. Crit Rev Anal Chem 2021; 53:483-497. [PMID: 34547945 DOI: 10.1080/10408347.2021.1964938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Electrospray ionization ion mobility mass spectrometry (ESI-IMS-MS) is a rapidly progressing analytical technique for the examination of complex compounds in the gas phase. ESI-IMS-MS separates isomers, provides structural information, and quantitatively identifies peptides, lipids, carbohydrates, polymers, and metabolites in biological samples. ESI-IMS-MS has pharmaceutical, environmental, and manufacturing applications quickly characterizing drugs, petroleum products, and metal macromolecules. This review provides the history of ESI-IMS-MS development and applications to date.
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Affiliation(s)
- Katie M. Kohoutek
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, USA
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3
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Bohl J, Sicard C, Rezaei H, Van der Rest G, Halgand F. Evidence of conformational landscape alteration and macromolecular complex formation in the early stages of in vitro human prion protein oxidation. Arch Biochem Biophys 2020; 690:108432. [PMID: 32663474 DOI: 10.1016/j.abb.2020.108432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 10/23/2022]
Abstract
Oxidative stress is proposed to be one of the major causes of neurodegenerative diseases. Cellular prion protein (PrP) oxidation has been widely studied using chemical reagents such as hydrogen peroxide. However, the experimental conditions used do not faithfully reflect the physiological environment of the cell. With the goal to explore the conformational landscape of PrP under oxidative stress, we conducted a set of experiments combining the careful control of the nature and the amount of ROS produced by a60Co γ-irradiation source. Characterization of the resulting protein species was achieved using a set of analytical techniques. Under our experimental condition hydroxyl radical are the main reactive species produced. The most important findings are i) the formation of molecular assemblies under oxidative stress, ii) the detection of a majority of unmodified monomer mixed with oxidized monomers in these molecular assemblies at low hydroxyl radical concentration, iii) the absence of significant oxidation on the monomer fraction after irradiation. Molecular assemblies are produced in small amounts and were shown to be an octamer. These results suggest either i) an active recruitment of intact monomers by molecular assemblies' oxidized monomers then inducing a structural change of their intact counterparts or ii) an intrinsic capability of intact monomer conformers to spontaneously associate to form stable molecular assemblies when oxidized monomers are present. Finally, abundances of the intact monomer conformers after irradiation were modified. This suggests that monomers of the molecular assemblies exchange structural information with intact irradiated monomer. All these results shed a new light on structural exchange information between PrP monomers under oxidative stress.
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Affiliation(s)
- Jan Bohl
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Cécile Sicard
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Human Rezaei
- Institut National de la Recherche Agronomique, UR892, Virologie Immunologie Moléculaires, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Guillaume Van der Rest
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France
| | - Frédéric Halgand
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay, France.
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4
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Transient multimers modulate conformer abundances of prion protein monomer through conformational selection. Sci Rep 2019; 9:12159. [PMID: 31434938 PMCID: PMC6704068 DOI: 10.1038/s41598-019-48377-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/01/2019] [Indexed: 01/15/2023] Open
Abstract
Prions are known to be involved in neurodegenerative pathologies such as Creutzfeld-Jakob disease. Current models point to a molecular event which rely on a transmissible structural change that leads to the production of β-sheet-rich prion conformer (PrPSc). PrPSc itself has the capability to trigger the structural rearrangement of the ubiquitously present prion (PrPc) substrate in a self-perpetuating cascade. In this article, we demonstrate that recombinant PrPc exists in a conformational equilibrium. The conformers’ abundances were shown to be dependent on PrPc concentration through the formation of transient multimers leading to conformational selection. The study of PrPc mutants that follow dedicated oligomerization pathways demonstrated that the conformers’ relative abundances are modified, thus reinforcing the assertion that the nature of conformers’ interactions orient the oligomerization pathways. Further this result can be viewed as the “signature” of an aborted oligomerization process. This discovery sheds a new light on the possible origin of prion protein diseases, namely that a change in prion protein structure could be transmitted through the formation of transient multimers having different conformer compositions. This could explain the selection of a transient multimeric type that could be viewed as the precursor of PrPSc responsible for structural information transmission, and strain apparition.
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Mitra G. Application of native mass spectrometry in studying intrinsically disordered proteins: A special focus on neurodegenerative diseases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140260. [PMID: 31382021 DOI: 10.1016/j.bbapap.2019.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022]
Abstract
Intrinsically disordered proteins (IDPs) are integral part of the proteome, regulating vital biological processes. Such proteins gained further visibility due to their key role in neurodegenerative diseases and cancer. IDPs however, escape structural characterization by traditional biophysical tools owing to their extreme flexibility and heterogeneity. In this review, we discuss the advantages of native mass spectrometry (MS) in analysing the atypical conformational dynamics of IDPs and recent advances made in the field. Especially, MS studies unravelling the conformational facets of IDPs involved in neurodegenerative diseases are highlighted. The limitations and the future promises of native MS while studying IDPs have been discussed.
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Affiliation(s)
- Gopa Mitra
- Clinical Proteomics Unit, Division of Molecular Medicine, St. John's Research Institute, St. John's National Academy of Health Sciences, 100 Feet Road, Koramangala, Bangalore 560034, Karnataka, India.
