1
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Jung JE, Ewing MA, Valentine SJ, Clemmer DE. Structural Insights into Linkage-Specific Ubiquitin Chains Using Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:982-991. [PMID: 38597281 DOI: 10.1021/jasms.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The structural characterization and differentiation of four types of oligoubiquitin conjugates [linear (Met1)-, Lys11-, Lys48-, Lys63-linked di-, tri-, and tetraubiquitin chains] using ion mobility mass spectrometry are reported. A comparison of collision cross sections for the same linkage of di-, tri-, and tetraubiquitin chains shows differences in conformational elongation for higher charge states due to the interplay of linkage-derived structure and Coulombic repulsion. For di- and triubiquitin chains, this elongation results in a single narrow feature representing an elongated conformation type for multiple higher charge state species. In contrast, higher charge state tetraubiquitin species do not form a single conformer type as readily. A comparison of different linkages in tetraubiquitin chains reveals greater similarity in conformation type at lower charge states; with increasing charge state, the four linkage types diverge in the relative proportions of elongated conformer types with Met1- ≥ Lys11- > Lys63- > Lys48-linkage. These differences in conformational trends could be discussed with respect to biological functions of linkage-specific polyubiquitinated proteins.
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Affiliation(s)
- Ji Eun Jung
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Forensic Chemistry Division, National Forensic Service, Wonju 26460, Korea
| | - Michael A Ewing
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Roche Infomatics, F. Hoffman-La Roche AG, Basel, CH 4070, Switzerland
| | - Stephen J Valentine
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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2
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Eldrid C, Cragnolini T, Ben-Younis A, Zou J, Raleigh DP, Thalassinos K. Linking Gas-Phase and Solution-Phase Protein Unfolding via Mobile Proton Simulations. Anal Chem 2022; 94:16113-16121. [PMID: 36350278 PMCID: PMC9685592 DOI: 10.1021/acs.analchem.2c03352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022]
Abstract
Native mass spectrometry coupled to ion mobility (IM-MS) combined with collisional activation (CA) of ions in the gas phase (in vacuo) is an important method for the study of protein unfolding. It has advantages over classical biophysical and structural techniques as it can be used to analyze small volumes of low-concentration heterogeneous mixtures while maintaining solution-like behavior and does not require labeling with fluorescent or other probes. It is unclear, however, whether the unfolding observed during collision activation experiments mirrors solution-phase unfolding. To bridge the gap between in vacuo and in-solution behavior, we use unbiased molecular dynamics (MD) to create in silico models of in vacuo unfolding of a well-studied protein, the N-terminal domain of ribosomal L9 (NTL9) protein. We utilize a mobile proton algorithm (MPA) to create 100 thermally unfolded and coulombically unfolded in silico models for observed charge states of NTL9. The unfolding behavior in silico replicates the behavior in-solution and is in line with the in vacuo observations; however, the theoretical collision cross section (CCS) of the in silico models was lower compared to that of the in vacuo data, which may reflect reduced sampling.
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Affiliation(s)
- Charles Eldrid
- School
of Biological Sciences, University of Southampton, SouthamptonSO16 1BJ, U.K.
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K.
| | - Tristan Cragnolini
- Institute
of Structural and Molecular Biology, Birkbeck College, University of London, LondonWC1E 7HX, U.K.
| | - Aisha Ben-Younis
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K.
| | - Junjie Zou
- Department
of Chemistry, Stony Brook University, 100 Nicolls Rd., Stony Brook, New York11794, United States
| | - Daniel P. Raleigh
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K.
- Department
of Chemistry, Stony Brook University, 100 Nicolls Rd., Stony Brook, New York11794, United States
| | - Konstantinos Thalassinos
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, LondonWC1E 6BT, U.K.
- Institute
of Structural and Molecular Biology, Birkbeck College, University of London, LondonWC1E 7HX, U.K.
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3
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Ujma J, Jhingree J, Norgate E, Upton R, Wang X, Benoit F, Bellina B, Barran P. Protein Unfolding in Freeze Frames: Intermediate States are Revealed by Variable-Temperature Ion Mobility-Mass Spectrometry. Anal Chem 2022; 94:12248-12255. [PMID: 36001095 PMCID: PMC9453741 DOI: 10.1021/acs.analchem.2c03066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The gas phase is an idealized laboratory for the study of protein structure, from which it is possible to examine stable and transient forms of mass-selected ions in the absence of bulk solvent. With ion mobility-mass spectrometry (IM-MS) apparatus built to operate at both cryogenic and elevated temperatures, we have examined conformational transitions that occur to the monomeric proteins: ubiquitin, lysozyme, and α-synuclein as a function of temperature and in source activation. We rationalize the experimental observations with a temperature-dependent framework model and comparison to known conformers. Data from ubiquitin show unfolding transitions that proceed through diverse and highly elongated intermediate states, which converge to more compact structures. These findings contrast with data obtained from lysozyme─a protein where (un)-folding plasticity is restricted by four disulfide linkages, although this is alleviated in its reduced form. For structured proteins, collision activation of the protein ions in-source enables subsequent "freezing" or thermal annealing of unfolding intermediates, whereas disordered proteins restructure substantially at 250 K even without activation, indicating that cold denaturation can occur without solvent. These data are presented in the context of a toy model framework that describes the relative occupancy of the available conformational space.
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Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jacquelyn Jhingree
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Emma Norgate
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Rosie Upton
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Xudong Wang
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Florian Benoit
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Bruno Bellina
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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4
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Gavriilidou AFM, Sokratous K, Yen HY, De Colibus L. High-Throughput Native Mass Spectrometry Screening in Drug Discovery. Front Mol Biosci 2022; 9:837901. [PMID: 35495635 PMCID: PMC9047894 DOI: 10.3389/fmolb.2022.837901] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field's recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.
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5
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Zviagin A, Kopysov V, Nagornova NS, Boyarkin OV. Tracking local and global structural changes in a protein by cold ion spectroscopy. Phys Chem Chem Phys 2022; 24:8158-8165. [PMID: 35332911 DOI: 10.1039/d2cp00217e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of native structures of proteins in the gas phase remains challenging due to the unpredictable conformational changes the molecules undergo during desolvation and ionization. We spectroscopically studied cryogenically cooled protonated protein ubiquitin and its microhydrated complexes prepared in the gas phase in a range of charge states under different ionization conditions. The UV spectra appear vibrationally resolved for the unfolded protein, but become redshifted and smooth for the native-like structures of ubiquitin. This spectroscopic change results from the H-bonding of the hydroxyl of Tyr to the amide group of Glu-51 in the compact structures; the minimum length of this bond was estimated to be ∼1.7 Å. IR spectroscopy reflects the global structural change by observing redshifts of free NH/OH-stretch vibrational transitions. Evaporative cooling of microhydrated complexes of ubiquitin keeps the protein chilly during ionization, enabling native-like conformers with up to eight protons to survive in the gas phase.