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6
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Laszlo KJ, Bush MF. Interpreting the Collision Cross Sections of Native-like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions. Anal Chem 2017. [PMID: 28636334 DOI: 10.1021/acs.analchem.7b01474] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of charge state on structures of native-like cations of serum albumin, streptavidin, avidin, and alcohol dehydrogenase were probed using cation-to-anion proton-transfer reactions (CAPTR), ion mobility, mass spectrometry, and complementary energy-dependent experiments. The CAPTR products all have collision cross-section (Ω) values that are within 5.5% of the original precursor cations. The first CAPTR event for each precursor yields products that have smaller Ω values and frequently exhibit the greatest magnitude of change in Ω resulting from a single CAPTR event. To investigate how the structures of the precursors affect the structures of the products, ions were activated as a function of energy prior to CAPTR. In each case, the Ω values of the activated precursors increase with increasing energy, but the Ω values of the CAPTR products are smaller than the activated precursors. To investigate the stabilities of the CAPTR products, the products were activated immediately prior to ion mobility. These results show that additional structures with smaller or larger Ω values can be populated and that the structures and stabilities of these ions depend most strongly on the identity of the protein and the charge state of the product, rather than the charge state of the precursor or the number of CAPTR events. Together, these results indicate that the excess charges initially present on native-like ions have a modest, but sometimes statistically significant, effect on their Ω values. Therefore, potential contributions from charge state should be considered when using experimental Ω values to elucidate structures in solution.
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Affiliation(s)
- 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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Laszlo KJ, Buckner JH, Munger EB, Bush MF. Native-Like and Denatured Cytochrome c Ions Yield Cation-to-Anion Proton Transfer Reaction Products with Similar Collision Cross-Sections. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1382-1391. [PMID: 28224394 PMCID: PMC5555649 DOI: 10.1007/s13361-017-1620-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 05/04/2023]
Abstract
The relationship between structures of protein ions, their charge states, and their original structures prior to ionization remains challenging to decouple. Here, we use cation-to-anion proton transfer reactions (CAPTR) to reduce the charge states of cytochrome c ions in the gas phase, and ion mobility to probe their structures. Ions were formed using a new temperature-controlled nanoelectrospray ionization source at 25 °C. Characterization of this source demonstrates that the temperature of the liquid sample is decoupled from that of the atmospheric pressure interface, which is heated during CAPTR experiments. Ionization from denaturing conditions yields 18+ to 8+ ions, which were each isolated and reacted with monoanions to generate all CAPTR products with charge states of at least 3+. The highest, intermediate, and lowest charge-state products exhibit collision cross-section distributions that are unimodal, multimodal, and unimodal, respectively. These distributions depend strongly on the charge state of the product, although those for the intermediate charge-state products also depend on that of the precursor. The distributions of the 3+ products are all similar, with averages that are less than half that of the 18+ precursor ions. Ionization of cytochrome c from native-like conditions yields 7+ and 6+ ions. The 3+ CAPTR products from these precursors have slightly more compact collision cross-section distributions that are indistinguishable from those for the 3+ CAPTR products from denaturing conditions. More broadly, these results indicate that the collision cross-sections of ions of this single domain protein depend strongly on charge state for charge states greater than ~4. Graphical Abstract ᅟ.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - John H Buckner
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
- Department of Chemistry, Carleton College, One North College Street, Northfield, MN, 55057, USA
| | - Eleanor B Munger
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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8
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Van der Rest G, Rezaei H, Halgand F. Monitoring Conformational Landscape of Ovine Prion Protein Monomer Using Ion Mobility Coupled to Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:303-314. [PMID: 27757822 DOI: 10.1007/s13361-016-1522-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 10/05/2016] [Accepted: 10/06/2016] [Indexed: 06/06/2023]
Abstract
Prion protein is involved in deadly neurodegenerative diseases. Its pathogenicity is linked to its structural conversion (α-helix to β-strand transition). However, recent studies suggest that prion protein can follow a plurality of conversion pathways, which hints towards different conformers that might coexist in solution. To gain insights on the plasticity of the ovine prion protein (PrP) monomer, wild type (A136, R154, Q171), mutants and deletions of ARQ were studied by traveling wave ion mobility experiments coupled to mass spectrometry. In order to perform the analysis of a large body of data sets, we designed and evaluated the performance of a processing pipeline based on Driftscope peak detection and a homemade script for automated peak assignment, annotation, and quantification on specific multiply charged protein data. Using this approach, we showed that in the gas phase, PrPs are represented by at least three conformer families differing in both charge state distribution and collisional cross-section, in agreement with the work of Hilton et al. (2010). We also showed that this plasticity is borne both by the N- and C-terminal domains. Effect of protein concentration, pH and temperature were also assessed, showing that (1) pH does not affect conformer distributions, (2) protein concentration modifies the conformational landscape of one mutant (I208M) only, and (3) heating leads to other unfolded species and to a modification of the conformer intensity ratios. Graphical Abstract ᅟ.
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Affiliation(s)
- Guillaume Van der Rest
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS UMR 8000, 91405, Orsay, France
| | - Human Rezaei
- Institut National de la Recherche Agronomique, UR892, Virologie Immunologie Moléculaires, Domaine de Vilvert, 78350, Jouy-en-Josas, France
| | - Frédéric Halgand
- Laboratoire de Chimie Physique, Université Paris Sud, CNRS UMR 8000, 91405, Orsay, France.
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9
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Abstract
In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.
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Affiliation(s)
- Jody C May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - Caleb B Morris
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
| | - John A McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University , Nashville, Tennessee 37235, United States
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10
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Laszlo KJ, Munger EB, Bush MF. Folding of Protein Ions in the Gas Phase after Cation-to-Anion Proton-Transfer Reactions. J Am Chem Soc 2016; 138:9581-8. [PMID: 27399988 PMCID: PMC4999245 DOI: 10.1021/jacs.6b04282] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The structure and folding of a protein in solution depends on noncovalent interactions within the protein and those with surrounding ions and molecules. Decoupling these interactions in solution is challenging, which has hindered the development of accurate physics-based models for structure prediction. Investigations of proteins in the gas phase can be used to selectively decouple factors affecting the structures of proteins. Here, we use cation-to-anion proton-transfer reactions (CAPTR) to reduce the charge states of denatured ubiquitin ions in the gas phase, and ion mobility to probe their structures. In CAPTR, a precursor charge state is selected (P) and reacted with monoanions to generate charge-reduced product ions (C). Following each CAPTR event, denatured ubiquitin ions (13+ to 6+) yield products that rapidly isomerize to structures that have smaller collision cross sections (Ω). The Ω values of CAPTR product ions depend strongly on C and very weakly on P. Pre- and post-CAPTR activation was then used to probe the potential-energy surfaces of the precursor and product ions, respectively. Post-CAPTR activation showed that ions of different P fold differently and populate different regions of the potential-energy surface of that ion. Finally, pre-CAPTR activation showed that the structures of protein ions can be indirectly investigated using ion mobility of their CAPTR product ions, even for subtle structural differences that are not apparent from ion mobility characterization of the activated precursor ions. More generally, these results show that CAPTR strongly complements existing techniques for characterizing the structures and dynamics of biological molecules in the gas phase.
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Affiliation(s)
- Kenneth J. Laszlo
- University of Washington, Department of Chemistry, Box 351700 Seattle, WA 98195-1700
| | - Eleanor B. Munger
- University of Washington, Department of Chemistry, Box 351700 Seattle, WA 98195-1700
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700 Seattle, WA 98195-1700
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11
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Lantsuzskaya EV, Krisilov AV, Levina AM. Structure of the cluster ions of ketones in the gas phase according to ion mobility spectrometry and ab initio calculations. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2015. [DOI: 10.1134/s0036024415100179] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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12
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Nyon MP, Prentice T, Day J, Kirkpatrick J, Sivalingam GN, Levy G, Haq I, Irving JA, Lomas DA, Christodoulou J, Gooptu B, Thalassinos K. An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of α1 -antitrypsin upon ligand binding. Protein Sci 2015; 24:1301-12. [PMID: 26011795 PMCID: PMC4534181 DOI: 10.1002/pro.2706] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/05/2015] [Accepted: 05/11/2015] [Indexed: 11/11/2022]
Abstract
Native mass spectrometry (MS) methods permit the study of multiple protein species within solution equilibria, whereas ion mobility (IM)-MS can report on conformational behavior of specific states. We used IM-MS to study a conformationally labile protein (α1 -antitrypsin) that undergoes pathological polymerization in the context of point mutations. The folded, native state of the Z-variant remains highly polymerogenic in physiological conditions despite only minor thermodynamic destabilization relative to the wild-type variant. Various data implicate kinetic instability (conformational lability within a native state ensemble) as the basis of Z α1 -antitrypsin polymerogenicity. We show the ability of IM-MS to track such disease-relevant conformational behavior in detail by studying the effects of peptide binding on α1 -antitrypsin conformation and dynamics. IM-MS is, therefore, an ideal platform for the screening of compounds that result in therapeutically beneficial kinetic stabilization of native α1 -antitrypsin. Our findings are confirmed with high-resolution X-ray crystallographic and nuclear magnetic resonance spectroscopic studies of the same event, which together dissect structural changes from dynamic effects caused by peptide binding at a residue-specific level. IM-MS methods, therefore, have great potential for further study of biologically relevant thermodynamic and kinetic instability of proteins and provide rapid and multidimensional characterization of ligand interactions of therapeutic interest.
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Affiliation(s)
- Mun Peak Nyon
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Tanya Prentice
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Jemma Day
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - John Kirkpatrick
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Ganesh N Sivalingam
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Geraldine Levy
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Imran Haq
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, United Kingdom
| | - James A Irving
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, United Kingdom
| | - David A Lomas
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, United Kingdom
| | - John Christodoulou
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
| | - Bibek Gooptu
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, WC1E 7HX, United Kingdom.,Division of Asthma, Allergy and Lung Biology, King's College London, Guy's Hospital, London, SE1 9RT, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, WC1E 7HX, United Kingdom
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13
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Structural Characterisation of Non-Deamidated Acidic Variants of Erwinia chrysanthemi L-asparaginase Using Small-Angle X-ray Scattering and Ion-Mobility Mass Spectrometry. Pharm Res 2015; 32:3636-48. [DOI: 10.1007/s11095-015-1722-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/20/2015] [Indexed: 02/04/2023]
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14
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Cumeras R, Figueras E, Davis CE, Baumbach JI, Gràcia I. Review on ion mobility spectrometry. Part 1: current instrumentation. Analyst 2015; 140:1376-90. [PMID: 25465076 PMCID: PMC4331213 DOI: 10.1039/c4an01100g] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ion Mobility Spectrometry (IMS) is a widely used and 'well-known' technique of ion separation in the gaseous phase based on the differences in ion mobilities under an electric field. All IMS instruments operate with an electric field that provides space separation, but some IMS instruments also operate with a drift gas flow that provides also a temporal separation. In this review we will summarize the current IMS instrumentation. IMS techniques have received an increased interest as new instrumentation and have become available to be coupled with mass spectrometry (MS). For each of the eight types of IMS instruments reviewed it is mentioned whether they can be hyphenated with MS and whether they are commercially available. Finally, out of the described devices, the six most-consolidated ones are compared. The current review article is followed by a companion review article which details the IMS hyphenated techniques (mainly gas chromatography and mass spectrometry) and the factors that make the data from an IMS device change as a function of device parameters and sampling conditions. These reviews will provide the reader with an insightful view of the main characteristics and aspects of the IMS technique.
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Affiliation(s)
- R Cumeras
- Institut de Microelectrònica de Barcelona, IMB-CNM (CSIC), Esfera UAB, Campus UAB s/n, E-08193 Bellaterra, Barcelona, Spain.