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Affiliation(s)
- Andrei Zviagin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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6
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Snyder DT, Jones BJ, Lin YF, Cooper-Shepherd DA, Hewitt D, Wildgoose J, Brown JM, Langridge JI, Wysocki VH. Surface-induced dissociation of protein complexes on a cyclic ion mobility spectrometer. Analyst 2021; 146:6861-6873. [PMID: 34632987 PMCID: PMC8574189 DOI: 10.1039/d1an01407b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We describe the implementation of a simple three-electrode surface-induced dissociation (SID) cell on a cyclic ion mobility spectrometer (cIMS) and demonstrate the utility of multipass mobility separations for resolving multiple conformations of protein complexes generated during collision-induced and surface-induced unfolding (CIU & SIU) experiments. In addition to CIU and SIU, SID of protein complexes is readily accomplished within the native instrument software and with no additional external power supplies by entering a single SID collision energy, a simplification in user experience compared to prior implementations. A set of cyclic homomeric protein complexes and a heterohexamer with known CID and SID behavior were analyzed to investigate mass and mobility resolution improvements, the latter of which improved by 20-50% (median: 33%) compared to a linear travelling wave device. Multiple passes of intact complexes, or their SID fragments, increased the mobility resolution by an average of 15% per pass, with the racetrack effect being observed after ∼3 or 4 passes, depending on the drift time spread of the analytes. Even with modest improvements to apparent mobility resolving power, multipass experiments were particularly useful for separating conformations produced from CIU and SIU experiments. We illustrate several examples where either (1) multipass experiments revealed multiple overlapping conformations previously unobserved or obscured due to limited mobility resolution, or (2) CIU or SIU conformations that appeared 'native' in a single pass experiment were actually slightly compacted or expanded, with the change only being measurable through multipass experiments. The work conducted here, the first utilization of multipass cyclic ion mobility for CIU, SIU, and SID of protein assemblies and a demonstration of a wholly integrated SIU/SID workflow, paves the way for widespread adoption of SID technology for native mass spectrometry and also improves our understanding of gas-phase protein complex CIU and SIU conformationomes.
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Affiliation(s)
- Dalton T Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Benjamin J Jones
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
| | - Yu-Fu Lin
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
| | | | - Darren Hewitt
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Jason Wildgoose
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Vicki H Wysocki
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
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7
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Eldrid C, Ben-Younis A, Ujma J, Britt H, Cragnolini T, Kalfas S, Cooper-Shepherd D, Tomczyk N, Giles K, Morris M, Akter R, Raleigh D, Thalassinos K. Cyclic Ion Mobility-Collision Activation Experiments Elucidate Protein Behavior in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1545-1552. [PMID: 34006100 PMCID: PMC8172447 DOI: 10.1021/jasms.1c00018] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Ion mobility coupled to mass spectrometry (IM-MS) is widely used to study protein dynamics and structure in the gas phase. Increasing the energy with which the protein ions are introduced to the IM cell can induce them to unfold, providing information on the comparative energetics of unfolding between different proteoforms. Recently, a high-resolution cyclic IM-mass spectrometer (cIM-MS) was introduced, allowing multiple, consecutive tandem IM experiments (IMn) to be carried out. We describe a tandem IM technique for defining detailed protein unfolding pathways and the dynamics of disordered proteins. The method involves multiple rounds of IM separation and collision activation (CA): IM-CA-IM and CA-IM-CA-IM. Here, we explore its application to studies of a model protein, cytochrome C, and dimeric human islet amyloid polypeptide (hIAPP), a cytotoxic and amyloidogenic peptide involved in type II diabetes. In agreement with prior work using single stage IM-MS, several unfolding events are observed for cytochrome C. IMn-MS experiments also show evidence of interconversion between compact and extended structures. IMn-MS data for hIAPP shows interconversion prior to dissociation, suggesting that the certain conformations have low energy barriers between them and transition between compact and extended forms.
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Affiliation(s)
- Charles Eldrid
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | - Aisha Ben-Younis
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | - Jakub Ujma
- Waters
Corporation, Wilmslow SK9 4AX, U.K.
| | - Hannah Britt
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | - Tristan Cragnolini
- Institute
of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, U.K.
| | - Symeon Kalfas
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
| | | | | | | | | | - Rehana Akter
- Department
of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Daniel Raleigh
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
- Department
of Chemistry, Stony Brook University, 100 Nicolls Road, Stony Brook, New York 11794, United States
| | - Konstantinos Thalassinos
- Institute
of Structural and Molecular Biology, Division of Bioscience, University College London, London, WC1E 6BT, U.K.
- Institute
of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, U.K.
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8
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Kit MCS, Carvalho VV, Vilseck JZ, Webb IK. Gas-Phase Ion/Ion Chemistry for Structurally Sensitive Probes of Gaseous Protein Ion Structure: Electrostatic and Electrostatic to Covalent Cross-Linking. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2021; 463:116549. [PMID: 33716558 PMCID: PMC7946065 DOI: 10.1016/j.ijms.2021.116549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Intramolecular interactions within a protein are key in maintaining protein tertiary structure and understanding how proteins function. Ion mobility-mass spectrometry (IM-MS) has become a widely used approach in structural biology since it provides rapid measurements of collision cross sections (CCS), which inform on the gas-phase conformation of the biomolecule under study. Gas-phase ion/ion reactions target amino acid residues with specific chemical properties and the modified sites can be identified by MS. In this study, electrostatically reactive, gas-phase ion/ion chemistry and IM-MS are combined to characterize the structural changes between ubiquitin electrosprayed from aqueous and denaturing conditions. The electrostatic attachment of sulfo-NHS acetate to ubiquitin via ion/ion reactions and fragmentation by electron-capture dissociation (ECD) provide the identification of the most accessible protonated sites within ubiquitin as the sulfonate group forms an electrostatic complex with accessible protonated side chains. The protonated sites identified by ECD from the different solution conditions are distinct and, in some cases, reflect the disruption of interactions such as salt bridges that maintain the native protein structure. This agrees with previously published literature demonstrating that a high methanol concentration at low pH causes the structure of ubiquitin to change from a native (N) state to a more elongated A state. Results using gas-phase, electrostatic cross-linking reagents also point to similar structural changes and further confirm the role of methanol and acid in favoring a more unfolded conformation. Since cross-linking reagents have a distance constraint for the two reactive sites, the data is valuable in guiding computational structures generated by molecular dynamics. The research presented here describes a promising strategy that can detect subtle changes in the local environment of targeted amino acid residues to inform on changes in the overall protein structure.
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Affiliation(s)
- Melanie Cheung See Kit
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
| | - Veronica V. Carvalho
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
| | - Jonah Z. Vilseck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Ian K. Webb
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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9
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Panczyk EM, Snyder DT, Ridgeway ME, Somogyi Á, Park MA, Wysocki VH. Surface-Induced Dissociation of Protein Complexes Selected by Trapped Ion Mobility Spectrometry. Anal Chem 2021; 93:5513-5520. [PMID: 33751887 DOI: 10.1021/acs.analchem.0c05373] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Native mass spectrometry (nMS), particularly in conjunction with gas-phase ion mobility spectrometry measurements, has proven useful as a structural biology tool for evaluating the stoichiometry, conformation, and topology of protein complexes. Here, we demonstrate the combination of trapped ion mobility spectrometry (TIMS) and surface-induced dissociation (SID) on a Bruker SolariX XR 15 T FT-ICR mass spectrometer for the structural analysis of protein complexes. We successfully performed SID on mobility-selected protein complexes, including the streptavidin tetramer and cholera toxin B with bound ligands. Additionally, TIMS-SID was employed on a mixture of the peptides desArg1 and desArg9 bradykinin to mobility-separate and identify the individual peptides. Importantly, results show that native-like conformations can be maintained throughout the TIMS analysis. The TIMS-SID spectra are analogous to SID spectra acquired using quadrupole mass selection, indicating little measurable, if any, structural rearrangement during mobility selection. Mobility parking was used on the ion or mobility of interest and 50-200 SID mass spectra were averaged. High-quality TIMS-SID spectra were acquired over a period of 2-10 min, comparable to or slightly longer than SID coupled with ion mobility on various instrument platforms in our laboratory. The ultrahigh resolving power of the 15 T FT-ICR allowed for the identification and relative quantification of overlapping SID fragments with the same nominal m/z based on isotope patterns, and it shows promise as a platform to probe small mass differences, such as protein/ligand binding or post-translational modifications. These results represent the potential of TIMS-SID-MS for the analysis of both protein complexes and peptides.