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15
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Remmele RL, Bee JS, Phillips JJ, Mo WD, Higazi DR, Zhang J, Lindo V, Kippen AD. Characterization of Monoclonal Antibody Aggregates and Emerging Technologies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1202.ch005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Richard L. Remmele
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jared S. Bee
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jonathan J. Phillips
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Wenjun David Mo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Daniel R. Higazi
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jifeng Zhang
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Vivian Lindo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Alistair D. Kippen
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
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16
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Bowers MT. Ion mobility spectrometry: A personal view of its development at UCSB. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2014; 370:75-95. [PMID: 25147478 PMCID: PMC4135396 DOI: 10.1016/j.ijms.2014.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Ion mobility is not a newly discovered phenomenon. It has roots going back to Langevin at the beginning of the 20th century. Our group initially got involved by accident around 1990 and this paper is a brief account of what has transpired here at UCSB the past 25 years in response to this happy accident. We started small, literally, with transition metal atomic ions and transitioned to carbon clusters, synthetic polymers, most types of biological molecules and eventually peptide and protein oligomeric assembly. Along the way we designed and built several generations of instruments, a process that is still ongoing. And perhaps most importantly we have incorporated theory with experiment from the beginning; a necessary wedding that allows an atomistic face to be put on the otherwise interesting but not fully informative cross section measurements.
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17
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Sivalingam GN, Yan J, Sahota H, Thalassinos K. Amphitrite: A program for processing travelling wave ion mobility mass spectrometry data. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2013; 345-347:54-62. [PMID: 25844045 PMCID: PMC4375678 DOI: 10.1016/j.ijms.2012.09.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/04/2012] [Accepted: 09/13/2012] [Indexed: 05/11/2023]
Abstract
Since the introduction of travelling wave (T-Wave)-based ion mobility in 2007 a large number of research laboratories have embraced the technique, particularly those working in the field of structural biology. The development of software to process the data generated from this technique, however, has been limited. We present a novel software package that enables the processing of T-Wave ion mobility data. The program can deconvolute components in a mass spectrum and uses this information to extract corresponding arrival time distributions (ATDs) with minimal user intervention. It can also be used to automatically create a collision cross section (CCS) calibration and apply this to subsequent files of interest. A number of applications of the software, and how it enhances the information content extracted from the raw data, are illustrated using model proteins.
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Affiliation(s)
- Ganesh N. Sivalingam
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Jun Yan
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Harpal Sahota
- Institute of Structural and Molecular Biology, Crystallography, Birkbeck College, London, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Corresponding author. Tel.: +44 20 7679 2197; fax: +44 20 7679 7193.
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18
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Williams DM, Pukala TL. Novel insights into protein misfolding diseases revealed by ion mobility-mass spectrometry. MASS SPECTROMETRY REVIEWS 2013; 32:169-187. [PMID: 23345084 DOI: 10.1002/mas.21358] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 05/23/2012] [Accepted: 05/29/2012] [Indexed: 06/01/2023]
Abstract
Amyloid disorders incorporate a wide range of human diseases arising from the failure of a specific peptide or protein to adopt, or remain in, its native functional conformational state. These pathological conditions, such as Parkinson's disease, Alzheimer's disease and Huntington's disease are highly debilitating, exact enormous costs on both individuals and society, and are predicted to increase in prevalence. Consequently, they form the focus of a topical and rich area of current scientific research. A major goal in attempts to understand and treat protein misfolding diseases is to define the structures and interactions of protein species intermediate between fully folded and aggregated, and extract a description of the aggregation process. This has proven a difficult task due to the inability of traditional structural biology approaches to analyze structurally heterogeneous systems. Continued developments in instrumentation and analytical approaches have seen ion mobility-mass spectrometry (IM-MS) emerge as a complementary approach for protein structure determination, and in some cases, a structural biology tool in its own right. IM-MS is well suited to the study of protein misfolding, and has already yielded significant structural information for selected amyloidogenic systems during the aggregation process. This review describes IM-MS for protein structure investigation, and provides a summary of current research highlighting how this methodology has unequivocally and unprecedentedly provided structural and mechanistic detail pertaining to the oligomerization of a variety of disease related proteins.
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Affiliation(s)
- Danielle M Williams
- School of Chemistry and Physics, The University of Adelaide, North Terrace, Adelaide, South Australia 5005, Australia
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19
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Matrix assisted laser desorption ionisation ion mobility separation mass spectrometry imaging of ex-vivo human skin. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12127-013-0124-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Kaaki W, Woudstra M, Gontero B, Halgand F. Exploration of CP12 conformational changes and of quaternary structural properties using electrospray ionization traveling wave ion mobility mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:179-186. [PMID: 23239332 DOI: 10.1002/rcm.6442] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 10/10/2012] [Accepted: 10/16/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE CP12 is a small chloroplast protein involved in the Benson-Calvin cycle. Since it was demonstrated that the CP12 protein shared different conformational properties between reduced and oxidized states we took advantage of the segregational properties of the Traveling Wave Ion Mobility (TWIM) guide to study subtle conformational changes related to redox changes. METHODS Electrospray ionization mass (ESI-MS) spectra of the CP12 protein were recorded in the positive ion mode using an ESI source fitted on a quadrupole time-of-flight (QToF) hybrid mass spectrometer equipped with a TWIM cell (Synapt HDMS G1, Waters Corp., Manchester) under non-denaturing conditions. Non-covalent experiments were performed using the same instrument without the use of the TWIM device. RESULTS Whatever the CP12 form studied, our results showed that CP12 protein was represented by two conformers in equilibrium that displayed very slight differences. These observations led us to propose that CP12 protein structure is rather undergoing transient subtle structural changes than having two different conformational populations in solution. In addition, using non-denaturing experiments, NAD and CP12 stoichiometry were determined with respect to the GAPDH tetramer and the redox state of CP12. CONCLUSIONS In this study we showed that the use of the segregational property of the ion mobility (TWIM, Synapt G1 HDMS, Waters, Manchester, UK) allowed differentiation of subtle conformational changes between redox states of the CP12 protein. Standard non-denaturing experiments revealed different binding stoichiometry according to the redox state of the CP12 protein.