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Affiliation(s)
- Erin M Panczyk
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dalton T Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Mark E Ridgeway
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Árpád Somogyi
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States.,Campus Chemical Instrument Center, Mass Spectrometry and Proteomics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Melvin A Park
- Bruker Daltonics Inc., Billerica, Massachusetts 01821, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States.,Campus Chemical Instrument Center, Mass Spectrometry and Proteomics, The Ohio State University, Columbus, Ohio 43210, United States
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10
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Austin CA, Inutan ED, Bohrer BC, Li J, Fischer JL, Wijerathne K, Foley CD, Lietz CB, Woodall DW, Imperial LF, Clemmer DE, Trimpin S, Larsen BS. Resolving Isomers of Star-Branched Poly(Ethylene Glycols) by IMS-MS Using Multiply Charged Ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:21-32. [PMID: 32510213 DOI: 10.1021/jasms.0c00045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ion mobility spectrometry (IMS) mass spectrometry (MS) centers on the ability to separate gaseous structures by size, charge, shape, and followed by mass-to-charge (m/z). For oligomeric structures, improved separation is hypothesized to be related to the ability to extend structures through repulsive forces between cations electrostatically bonded to the oligomers. Here we show the ability to separate differently branched multiply charged ions of star-branched poly(ethylene glycol) oligomers (up to 2000 Da) regardless of whether formed by electrospray ionization (ESI) charged solution droplets or from charged solid particles produced directly from a surface by matrix-assisted ionization. Detailed structural characterization of isomers of the star-branched compositions was first established using a home-built high-resolution ESI IMS-MS instrument. The doubly charged ions have well-resolved drift times, achieving separation of isomers and also allowing differentiation of star-branched versus linear oligomers. An IMS-MS "snapshot" approach allows visualization of architectural dispersity and (im)purity of samples in a straightforward manner. Analyses capabilities are shown for different cations and ionization methods using commercially available traveling wave IMS-MS instruments. Analyses directly from surfaces using the new ionization processes are, because of the multiply charging, not only associated with the benefits of improved gas-phase separations, relative to that of ions produced by matrix-assisted laser desorption/ionization, but also provide the potential for spatially resolved measurements relative to ESI and other ionization methods.
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Affiliation(s)
- Calvin A Austin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Ellen D Inutan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Brian C Bohrer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jing Li
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Joshua L Fischer
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Kanchana Wijerathne
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Casey D Foley
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Christopher B Lietz
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Daniel W Woodall
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Lorelie F Imperial
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sarah Trimpin
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Barbara S Larsen
- DuPont, Nutrition & Biosciences, Wilmington, Delaware 19808, United States
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11
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Inutan ED, Jarois DR, Lietz CB, El-Baba TJ, Elia EA, Karki S, Sampat AAS, Foley CD, Clemmer DE, Trimpin S. Comparison of gaseous ubiquitin ion structures obtained from a solid and solution matrix using ion mobility spectrometry/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35 Suppl 1:e8793. [PMID: 32220130 DOI: 10.1002/rcm.8793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 03/24/2020] [Accepted: 03/24/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Examining surface protein conformations, and especially achieving this with spatial resolution, is an important goal. The recently discovered ionization processes offer spatial-resolution measurements similar to matrix-assisted laser desorption/ionization (MALDI) and produce charge states similar to electrospray ionization (ESI) extending higher-mass protein applications directly from surfaces on high-performance mass spectrometers. Studying a well-interrogated protein by ion mobility spectrometry-mass spectrometry (IMS-MS) to access effects on structures using a solid vs. solvent matrix may provide insights. METHODS Ubiquitin was studied by IMS-MS using new ionization processes with commercial and homebuilt ion sources and instruments (Waters SYNAPT G2(S)) and homebuilt 2 m drift-tube instrument; MS™ sources). Mass-to-charge and drift-time (td )-measurements are compared for ubiquitin ions obtained by inlet and vacuum ionization using laserspray ionization (LSI), matrix- (MAI) and solvent-assisted ionization (SAI), respectively, and compared with those from ESI under conditions that are most comparable. RESULTS Using the same solution conditions with SYNAPT G2(S) instruments, td -distributions of various ubiquitin charge states from MAI, LSI, and SAI are similar to those from ESI using a variety of solvents, matrices, extraction voltages, a laser, and temperature only, showing subtle differences in more compact features within the elongated distribution of structures. However, on a homebuilt drift-tube instrument, within the elongated distribution of structures, both similar and different td -distributions are observed for ubiquitin ions obtained by MAI and ESI. MAI-generated ions are frequently narrower in their td -distributions. CONCLUSIONS Direct comparisons between ESI and the new ionization methods operational directly from surfaces suggest that the protein in its solution structure prior to exposure to the ionization event is either captured (frozen out) at the time of crystallization, or that the protein in the solid matrix is associated with sufficient solvent to maintain the solution structure, or, alternatively, that the observed structures are those related to what occurs in the gas phase with ESI- or MAI-generated ions and not with the solution structures.
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Affiliation(s)
- Ellen D Inutan
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
- Mindanao State University-Iligan Institute of Technology, Iligan City, Philippines
| | - Dean R Jarois
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | | | - Santosh Karki
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | | | - Casey D Foley
- Department of Chemistry, Wayne State University, Detroit, MI, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, USA
| | - Sarah Trimpin
- MSTM, LLC, Newark, DE, USA
- Department of Chemistry, Wayne State University, Detroit, MI, USA
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12
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Eldrid C, Thalassinos K. Developments in tandem ion mobility mass spectrometry. Biochem Soc Trans 2020; 48:2457-2466. [PMID: 33336686 PMCID: PMC7752082 DOI: 10.1042/bst20190788] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 01/09/2023]
Abstract
Ion Mobility (IM) coupled to mass spectrometry (MS) is a useful tool for separating species of interest out of small quantities of heterogenous mixtures via a combination of m/z and molecular shape. While tandem MS instruments are common, instruments which employ tandem IM are less so with the first commercial IM-MS instrument capable of multiple IM selection rounds being released in 2019. Here we explore the history of tandem IM instruments, recent developments, the applications to biological systems and expected future directions.
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Affiliation(s)
- Charles Eldrid
- Institute of Structural and Molecular Biology, UCL, Gower St, London WC1E 6BT, U.K
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, UCL, Gower St, London WC1E 6BT, U.K
- Institute of Structural and Molecular Biology, Birkbeck University, Malet Place, London WC1E 7HX, U.K
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13
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Raab SA, El-Baba TJ, Woodall DW, Liu W, Liu Y, Baird Z, Hales DA, Laganowsky A, Russell DH, Clemmer DE. Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements. J Am Chem Soc 2020; 142:17372-17383. [PMID: 32866376 DOI: 10.1021/jacs.0c05365] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chymotrypsin inhibitor 2 (CI-2) is a classic model for two-state cooperative protein folding and is one of the most extensively studied systems. Alan Fersht, a pioneer in the field of structural biology, has studied the wild-type (wt) and over 100 mutant forms of CI-2 with traditional analytical and biochemical techniques. Here, we examine wt CI-2 and three mutant forms (A16G, K11A, L32A) to demonstrate the utility of variable-temperature (vT) electrospray ionization (ESI) paired with ion mobility spectrometry (IMS) and mass spectrometry (MS) to map the free energy folding landscape. As the solution temperature is increased, the abundance of each of the six ESI charge states for wt CI-2 and each mutant is found to vary independently. These results require that at least six unique types of CI-2 solution conformers are present. Ion mobility analysis reveals that within each charge state there are additional conformers having distinct solution temperature profiles. A model of the data at ∼30 different temperatures for all four systems suggests the presence of 41 unique CI-2 solution conformations. A thermodynamic analysis of this system yields values of ΔCp as well as ΔG, ΔH, and ΔS for each state at every temperature studied. Detailed energy landscapes derived from these data provide a rare glimpse into Anfinsen's thermodynamic hypothesis and the process of thermal denaturation, normally thought of as a cooperative two-state transition involving the native state and unstructured denatured species. Specifically, as the temperature is varied, the entropies and enthalpies of different conformers undergo dramatic changes in magnitude and relative order to maintain the delicate balance associated with equilibrium.
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Affiliation(s)
- Shannon A Raab
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Tarick J El-Baba
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Daniel W Woodall
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
| | - Wen Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Zane Baird
- Baxter Healthcare Corporation, 927 South Curry Pike, Bloomington, Indiana 47403, United States
| | - David A Hales
- Department of Chemistry, Hendrix College, Conway, Arkansas 72032, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 Kirkwood Avenue, Bloomington, Indiana 47401, United States
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14
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Comby-Zerbino C, Bertorelle F, Dugourd P, Antoine R, Chirot F. Structure and Charge Heterogeneity in Isomeric Au25(MBA)18 Nanoclusters—Insights from Ion Mobility and Mass Spectrometry. J Phys Chem A 2020; 124:5840-5848. [DOI: 10.1021/acs.jpca.0c03131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Clothilde Comby-Zerbino
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5306, Institut Lumière Matière, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Franck Bertorelle
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5306, Institut Lumière Matière, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Philippe Dugourd
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5306, Institut Lumière Matière, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Rodolphe Antoine
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5306, Institut Lumière Matière, 5 rue de la Doua, Villeurbanne F-69100, France
| | - Fabien Chirot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5280, Institut des Sciences Analytiques, 5 rue de la Doua, Villeurbanne F-69100, France
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15
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Gantman T, Goldstein M, Segev E, Gerber RB. Conformers of Ubiquitin 6+ for Different Charge Distributions: Atomistic Structures and Ion Mobility Cross Sections. J Phys Chem B 2019; 123:6401-6409. [DOI: 10.1021/acs.jpcb.9b02720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tamara Gantman
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Moshe Goldstein
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Computer Science, Jerusalem College of Technology (JCT), Jerusalem 9372115, Israel
| | - Elad Segev
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Applied Mathematics, Holon Institute of Technology, Holon 5810201, Israel
| | - R. Benny Gerber
- The Fritz Haber Research Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697, United States
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16
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Rolland AD, Prell JS. Computational Insights into Compaction of Gas-Phase Protein and Protein Complex Ions in Native Ion Mobility-Mass Spectrometry. Trends Analyt Chem 2019; 116:282-291. [PMID: 31983791 PMCID: PMC6979403 DOI: 10.1016/j.trac.2019.04.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) is a rapidly growing field for studying the composition and structure of biomolecules and biomolecular complexes using gas-phase methods. Typically, ions are formed in native IM-MS using gentle nanoelectrospray ionization conditions, which in many cases can preserve condensed-phase stoichiometry. Although much evidence shows that large-scale condensed-phase structure, such as quaternary structure and topology, can also be preserved, it is less clear to what extent smaller-scale structure is preserved in native IM-MS. This review surveys computational and experimental efforts aimed at characterizing compaction and structural rearrangements of protein and protein complex ions upon transfer to the gas phase. A brief summary of gas-phase compaction results from molecular dynamics simulations using multiple common force fields and a wide variety of protein ions is presented and compared to literature IM-MS data.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon,
Eugene, OR, USA 97403-1252
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17
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Giles K, Ujma J, Wildgoose J, Pringle S, Richardson K, Langridge D, Green M. A Cyclic Ion Mobility-Mass Spectrometry System. Anal Chem 2019; 91:8564-8573. [PMID: 31141659 DOI: 10.1021/acs.analchem.9b01838] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Improvements in the performance and availability of commercial instrumentation have made ion mobility-mass spectrometry (IM-MS) an increasingly popular approach for the structural analysis of ionic species as well as for separation of complex mixtures. Here, a new research instrument is presented which enables complex experiments, extending the current scope of IM technology. The instrument is based on a Waters SYNAPT G2-S i IM-MS platform, with the IM separation region modified to accept a cyclic ion mobility (cIM) device. The cIM region consists of a 98 cm path length, closed-loop traveling wave (TW)-enabled IM separator positioned orthogonally to the main ion optical axis. A key part of this geometry and its flexibility is the interface between the ion optical axis and the cIM, where a planar array of electrodes provides control over the TW direction and subsequent ion motion. On either side of the array, there are ion guides used for injection, ejection, storage, and activation of ions. In addition to single and multipass separations around the cIM, providing selectable mobility resolution, the instrument design and control software enable a range of "multifunction" experiments such as mobility selection, activation, storage, IMS n, and importantly custom combinations of these functions. Here, the design and performance of the cIM-MS instrument is highlighted, with a mobility resolving power of approximately 750 demonstrated for 100 passes around the cIM device using a reverse sequence peptide pair. The multifunction capabilities are demonstrated through analysis of three isomeric pentasaccharide species and the small protein ubiquitin.
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Affiliation(s)
- Kevin Giles
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jakub Ujma
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jason Wildgoose
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Steven Pringle
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Keith Richardson
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - David Langridge
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Martin Green
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
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18
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Eldrid C, Ujma J, Kalfas S, Tomczyk N, Giles K, Morris M, Thalassinos K. Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device. Anal Chem 2019; 91:7554-7561. [PMID: 31117399 PMCID: PMC7006968 DOI: 10.1021/acs.analchem.8b05641] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Ion
mobility mass spectrometry (IM-MS) allows separation of native
protein ions into “conformational families”. Increasing
the IM resolving power should allow finer structural information to
be obtained and can be achieved by increasing the length of the IM
separator. This, however, increases the time that protein ions spend
in the gas phase and previous experiments have shown that the initial
conformations of small proteins can be lost within tens of milliseconds.
Here, we report on investigations of protein ion stability using a
multipass traveling wave (TW) cyclic IM (cIM) device. Using this device,
minimal structural changes were observed for Cytochrome C after hundreds
of milliseconds, while no changes were observed for a larger multimeric
complex (Concanavalin A). The geometry of the instrument (Q-cIM-ToF)
also enables complex tandem IM experiments to be performed, which
were used to obtain more detailed collision-induced unfolding pathways
for Cytochrome C. The instrument geometry provides unique capabilities
with the potential to expand the field of protein analysis via IM-MS.
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Affiliation(s)
- Charles Eldrid
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Jakub Ujma
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Symeon Kalfas
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom
| | - Nick Tomczyk
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Kevin Giles
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Mike Morris
- Waters Corporation , Wilmslow , SK9 4AX , United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences , University College London , London , WC1E 6BT , United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College , University of London , London , WC1E 7HX , United Kingdom
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19
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Eaton RM, Allen SJ, Bush MF. Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility Implemented Using Structures for Lossless Ion Manipulations (SLIM). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1115-1125. [PMID: 30963456 DOI: 10.1007/s13361-019-02170-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Tandem ion mobility (IM) enables the characterization of subpopulations of ions from larger ensembles, including differences that cannot be resolved in a single dimension of IM. Tandem IM consists of at least two IM regions that are each separated by an ion selection region. In many implementations of tandem IM, ions eluting from a dimension of separation are filtered and immediately transferred to the subsequent dimension of separation (selection-only experiments). We recently reported a mode of operation in which ions eluting from a dimension are trapped prior to the subsequent dimension (selection-trapping experiments), which was implemented on an instrument constructed using the structures for lossless ion manipulations (SLIM) architecture. Here, we use a combination of experiments and trajectory simulations to characterize aspects of the selection, trapping, and separation processes underlying these modes of operation. For example, the actual temporal profile of filtered ions can be very similar to the width of the waveforms used for selection, but depending on experimental parameters, can differ by up to ± 500 μs. Experiments and simulations indicate that ions in selection-trapping experiments can be spatially focused between dimensions, which removes the broadening that occurred during the preceding dimension. During focusing, individual ions are thermalized, which aligns and establishes common initial conditions for the subsequent dimension. Therefore, selection-trapping experiments appear to offer significant advantages relative to selection-only experiments, which we anticipate will become more pronounced in future experiments that make use of longer IM separations, additional dimensions of analysis, and the outcomes of this study. Graphical Abstract.