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Affiliation(s)
- Wassim Kaaki
- Unité de Bioénergétique et Ingénierie des Protéines (UMR 7281), Institut de Microbiologie de la Méditerranée, CNRS & AMU Aix-Marseille Univ, France
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21
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Rozbesky D, Sovova Z, Marcoux J, Man P, Ettrich R, Robinson CV, Novak P. Structural model of lymphocyte receptor NKR-P1C revealed by mass spectrometry and molecular modeling. Anal Chem 2013; 85:1597-604. [PMID: 23249299 DOI: 10.1021/ac302860m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
NKR-P1C is an activating immune receptor expressed on the surface of mouse natural killer cells. It has been widely used as a marker for NK cell identification in different mice strains. Recently we solved a crystal structure of the C-type lectin-like domain of a homologous protein, NKR-P1A, using X-ray crystallography and also described the strategy for rapid characterization of the protein conformation in solution. This procedure utilized chemical cross-linking, hydrogen/deuterium exchange, and molecular modeling. It was found that the solution structure differs from the crystal structure in the conformation of the loop region. The loop, detached from the protein compact core in the crystal structure, is closely attached to the core of the protein in solution. Here we present and interpret the solution structure of the C-type lectin-like domain of NKR-P1C using chemical cross-linking and molecular modeling. The validation of the model and conformation of the loop region in NKR-P1C were addressed using ion-mobility mass spectrometry.
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Affiliation(s)
- Daniel Rozbesky
- Department of Biochemistry, Charles University, Prague, Czech Republic
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22
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Sokratous K, Layfield R, Oldham NJ. The effects of cation adduction upon the conformation of three-helix bundle protein domains. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12127-012-0114-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Takebayashi K, Hirose K, Izumi Y, Bamba T, Fukusaki E. Application of ion mobility-mass spectrometry to microRNA analysis. J Biosci Bioeng 2012. [PMID: 23201507 DOI: 10.1016/j.jbiosc.2012.10.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Liquid chromatography/mass spectrometry is widely used for studying sequence determination and modification analysis of small RNAs. However, the efficiency of liquid chromatography-based separation of intact small RNA species is insufficient, since the physiochemical properties among small RNAs are very similar. In this study, we focused on ion mobility-mass spectrometry (IM-MS), which is a gas-phase separation technique coupled with mass spectrometry; we have evaluated the utility of IM-MS for microRNA (miRNA) analysis. A multiply charged deprotonated ion derived from an 18-24-nt-long miRNA was formed by electrospray ionization, and then the time, called the "drift time", taken by each ion to migrate through a buffer gas was measured. Each multivalent ion was temporally separated on the basis of the charge state and structural formation; 3 types of unique mass-mobility correlation patterns (i.e., chainlike-form, hairpin-form, and dimer-form) were present on the two-dimensional mobility-mass spectrum. Moreover, we found that the ion size (sequence length) and the secondary structures of the small RNAs strongly contributed to the IM-MS-based separation, although solvent conditions such as pH had no effect. Therefore, sequence isomers could also be discerned by the selection of each specific charged ion, i.e., the 6(-) charged ion reflected a majority among chainlike-, hairpin-, and other structures. We concluded that the IM-MS provides additional capability for separation; thus, this analytical method will be a powerful tool for comprehensive small RNA analysis.
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Affiliation(s)
- Kosuke Takebayashi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
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24
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Lorenzi M, Sylvi L, Gerbaud G, Mileo E, Halgand F, Walburger A, Vezin H, Belle V, Guigliarelli B, Magalon A. Conformational selection underlies recognition of a molybdoenzyme by its dedicated chaperone. PLoS One 2012. [PMID: 23185350 PMCID: PMC3501500 DOI: 10.1371/journal.pone.0049523] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Molecular recognition is central to all biological processes. Understanding the key role played by dedicated chaperones in metalloprotein folding and assembly requires the knowledge of their conformational ensembles. In this study, the NarJ chaperone dedicated to the assembly of the membrane-bound respiratory nitrate reductase complex NarGHI, a molybdenum-iron containing metalloprotein, was taken as a model of dedicated chaperone. The combination of two techniques ie site-directed spin labeling followed by EPR spectroscopy and ion mobility mass spectrometry, was used to get information about the structure and conformational dynamics of the NarJ chaperone upon binding the N-terminus of the NarG metalloprotein partner. By the study of singly spin-labeled proteins, the E119 residue present in a conserved elongated hydrophobic groove of NarJ was shown to be part of the interaction site. Moreover, doubly spin-labeled proteins studied by pulsed double electron-electron resonance (DEER) spectroscopy revealed a large and composite distribution of inter-label distances that evolves into a single preexisting one upon complex formation. Additionally, ion mobility mass spectrometry experiments fully support these findings by revealing the existence of several conformers in equilibrium through the distinction of different drift time curves and the selection of one of them upon complex formation. Taken together our work provides a detailed view of the structural flexibility of a dedicated chaperone and suggests that the exquisite recognition and binding of the N-terminus of the metalloprotein is governed by a conformational selection mechanism.