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Affiliation(s)
- Rachel M Eaton
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Samuel J Allen
- 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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20
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Peters I, Metwally H, Konermann L. Mechanism of Electrospray Supercharging for Unfolded Proteins: Solvent-Mediated Stabilization of Protonated Sites During Chain Ejection. Anal Chem 2019; 91:6943-6952. [DOI: 10.1021/acs.analchem.9b01470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Insa Peters
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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21
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McKenna KR, Li L, Baker AG, Ujma J, Krishnamurthy R, Liotta CL, Fernández FM. Carbohydrate isomer resolutionviamulti-site derivatization cyclic ion mobility-mass spectrometry. Analyst 2019; 144:7220-7226. [DOI: 10.1039/c9an01584a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cyclic ion mobility-tandem mass spectrometry enhances the separation and identification of small carbohydrate isomers.
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Affiliation(s)
- Kristin R. McKenna
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | - Li Li
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | | | | | | | - Charles L. Liotta
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | - Facundo M. Fernández
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
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22
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Choi CM, MacAleese L, Dugourd P, Choi MC, Chirot F. Photo-induced linkage isomerization in the gas phase probed by tandem ion mobility and laser spectroscopy. Phys Chem Chem Phys 2018; 20:12223-12228. [PMID: 29687123 DOI: 10.1039/c8cp01833b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Ruthenium complexes involving sulfoxide ligands can undergo linkage isomerization upon light absorption, accompanied by dramatic changes in their optical properties. These remarkable photochromic properties are sensitive to the nature of the ligand as well as to that of the solvent. We used tandem ion mobility spectrometry coupled to mass spectrometry to gain direct experimental insight into the isomerization pathways connecting the different linkage isomers of an isolated ruthenium complex with two dimethyl-sulfoxide ligands. We find that the isomerization behavior of the solvent-free complex differs from that previously reported in the solution-phase, which is in line with recent theoretical predictions.
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Affiliation(s)
- Chang Min Choi
- Mass Spectrometry and Advanced Instrumentation Research Group, Div. of Scientific Instrumentation, Korea Basic Science Institute, Cheongju, Republic of Korea
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23
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May JC, Jurneczko E, Stow SM, Kratochvil I, Kalkhof S, McLean JA. Conformational Landscapes of Ubiquitin, Cytochrome c, and Myoglobin: Uniform Field Ion Mobility Measurements in Helium and Nitrogen Drift Gas. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2018; 427:79-90. [PMID: 29915518 PMCID: PMC6003721 DOI: 10.1016/j.ijms.2017.09.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In this study, a commercial uniform field drift tube ion mobility-mass spectrometer (IM-MS) was utilized to measure the gas-phase conformational populations of three well-studied proteins: ubiquitin (8566 Da), cytochrome c (12,359 Da), and myoglobin in both apo and holo forms (16,951 and 17,567 Da, respectively) in order to evaluate the use of this technology for broadscale structural proteomics applications. Proteins were electrosprayed from either acidic organic (pH ~3) or aqueous buffered (pH ~6.6) solution phase conditions, which generated a wide range of cation charge states corresponding to both extended (unfolded) and compact (folded) gas-phase conformational populations. Corresponding collision cross section (CCS) measurements were compiled for significant ion mobility peak features observed at each charge state in order to map the conformational landscapes of these proteins in both helium and nitrogen drift gases. It was observed that the conformational landscapes were similar in both drift gases, with differences being attributed primarily to ion heating during helium operation due to the necessity of operating the instrument with higher pressure differentials. Higher resolving powers were observed in nitrogen, which allowed for slightly better structural resolution of closely-spaced conformer populations. The instrumentation was found to be particularly adept at measuring low abundance conformers which are only present under gentle conditions which minimize ion heating. This work represents the single largest ion mobility CCS survey published to date for these three proteins with 266 CCS values and 117 ion mobility spectra, many of which have not been previously reported.
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Affiliation(s)
- Jody C. May
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Integrative Biosystems Research and Education, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, 37235, United States
| | - Ewa Jurneczko
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Integrative Biosystems Research and Education, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, 37235, United States
| | - Sarah M. Stow
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Integrative Biosystems Research and Education, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, 37235, United States
| | - Isabel Kratochvil
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Kalkhof
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, 04318 Leipzig, Germany
| | - John A. McLean
- Department of Chemistry, Center for Innovative Technology, Vanderbilt Institute for Integrative Biosystems Research and Education, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, 37235, United States
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24
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Morrison LJ, Chai W, Rosenberg JA, Henkelman G, Brodbelt JS. Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry. Phys Chem Chem Phys 2018; 19:20057-20074. [PMID: 28722742 DOI: 10.1039/c7cp04073c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Determination of structure and folding of certain classes of proteins remains intractable by conventional structural characterization strategies and has spurred the development of alternative methodologies. Mass spectrometry-based approaches have a unique capacity to differentiate protein heterogeneity due to the ability to discriminate populations, whether minor or major, featuring modifications or complexation with non-covalent ligands on the basis of m/z. Cleavage of the peptide backbone can be further utilized to obtain residue-specific structural information. Here, hydrogen elimination monitoring (HEM) upon ultraviolet photodissociation (UVPD) of proteins transferred to the gas phase via nativespray ionization is introduced as an innovative approach to deduce backbone hydrogen bonding patterns. Using well-characterized peptides and a series of proteins, prediction of the engagement of the amide carbonyl oxygen of the protein backbone in hydrogen bonding using UVPD-HEM is demonstrated to show significant agreement with the hydrogen-bonding motifs derived from molecular dynamics simulations and X-ray crystal structures.
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25
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Majuta SN, Maleki H, Kiani Karanji A, Attanyake K, Loch E, Valentine SJ. Magnifying ion mobility spectrometry-mass spectrometry measurements for biomolecular structure studies. Curr Opin Chem Biol 2018; 42:101-110. [PMID: 29241076 PMCID: PMC6500794 DOI: 10.1016/j.cbpa.2017.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 12/31/2022]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) provides information about the structures of gas-phase ions in the form of a collision cross section (CCS) with a neutral buffer gas. Indicating relative ion size, a CCS value alone is of limited utility. Although such information can be used to propose different conformer types, finer details of structure are not captured. The increased accessibility of IMS-MS measurements with commercial instrumentation in recent years has ballooned its usage in combination with separate measurements to provide enhanced data from which greater structural inferences can be drawn. This short review presents recent outstanding developments in scientific research that employs complementary measurements that when combined with IMS-MS data are used to characterize the structures of a wide range of compounds.
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Affiliation(s)
- Sandra N Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Hossein Maleki
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Ahmad Kiani Karanji
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Kushani Attanyake
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Elinore Loch
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, WV 26506, United States.
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26
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Chandler SA, Benesch JL. Mass spectrometry beyond the native state. Curr Opin Chem Biol 2017; 42:130-137. [PMID: 29288996 DOI: 10.1016/j.cbpa.2017.11.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022]
Abstract
Native mass spectrometry allows the study of proteins by probing in vacuum the interactions they form in solution. It is a uniquely useful approach for structural biology and biophysics due to the high resolution of separation it affords, allowing the concomitant interrogation of multiple protein components with high mass accuracy. At its most basic, native mass spectrometry reports the mass of intact proteins and the assemblies they form in solution. However, the opportunities for more detailed characterisation are extensive, enabled by the exquisite control of ion motion that is possible in vacuum. Here we describe recent developments in mass spectrometry approaches to the structural interrogation of proteins both in, and beyond, their native state.