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Affiliation(s)
- Magali Lorenzi
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Léa Sylvi
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Guillaume Gerbaud
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Elisabetta Mileo
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Frédéric Halgand
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Anne Walburger
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Hervé Vezin
- Laboratoire de Spectrochimie Infrarouge et Raman (UMR8516), Villeneuve d'Ascq, France
| | - Valérie Belle
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
- * E-mail: (VB); (AM)
| | - Bruno Guigliarelli
- Unité de Bioénergétique et Ingénierie des Protéines (UMR7281), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
| | - Axel Magalon
- Laboratoire de Chimie Bactérienne (UMR7283), Institut de Microbiologie de la Méditerranée, CNRS & Aix-Marseille Univ, Marseille, France
- * E-mail: (VB); (AM)
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25
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Nyon M, Segu L, Cabrita L, Lévy G, Kirkpatrick J, Roussel B, Patschull A, Barrett T, Ekeowa U, Kerr R, Waudby C, Kalsheker N, Hill M, Thalassinos K, Lomas D, Christodoulou J, Gooptu B. Structural dynamics associated with intermediate formation in an archetypal conformational disease. Structure 2012; 20:504-12. [PMID: 22405009 PMCID: PMC3314904 DOI: 10.1016/j.str.2012.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 12/02/2011] [Accepted: 01/03/2012] [Indexed: 11/21/2022]
Abstract
In conformational diseases, native protein conformers convert to pathological intermediates that polymerize. Structural characterization of these key intermediates is challenging. They are unstable and minimally populated in dynamic equilibria that may be perturbed by many analytical techniques. We have characterized a forme fruste deficiency variant of α1-antitrypsin (Lys154Asn) that forms polymers recapitulating the conformer-specific neo-epitope observed in polymers that form in vivo. Lys154Asn α1-antitrypsin populates an intermediate ensemble along the polymerization pathway at physiological temperatures. Nuclear magnetic resonance spectroscopy was used to report the structural and dynamic changes associated with this. Our data highlight an interaction network likely to regulate conformational change and do not support the recent contention that the disease-relevant intermediate is substantially unfolded. Conformational disease intermediates may best be defined using powerful but minimally perturbing techniques, mild disease mutants, and physiological conditions.
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Affiliation(s)
- Mun Peak Nyon
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Lakshmi Segu
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Géraldine R. Lévy
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - John Kirkpatrick
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Benoit D. Roussel
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
| | - Anathe O.M. Patschull
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Tracey E. Barrett
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
| | - Ugo I. Ekeowa
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
| | - Richard Kerr
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - Noor Kalsheker
- Division of Clinical Chemistry, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Marian Hill
- Division of Clinical Chemistry, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
| | - David A. Lomas
- Department of Medicine, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, UK
- Corresponding author
| | - John Christodoulou
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- ISMB, Division of Biosciences, University College London, London, WC1E 6BT, UK
- Corresponding author
| | - Bibek Gooptu
- Institute of Structural and Molecular Biology (ISMB), Department of Biological Sciences, Birkbeck College, London, WC1E 7HX, UK
- Corresponding author
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26
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Atmanene C, Petiot-Bécard S, Zeyer D, Van Dorsselaer A, Vivat Hannah V, Sanglier-Cianférani S. Exploring Key Parameters to Detect Subtle Ligand-Induced Protein Conformational Changes Using Traveling Wave Ion Mobility Mass Spectrometry. Anal Chem 2012; 84:4703-10. [DOI: 10.1021/ac203223h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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27
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Salbo R, Bush MF, Naver H, Campuzano I, Robinson CV, Pettersson I, Jørgensen TJD, Haselmann KF. Traveling-wave ion mobility mass spectrometry of protein complexes: accurate calibrated collision cross-sections of human insulin oligomers. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:1181-1193. [PMID: 22499193 DOI: 10.1002/rcm.6211] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE The collision cross-section (Ω) of a protein or protein complex ion can be measured using traveling-wave (T-wave) ion mobility (IM) mass spectrometry (MS) via calibration with compounds of known Ω. The T-wave Ω-values depend strongly on instrument parameters and calibrant selection. Optimization of instrument parameters and calibration standards are crucial for obtaining accurate T-wave Ω-values. METHODS Human insulin and the fast-acting insulin aspart under native-like conditions (ammonium acetate, physiological pH) were analyzed on Waters SYNAPT G1 and G2 HDMS instruments. The calibrated T-wave Ω-values of insulin monomer, dimer, and hexamer ions were measured using many different combinations of denatured and native-like calibrants (masses between 2.85 and 256 kDa) and T-wave conditions. Drift-tube Ω-values were obtained on a modified SYNAPT G1. RESULTS Insulin T-wave Ω-values were measured at 26 combinations of T-wave velocity and amplitude. Optimal sets of calibrants were identified that yield Ω-values with minimal dependence on T-wave conditions and calibration plots with high R(2)-values. The T-wave Ω-values determined under conditions satisfying these criteria had absolute errors <2%. Structural differences between human insulin and fast-acting insulin aspart were probed with IM-MS. Insulin aspart monomers have increased flexibility, while hexamers are more compact than human insulin. CONCLUSIONS Accurate T-wave Ω-values that are indistinguishable from drift-tube values are obtained when using (1) native-like calibrants with masses that closely bracket that of the analyte, (2) T-wave velocities that maximize the R(2) of the calibration plot for those calibrants, and (3) at least three replicates at T-wave velocities that yield calibration plots with high R(2).
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Affiliation(s)
- Rune Salbo
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, Måløv, Denmark
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28
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Lalli PM, Iglesias BA, Deda DK, Toma HE, de Sa GF, Daroda RJ, Araki K, Eberlin MN. Resolution of isomeric multi-ruthenated porphyrins by travelling wave ion mobility mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:263-268. [PMID: 22223311 DOI: 10.1002/rcm.5314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The ability of travelling wave ion mobility mass spectrometry (TWIM-MS) to resolve cationic meta/para and cis/trans isomers of mono-, di-, tri- and tetra-ruthenated supramolecular porphyrins was investigated. All meta isomers were found to be more compact than the para isomers and therefore mixtures of all isomeric pairs could be properly resolved with baseline or close to baseline peak-to-peak resolution (R(p-p)). Di-substituted cis/trans isomers were found, however, to present very similar drift times and could not be resolved. N(2) and CO(2) were tested as the drift gas, and similar α but considerably better values of R(p) and R(p-p) were always observed for CO(2).