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Affiliation(s)
- Shane A Chandler
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK
| | - Justin Lp Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, UK.
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27
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Wagner ND, Clemmer DE, Russell DH. ESI-IM-MS and Collision-Induced Unfolding That Provide Insight into the Linkage-Dependent Interfacial Interactions of Covalently Linked Diubiquitin. Anal Chem 2017; 89:10094-10103. [DOI: 10.1021/acs.analchem.7b02932] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicole D. Wagner
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David E. Clemmer
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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28
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Allen SJ, Eaton RM, Bush MF. Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome c. Anal Chem 2017. [PMID: 28636328 DOI: 10.1021/acs.analchem.7b01234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ion mobility (IM) is a gas-phase separation technique that is used to determine the collision cross sections of native-like ions of proteins and protein complexes, which are in turn used as restraints for modeling the structures of those analytes in solution. Here, we evaluate the stability of native-like ions using tandem IM experiments implemented using structures for lossless ion manipulations (SLIM). In this implementation of tandem IM, ions undergo a first dimension of IM up to a switch that is used to selectively transmit ions of a desired mobility. Selected ions are accumulated in a trap and then released after a delay to initiate the second dimension of IM. For delays ranging from 16 to 33 231 ms, the collision cross sections of native-like, 7+ cytochrome c ions increase monotonically from 15.1 to 17.1 nm2. The largest products formed in these experiments at near-ambient temperature are still far smaller than those formed in energy-dependent experiments (∼21 nm2). However, the collision cross section increases by ∼2% between delay times of 16 and 211 ms, which may have implications for other IM experiments on these time scales. Finally, two subpopulations from the full population were each mobility selected and analyzed as a function of delay time, showing that the three populations can be differentiated for at least 1 s. Together, these results suggest that elements of native-like structure can have long lifetimes at near-ambient temperature in the gas phase but that gas-phase dynamics should be considered when interpreting results from IM.
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Affiliation(s)
- Samuel J Allen
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Rachel M Eaton
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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29
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Daly S, Knight G, Halim MA, Kulesza A, Choi CM, Chirot F, MacAleese L, Antoine R, Dugourd P. Action-FRET of a Gaseous Protein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:38-49. [PMID: 27506208 PMCID: PMC5174150 DOI: 10.1007/s13361-016-1449-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 05/03/2023]
Abstract
Mass spectrometry is an extremely powerful technique for analysis of biological molecules, in particular proteins. One aspect that has been contentious is how much native solution-phase structure is preserved upon transposition to the gas phase by soft ionization methods such as electrospray ionization. To address this question-and thus further develop mass spectrometry as a tool for structural biology-structure-sensitive techniques must be developed to probe the gas-phase conformations of proteins. Here, we report Förster resonance energy transfer (FRET) measurements on a ubiquitin mutant using specific photofragmentation as a reporter of the FRET efficiency. The FRET data is interpreted in the context of circular dichroism, molecular dynamics simulation, and ion mobility data. Both the dependence of the FRET efficiency on the charge state-where a systematic decrease is observed-and on methanol concentration are considered. In the latter case, a decrease in FRET efficiency with methanol concentration is taken as evidence that the conformational ensemble of gaseous protein cations retains a memory of the solution phase conformational ensemble upon electrospray ionization. Graphical Abstract ᅟ.
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Affiliation(s)
- Steven Daly
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
| | - Geoffrey Knight
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
| | - Mohamed Abdul Halim
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
| | - Alexander Kulesza
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
| | - Chang Min Choi
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
| | - Fabien Chirot
- Institut des Sciences Analytiques, Université Lyon 1 - CNRS, Université de Lyon, 69622, Villeurbanne Cedex, France
| | - Luke MacAleese
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
| | - Rodolphe Antoine
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France
| | - Philippe Dugourd
- Institut Lumière Matière, Université Lyon 1-CNRS, Université de Lyon, 69622, Villeurbanne cedex, France.
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30
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Ujma J, Giles K, Morris M, Barran PE. New High Resolution Ion Mobility Mass Spectrometer Capable of Measurements of Collision Cross Sections from 150 to 520 K. Anal Chem 2016; 88:9469-9478. [DOI: 10.1021/acs.analchem.6b01812] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jakub Ujma
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
for Biotechnology, University of Manchester, Manchester M1 7DN, U.K
| | | | | | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
for Biotechnology, University of Manchester, Manchester M1 7DN, U.K
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31
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Schlathölter T, Reitsma G, Egorov D, Gonzalez-Magaña O, Bari S, Boschman L, Bodewits E, Schnorr K, Schmid G, Schröter CD, Moshammer R, Hoekstra R. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Thomas Schlathölter
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Geert Reitsma
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Max-Born-Institute; Max Born Strasse 2A 12489 Berlin Germany
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Olmo Gonzalez-Magaña
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sadia Bari
- European XFEL GmbH; Holzkoppel 4 22869 Schenefeld Germany
- DESY; Notkestraße 85 22607 Hamburg Germany
| | - Leon Boschman
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Kapteyn Institute; Landleven 12 9747 AD Groningen The Netherlands
| | - Erwin Bodewits
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Kirsten Schnorr
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Georg Schmid
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | | | - Robert Moshammer
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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32
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Gray C, Thomas B, Upton R, Migas L, Eyers C, Barran P, Flitsch S. Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochim Biophys Acta Gen Subj 2016; 1860:1688-709. [DOI: 10.1016/j.bbagen.2016.02.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/21/2022]
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33
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Schlathölter T, Reitsma G, Egorov D, Gonzalez-Magaña O, Bari S, Boschman L, Bodewits E, Schnorr K, Schmid G, Schröter CD, Moshammer R, Hoekstra R. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses. Angew Chem Int Ed Engl 2016; 55:10741-5. [DOI: 10.1002/anie.201605335] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Thomas Schlathölter
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Geert Reitsma
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Max-Born-Institute; Max Born Strasse 2A 12489 Berlin Germany
| | - Dmitrii Egorov
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Olmo Gonzalez-Magaña
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Sadia Bari
- European XFEL GmbH; Holzkoppel 4 22869 Schenefeld Germany
- DESY; Notkestraße 85 22607 Hamburg Germany
| | - Leon Boschman
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Kapteyn Institute; Landleven 12 9747 AD Groningen The Netherlands
| | - Erwin Bodewits
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Kirsten Schnorr
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Georg Schmid
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | | | - Robert Moshammer
- Max-Planck-Institut für Kernphysik; Saupfercheckweg 1 69117 Heidelberg Germany
| | - Ronnie Hoekstra
- Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
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34
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López A, Vilaseca M, Madurga S, Varese M, Tarragó T, Giralt E. Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:504-511. [PMID: 27434808 DOI: 10.1002/jms.3777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 03/29/2016] [Accepted: 04/20/2016] [Indexed: 06/06/2023]
Abstract
Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confer IMMS great potential for the study of proteins in slow (µs-ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here, we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP) - a model of a large dynamic enzyme in the µs-ms range - by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision-induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas-phase collapsed form of POP was also detected. Therefore, our findings not only support the potential of IMMS for the study of multiple co-existing conformations of large proteins in slow dynamic equilibrium in solution but also stress the need for careful data analysis to avoid artifacts. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Abraham López
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Sergio Madurga
- Department of Physical Chemistry and Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Teresa Tarragó
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Iproteos, S.L., Barcelona Science Park, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Organic Chemistry, University of Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
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35
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Bartman CE, Metwally H, Konermann L. Effects of Multidentate Metal Interactions on the Structure of Collisionally Activated Proteins: Insights from Ion Mobility Spectrometry and Molecular Dynamics Simulations. Anal Chem 2016; 88:6905-13. [DOI: 10.1021/acs.analchem.6b01627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Claire E. Bartman
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department
of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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36
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Wagner ND, Kim D, Russell DH. Increasing Ubiquitin Ion Resistance to Unfolding in the Gas Phase Using Chloride Adduction: Preserving More "Native-Like" Conformations Despite Collisional Activation. Anal Chem 2016; 88:5934-40. [PMID: 27137645 DOI: 10.1021/acs.analchem.6b00871] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Electrospray ionization (ESI) of ubiquitin from acidified (0.1%) aqueous solution produces abundant ubiquitin-chloride adduct ions, [M + nH + xCl]((n - x)+), that upon mild heating react via elimination of neutral HCl. Ion mobility collision cross section (CCS) measurements show that ubiquitin ions retaining chloride adducts exhibit CCS values similar to those of the "native-state" of the protein. Coupled with results from recent molecular dynamics (MD) simulations for the evolution of a salt-containing electrospray droplet, this study provides a more complete picture for how the presence of salts affects the evolution of protein conformers in the final stages of dehydration of the ESI process and within the instrument.
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Affiliation(s)
- Nicole D Wagner
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - Doyong Kim
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States
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37
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González Flórez AI, Mucha E, Ahn DS, Gewinner S, Schöllkopf W, Pagel K, von Helden G. Charge-Induced Unzipping of Isolated Proteins to a Defined Secondary Structure. Angew Chem Int Ed Engl 2016; 55:3295-9. [PMID: 26847383 PMCID: PMC4770441 DOI: 10.1002/anie.201510983] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 11/08/2022]
Abstract
Here we present a combined experimental and theoretical study on the secondary structure of isolated proteins as a function of charge state. In infrared spectra of the proteins ubiquitin and cytochrome c, amide I (C=O stretch) and amide II (N-H bend) bands can be found at positions that are typical for condensed-phase proteins. For high charge states a new band appears, substantially red-shifted from the amide II band observed at lower charge states. The observations are interpreted in terms of Coulomb-driven transitions in secondary structures from mostly helical to extended C5 -type hydrogen-bonded structures. Support for this interpretation comes from simple energy considerations as well as from quantum chemical calculations on model peptides. This transition in secondary structure is most likely universal for isolated proteins that occur in mass spectrometric experiments.
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Affiliation(s)
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Doo-Sik Ahn
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany
- Institut für Chemie und Biochemie der Freien Universität Berlin, Takustrasse 3, 14195, Berlin, Germany
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195, Berlin, Germany.
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38
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González Flórez AI, Mucha E, Ahn DS, Gewinner S, Schöllkopf W, Pagel K, von Helden G. Ladungsinduziertes Entwinden isolierter Proteine zu einer definierten Sekundärstruktur. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201510983] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Eike Mucha
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Doo-Sik Ahn
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Sandy Gewinner
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Wieland Schöllkopf
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Kevin Pagel
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
- Institut für Chemie und Biochemie der Freien Universität Berlin; Takustraße 3 14195 Berlin Deutschland
| | - Gert von Helden
- Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
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39
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Morrison LJ, Brodbelt JS. Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry. Analyst 2016; 141:166-76. [PMID: 26596460 PMCID: PMC4679510 DOI: 10.1039/c5an01819f] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Characterization of all gas-phase charge sites of natively sprayed proteins and peptides is demonstrated using 193 nm UVPD. The high sequence coverage offered by UVPD is exploited for the accurate determination of charge sites in protein systems up to 18 kDa, allowing charge site to be studied as a function of protein conformation and the presence of disulfide bonds. Charging protons are found on both basic sidechains and on the amide backbone of less basic amino acids such as serine, glutamine, and proline. UVPD analysis was performed on the 3+ charge state of melittin, the 5+ to 8+ charge states of ubiquitin, and the 8+ charge state of reduced and oxidized β-lactoglobulin. The location of charges in gas-phase proteins is known to impact structure; molecular modeling of different charge site motifs of 3+ melittin demonstrates how placement of protons in simulations can dramatically impact the predicted structure of the molecule. The location of positive charge sites in ubiquitin and β-lactoglobulin are additionally found to depend on the presence or absence of salt-bridges, columbic repulsion across the length of the peptide, and protein conformation. Charge site isomers are demonstrated for ubiquitin and β-lactoglobulin but found to be much less numerous than previously predicted.
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40
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Göth M, Lermyte F, Schmitt XJ, Warnke S, von Helden G, Sobott F, Pagel K. Gas-phase microsolvation of ubiquitin: investigation of crown ether complexation sites using ion mobility-mass spectrometry. Analyst 2016; 141:5502-10. [DOI: 10.1039/c6an01377e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The influence of side chain to backbone interactions on the gas-phase structure of ubiquitin and ubiquitin lysine-to-arginine mutants was analysed.
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Affiliation(s)
- Melanie Göth
- Department of Biology
- Chemistry
- Pharmacy
- Freie Universität Berlin
- 14195 Berlin
| | - Frederik Lermyte
- Biomolecular and Analytical Mass Spectrometry
- Chemistry Department
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - Xiao Jakob Schmitt
- Department of Molecular Physics
- Fritz Haber Institute of the Max Planck Society
- 14195 Berlin
- Germany
| | - Stephan Warnke
- Department of Molecular Physics
- Fritz Haber Institute of the Max Planck Society
- 14195 Berlin
- Germany
| | - Gert von Helden
- Department of Molecular Physics
- Fritz Haber Institute of the Max Planck Society
- 14195 Berlin
- Germany
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry
- Chemistry Department
- University of Antwerp
- 2020 Antwerp
- Belgium
| | - Kevin Pagel
- Department of Biology
- Chemistry
- Pharmacy
- Freie Universität Berlin
- 14195 Berlin
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41
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Liu FC, Kirk SR, Bleiholder C. On the structural denaturation of biological analytes in trapped ion mobility spectrometry – mass spectrometry. Analyst 2016; 141:3722-30. [DOI: 10.1039/c5an02399h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trapped ion mobility spectra recorded for ubiquitin are consistent with structures reported for the native state by NMR.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Samuel R. Kirk
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
- Institute of Molecular Biophysics
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42
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Stover ML, Plummer CE, Miller SR, Cassady CJ, Dixon DA. Gas-Phase Acidities of Phosphorylated Amino Acids. J Phys Chem B 2015; 119:14604-21. [DOI: 10.1021/acs.jpcb.5b08616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michele L. Stover
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Chelsea E. Plummer
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Sean R. Miller
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Carolyn J. Cassady
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
| | - David A. Dixon
- Chemistry
Department, Shelby
Hall, The University of Alabama, Shelby Hall, Box
870336, Tuscaloosa, Alabama 35487-0336, United States
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43
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Chen SH, Russell DH. How Closely Related Are Conformations of Protein Ions Sampled by IM-MS to Native Solution Structures? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1433-43. [PMID: 26115967 DOI: 10.1007/s13361-015-1191-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 05/07/2015] [Accepted: 05/13/2015] [Indexed: 05/25/2023]
Abstract
Here, we critically evaluate the effects of changes in the ion internal energy (E(int)) on ion-neutral collision cross sections (CCS) of ions of two structurally diverse proteins, specifically the [M + 6H](6+) ion of ubiquitin (ubq(6+)), the [M + 5H](5+) ion of the intrinsically disordered protein (IDP) apo-metallothionein-2A (MT), and its partially- and fully-metalated isoform, the [CdiMT](5+) ion. The ion-neutral CCS for ions formed by "native-state" ESI show a strong dependence on E(int). Collisional activation is used to increase E(int) prior to the ions entering and within the traveling wave (TW) ion mobility analyzer. Comparisons of experimental CCSs with those generated by molecular dynamics (MD) simulation for solution-phase ions and solvent-free ions as a function of temperature provide new insights about conformational preferences and retention of solution conformations. The E(int)-dependent CCSs, which reveal increased conformational diversity of the ion population, are discussed in terms of folding/unfolding of solvent-free ions. For example, ubiquitin ions that have low internal energies retain native-like conformations, whereas ions that are heated by collisional activation possess higher internal energies and yield a broader range of CCS owing to increased conformational diversity due to losses of secondary and tertiary structures. In contrast, the CCS profile for the IDP apoMT is consistent with kinetic trapping of an ion population composed of a wide range of conformers, and as the E(int) is increased, these structurally labile conformers unfold to an elongated conformation.