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Affiliation(s)
- Priscila M Lalli
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP 13083-970, Campinas, SP, Brazil
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29
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Jenner M, Ellis J, Huang WC, Lloyd Raven E, Roberts GCK, Oldham NJ. Detection of a Protein Conformational Equilibrium by Electrospray Ionisation-Ion Mobility-Mass Spectrometry. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Halgand F, Habchi J, Cravello L, Martinho M, Guigliarelli B, Longhi S. Dividing to unveil protein microheterogeneities: traveling wave ion mobility study. Anal Chem 2011; 83:7306-15. [PMID: 21800924 DOI: 10.1021/ac200994c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Overexpression of a protein in a foreign host is often the only route toward an exhaustive characterization, especially when purification from the natural source(s) is hardly achievable. The key issue in these studies relies on quality control of the purified recombinant protein to precisely determining its identity as well as any undesirable microheterogeneities. While standard proteomics approaches preclude unbiased search for modifications, the optional technique of top-down tandem mass spectrometry (MSMS) requires the use of highly accurate and highly resolved experiments to reveal subtle sequence modifications. In the present study, the top-down MSMS approach combined with traveling wave ion mobility (TWIM) separation was evaluated for its ability to achieve high sequence coverage and to reveal subtle microheterogeneities that were hitherto only accessible with Fourier-transform ion cyclotron resonance-MS instruments. The power of this approach is herein illustrated in an in-depth analysis of both the wild type and K496C variant of the recombinant X domain (XD; aa's 459-507) of the measles virus phosphoprotein expressed in Escherichia coli . Using top-down MSMS combined with TWIM, we show that XD samples occasionally exhibit a microheterogeneity that could not be anticipated from the nucleotide sequence of the encoding constructs and that likely reflects a genetic drift, neutral or not, occurring during expression. In addition, a 1-oxyl-2,2,5,5-tetramethyl-δ3-pyrroline-3-methyl methanethiosulfonate nitroxide probe that was grafted onto the K496C XD variant was shown to undergo oxidation and/or protonation in the electrospray ionization source, leading to artifactual mass increases.
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Affiliation(s)
- F Halgand
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Equipe de Protéomique Fonctionnelle et Dynamique, UPR 9036-CNRS, 31 Chemin Joseph Aiguier, 13420 Marseille Cedex, France.
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31
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Chan YT, Li X, Yu J, Carri GA, Moorefield CN, Newkome GR, Wesdemiotis C. Design, synthesis, and traveling wave ion mobility mass spectrometry characterization of iron(II)- and ruthenium(II)-terpyridine metallomacrocycles. J Am Chem Soc 2011; 133:11967-76. [PMID: 21718066 DOI: 10.1021/ja107307u] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New metallomacrocycles composed of 2,2':6',2″-terpyridine (tpy) ligands and Ru(II) or Fe(II) transition metal ions were prepared by stepwise directed assembly and characterized by 2D diffusion NMR spectroscopy (DOSY), electrospray ionization traveling wave ion mobility mass spectrometry (ESI TWIM MS), and molecular modeling. The supramolecular polymers synthesized include a homonuclear all-Ru hexamer as well as heteronuclear hexamer and nonamer with alternating Ru/Ru/Fe metal centers. ESI MS yields several charge states from each supramacromolecule. If ESI is interfaced with TWIM MS, overlapping charge states and the isomeric components of an individual charge state are separated based on their unique drift times through the TWIM region. From experimentally measured drift times, collision cross-sections can be deduced. The collision cross-sections obtained for the synthesized supramacromolecules are in good agreement with those predicted by molecular modeling for macrocyclic structures. Similarly, the hydrodynamic radii of the synthesized complexes derived from 2D DOSY NMR experiments agree excellently with the radii calculated for macrocyclic architectures, confirming the ESI TWIM MS finding. ESI TWIM MS and 2D DOSY NMR spectroscopy provide an alternative approach for the structural analysis of supramolecules that are difficult or impossible to crystallize, such as the large macrocyclic assemblies investigated. ESI TWIM MS will be particularly valuable for the characterization of supramolecular assemblies not available in the quantity or purity required for NMR studies.
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Affiliation(s)
- Yi-Tsu Chan
- Departments of Polymer Science, The University of Akron, Akron, Ohio, 44325, USA
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Jenner M, Ellis J, Huang WC, Lloyd Raven E, Roberts GCK, Oldham NJ. Detection of a Protein Conformational Equilibrium by Electrospray Ionisation-Ion Mobility-Mass Spectrometry. Angew Chem Int Ed Engl 2011; 50:8291-4. [DOI: 10.1002/anie.201101077] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2011] [Revised: 05/25/2011] [Indexed: 01/23/2023]
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Li X, Guo L, Casiano-Maldonado M, Zhang D, Wesdemiotis C. Top-Down Multidimensional Mass Spectrometry Methods for Synthetic Polymer Analysis. Macromolecules 2011. [DOI: 10.1021/ma200542p] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Li Guo
- Department of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | | | - Donghui Zhang
- Department of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Harvey SR, Macphee CE, Barran PE. Ion mobility mass spectrometry for peptide analysis. Methods 2011; 54:454-61. [PMID: 21669288 DOI: 10.1016/j.ymeth.2011.05.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/04/2011] [Accepted: 05/22/2011] [Indexed: 02/03/2023] Open
Abstract
The use of ion mobility mass spectrometry has grown rapidly over the last two decades. This powerful analytical platform now forms an attractive prospect for comprehensive analysis of many different molecular species, including chemically complex biological molecules. This paper describes the application of IM-MS to the study of peptides. We focus on three different ion mobility devices that are most frequently found in tandem with mass spectrometers. These are instruments using linear drift tubes (LDT), those using travelling wave ion guides (TWIGS) and those employing high field asymmetric ion mobility spectrometry (FAIMS). Each technique is described. Examples are given on the use of IM-MS for the determination of peptide structure, the study of peptides that form amyloid fibrils, and the study of complex peptide mixtures in proteomic investigations. We describe and comment on the methodologies used and the outlook for this developing analytical technique.
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Affiliation(s)
- Sophie R Harvey
- The School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
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Giganti VG, Kundoor S, Best WA, Angel LA. Ion mobility-mass spectrometry study of folded ubiquitin conformers induced by treatment with cis-[Pd(en)(H2O2]2+. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:300-309. [PMID: 21472589 DOI: 10.1007/s13361-010-0044-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 12/09/2010] [Accepted: 12/09/2010] [Indexed: 05/30/2023]
Abstract
Ion mobility-mass spectrometry is used to study the new conformers of bovine ubiquitin (Ub) and the palladium(II) binding sites after the incubation with cis-[Pd(en)(H(2)O)(2)](2+) where en = ethylenediamine. Palladium(II) complexes are potentially useful proteomic reagents because they selectively bind to the side groups of methionine and histidine and hydrolytically cleave the peptide bond. Incubating 1.0 mM solution of Ub with 10.0 molar excess of cis-[Pd(en)(H(2)O)(2)](2+) results with one to four Pd(2+) or Pd(en)(2+) being attached to intact Ub and two conformer families at each of the 4+ to 11+ charge states. The 4+ and 5+ species exhibit a compact form, which is also observed in untreated Ub, and a new highly folded conformer. The 6+ to 10+ exhibit an elongated form, also observed in Ub, and a new partially folded conformer. The new conformers are shown to be more stable if they contain at least one Pd(2+), rather than all Pd(en)(2+). IM-MS/MS of [UbPd(2)en+5H](9+) shows that both the partially folded and elongated conformers first lose the en ligand, followed by dissociating into product ions that indicate that Met1, Glu51/Asp52, His68, and Glu16 are binding sites for Pd(2+). These results suggest that Pd(2+) is simultaneously binding to multiple side groups across different regions of Ub. This type of sequestering of Pd(2+) probably reduces the efficiency of Pd(2+) ions to selectively cleave Ub because it prevents Pd(2+) anchoring to only Met or His and to an adjacent backbone amide nitrogen and forming the "activated complex" necessary for specific peptide bond cleavage.
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Li X, Chan YT, Newkome GR, Wesdemiotis C. Gradient Tandem Mass Spectrometry Interfaced with Ion Mobility Separation for the Characterization of Supramolecular Architectures. Anal Chem 2011; 83:1284-90. [DOI: 10.1021/ac1022875] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xiaopeng Li
- Departments of Chemistry and ‡Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Yi-Tsu Chan
- Departments of Chemistry and ‡Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - George R. Newkome
- Departments of Chemistry and ‡Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Chrys Wesdemiotis
- Departments of Chemistry and ‡Polymer Science, The University of Akron, Akron, Ohio 44325, United States
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Perera S, Li X, Guo M, Wesdemiotis C, Moorefield CN, Newkome GR. Sterically congested, hexameric tetrakispyridinyl-PdII/CdII-metallomacrocycles: self-assembly and structural characterization. Chem Commun (Camb) 2011; 47:4658-60. [DOI: 10.1039/c1cc10649j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Santos LFA, Iglesias AH, Pilau EJ, Gomes AF, Gozzo FC. Traveling-wave ion mobility mass spectrometry analysis of isomeric modified peptides arising from chemical cross-linking. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:2062-2069. [PMID: 20864354 DOI: 10.1016/j.jasms.2010.08.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 08/19/2010] [Accepted: 08/24/2010] [Indexed: 05/29/2023]
Abstract
Traveling-wave ion mobility (TWIM) coupled to mass spectrometry (MS) has emerged as a powerful tool for structural and conformational analysis of proteins and peptides, allowing the analysis of isomeric peptides (or proteins) with the same sequence but modified at different residues. This work demonstrates the use of the novel TWIM-MS technique to separate isomeric peptide ions derived from chemical cross-linking experiments, which enables the acquisition of distinct product ion spectra for each isomer, clearly indicating modification on different sites. Experiments were performed with four synthetic peptides, for which variable degrees of mobility separation were achieved. In cases of partially overlapping mobility arrival time distributions (ATDs), extracting the ATDs of fragment ions belonging to each individual isomer allowed their separation into two distinct ATDs. Accumulation over regions from the specific ATDs generates the product ion spectrum of each isomer, or a spectrum highly enriched in their fragments. The population of both modified peptide isomers was correlated with the intrinsic reactivities of different Lys residues from reactions conducted at different pH conditions.
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Affiliation(s)
- Luiz F A Santos
- Institute of Chemistry, University of Campinas and Instituto Nacional de Ciencia e Tecnologia de Bioanalitica, Sao Paulo, Brazil
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Bagal D, Valliere-Douglass JF, Balland A, Schnier PD. Resolving Disulfide Structural Isoforms of IgG2 Monoclonal Antibodies by Ion Mobility Mass Spectrometry. Anal Chem 2010; 82:6751-5. [DOI: 10.1021/ac1013139] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dhanashri Bagal
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Process and Product Development, Amgen, Seattle, Washington 98119
| | - John F. Valliere-Douglass
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Process and Product Development, Amgen, Seattle, Washington 98119
| | - Alain Balland
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Process and Product Development, Amgen, Seattle, Washington 98119
| | - Paul D. Schnier
- Molecular Structure, Amgen, Thousand Oaks, California 91320, and Process and Product Development, Amgen, Seattle, Washington 98119
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