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Affiliation(s)
- Shu-Hua Chen
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
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44
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Schennach M, Breuker K. Probing Protein Structure and Folding in the Gas Phase by Electron Capture Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1059-67. [PMID: 25868904 PMCID: PMC4475247 DOI: 10.1007/s13361-015-1088-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/19/2015] [Accepted: 01/27/2015] [Indexed: 05/11/2023]
Abstract
The established methods for the study of atom-detailed protein structure in the condensed phases, X-ray crystallography and nuclear magnetic resonance spectroscopy, have recently been complemented by new techniques by which nearly or fully desolvated protein structures are probed in gas-phase experiments. Electron capture dissociation (ECD) is unique among these as it provides residue-specific, although indirect, structural information. In this Critical Insight article, we discuss the development of ECD for the structural probing of gaseous protein ions, its potential, and limitations.
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Affiliation(s)
- Moritz Schennach
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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45
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Bleiholder C, Johnson NR, Contreras S, Wyttenbach T, Bowers MT. Molecular Structures and Ion Mobility Cross Sections: Analysis of the Effects of He and N2 Buffer Gas. Anal Chem 2015; 87:7196-203. [DOI: 10.1021/acs.analchem.5b01429] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Nicholas R. Johnson
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Stephanie Contreras
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Thomas Wyttenbach
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and
Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
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46
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Wyttenbach T, Bleiholder C, Anderson SE, Bowers MT. A new algorithm to characterise the degree of concaveness of a molecular surface relevant in ion mobility spectrometry. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1042935] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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47
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Pierson NA, Clemmer DE. An IMS-IMS threshold method for semi-quantitative determination of activation barriers: Interconversion of proline cis↔trans forms in triply protonated bradykinin. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 377:646-654. [PMID: 25838788 PMCID: PMC4378547 DOI: 10.1016/j.ijms.2014.07.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Collisional activation of selected conformations by multidimensional ion mobility spectrometry (IMS-IMS), combined with mass spectrometry (MS), is described as a method to determine semi-quantitative activation energies for interconversion of different structures of the nonapeptide bradykinin (BK, Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg). This analysis is based on a calibration involving collision-induced dissociation measurements of ions with known dissociation energies (i.e., "thermometer" ions) such as leucine enkephalin, BK, and amino acid-metal cation systems. The energetic barriers between six conformations of [BK+3H]3+ range from 0.23 ±0.01 to 0.55 ±0.03 eV. Prior results indicate that the major peaks in the IMS distributions correspond to specific combinations of cis and trans configurations of the three proline residues in the peptide sequence. The analysis allows us to directly assess pathways for specific transitions. The combination of structural assignments, experimentally determined barrier heights, onset of the quasi-equilibrium region, and dissociation threshold are used to derive a semi-quantitative potential energy surface for main features of [BK+3H]3+.
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Affiliation(s)
- Nicholas A. Pierson
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405 United States
| | - David E. Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405 United States
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48
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Ridgeway ME, Silveira JA, Meier JE, Park MA. Microheterogeneity within conformational states of ubiquitin revealed by high resolution trapped ion mobility spectrometry. Analyst 2015; 140:6964-72. [DOI: 10.1039/c5an00841g] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The present work employs trapped ion mobility spectrometry (TIMS) for the analysis of ubiquitin ions known to display a multitude of previously unresolved interchangeable conformations upon electrospray ionization.
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49
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Shi H, Atlasevich N, Merenbloom SI, Clemmer DE. Solution dependence of the collisional activation of ubiquitin [M + 7H](7+) ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:2000-8. [PMID: 24658799 PMCID: PMC4171273 DOI: 10.1007/s13361-014-0834-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/31/2013] [Accepted: 01/10/2014] [Indexed: 05/12/2023]
Abstract
The solution dependence of gas-phase unfolding for ubiquitin [M + 7H](7+) ions has been studied by ion mobility spectrometry-mass spectrometry (IMS-MS). Different acidic water:methanol solutions are used to favor the native (N), more helical (A), or unfolded (U) solution states of ubiquitin. Unfolding of gas-phase ubiquitin ions is achieved by collisional heating and newly formed structures are examined by IMS. With an activation voltage of 100 V, a selected distribution of compact structures unfolds, forming three resolvable elongated states (E1-E3). The relative populations of these elongated structures depend strongly on the solution composition. Activation of compact ions from aqueous solutions known to favor N-state ubiquitin produces mostly the E1 type elongated state, whereas activation of compact ions from methanol containing solutions that populate A-state ubiquitin favors the E3 elongated state. Presumably, this difference arises because of differences in precursor ion structures emerging from solution. Thus, it appears that information about solution populations can be retained after ionization, selection, and activation to produce the elongated states. These data as well as others are discussed.
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50
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Hendricks N, Lareau NM, Stow SM, McLean JA, Julian RR. Bond-specific dissociation following excitation energy transfer for distance constraint determination in the gas phase. J Am Chem Soc 2014; 136:13363-70. [PMID: 25174489 PMCID: PMC4183596 DOI: 10.1021/ja507215q] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Indexed: 01/02/2023]
Abstract
Herein, we report chemistry that enables excitation energy transfer (EET) to be accurately measured via action spectroscopy on gaseous ions in an ion trap. It is demonstrated that EET between tryptophan or tyrosine and a disulfide bond leads to excited state, homolytic fragmentation of the disulfide bond. This phenomenon exhibits a tight distance dependence, which is consistent with Dexter exchange transfer. The extent of fragmentation of the disulfide bond can be used to determine the distance between the chromophore and disulfide bond. The chemistry is well suited for the examination of protein structure in the gas phase because native amino acids can serve as the donor/acceptor moieties. Furthermore, both tyrosine and tryptophan exhibit unique action spectra, meaning that the identity of the donating chromophore can be easily determined in addition to the distance between donor/acceptor. Application of the method to the Trpcage miniprotein reveals distance constraints that are consistent with a native-like fold for the +2 charge state in the gas phase. This structure is stabilized by several salt bridges, which have also been observed to be important previously in proteins that retain native-like structures in the gas phase. The ability of this method to measure specific distance constraints, potentially at numerous positions if combined with site-directed mutagenesis, significantly enhances our ability to examine protein structure in the gas phase.
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Affiliation(s)
- Nathan
G. Hendricks
- Department
of Chemistry, University of California, Riverside, California 92521, United States
| | - Nichole M. Lareau
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology (VICB), and
Vanderbilt Institute for Integrative Biosystems Research and Education
(VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sarah M. Stow
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology (VICB), and
Vanderbilt Institute for Integrative Biosystems Research and Education
(VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology (VICB), and
Vanderbilt Institute for Integrative Biosystems Research and Education
(VIIBRE), Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ryan R. Julian
- Department
of Chemistry, University of California, Riverside, California 92521, United States
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