Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry

Abstract

Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving non-covalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and inter-molecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with pre-activation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-bindingmore » and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.« less

Authors:
 [1];  [1];  [2];  [2];  [2]; ORCiD logo [1]
+ Show Author Affiliations
  1. Univ. of California, Los Angeles, CA (United States)
  2. Univ. of Texas, Austin, TX (United States)
Publication Date:
Research Org.:
Univ. of California, Los Angeles, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1463126
Grant/Contract Number:  
FC03-02ER63421
Resource Type:
Accepted Manuscript
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 89; Journal Issue: 5; Journal ID: ISSN 0003-2700
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Li, Huilin, Sheng, Yuewei, McGee, William, Cammarata, Michael, Holden, Dustin, and Loo, Joseph A. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. United States: N. p., 2017. Web. doi:10.1021/acs.analchem.6b02377.
Copy to clipboard
Li, Huilin, Sheng, Yuewei, McGee, William, Cammarata, Michael, Holden, Dustin, & Loo, Joseph A. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. United States. https://doi.org/10.1021/acs.analchem.6b02377
Copy to clipboard
Li, Huilin, Sheng, Yuewei, McGee, William, Cammarata, Michael, Holden, Dustin, and Loo, Joseph A. Tue . "Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry". United States. https://doi.org/10.1021/acs.analchem.6b02377. https://www.osti.gov/servlets/purl/1463126.
Copy to clipboard
@article{osti_1463126,
title = {Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry},
author = {Li, Huilin and Sheng, Yuewei and McGee, William and Cammarata, Michael and Holden, Dustin and Loo, Joseph A.},
abstractNote = {Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving non-covalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and inter-molecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with pre-activation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-binding and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.},
doi = {10.1021/acs.analchem.6b02377},
journal = {Analytical Chemistry},
number = 5,
volume = 89,
place = {United States},
year = {Tue Feb 07 00:00:00 EST 2017},
month = {Tue Feb 07 00:00:00 EST 2017}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/acs.analchem.6b02377
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 52 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Native mass spectrometry: a bridge between interactomics and structural biology
journal, October 2008

Native protein mass spectrometry: from intact oligomers to functional machineries
journal, October 2004

Probing allosteric mechanisms using native mass spectrometry
journal, October 2015

Mass spectrometry supported determination of protein complex structure
journal, April 2013

  • Walzthoeni, Thomas; Leitner, Alexander; Stengel, Florian
  • Current Opinion in Structural Biology, Vol. 23, Issue 2
  • DOI: 10.1016/j.sbi.2013.02.008

Mass Spectrometry of Protein Complexes: From Origins to Applications
journal, April 2015

Dissecting the Large Noncovalent Protein Complex GroEL with Surface-Induced Dissociation and Ion Mobility–Mass Spectrometry
journal, August 2013

  • Zhou, Mowei; Jones, Christopher M.; Wysocki, Vicki H.
  • Analytical Chemistry, Vol. 85, Issue 17
  • DOI: 10.1021/ac401497c

Stepwise evolution of protein native structure with electrospray into the gas phase, 10-12 to 102 s
journal, November 2008

  • Breuker, K.; McLafferty, F. W.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 47
  • DOI: 10.1073/pnas.0807005105

Electron-capture dissociation and ion mobility mass spectrometry for characterization of the hemoglobin protein assembly: ECD & IM for Hemoglobin
journal, July 2015

  • Cui, Weidong; Zhang, Hao; Blankenship, Robert E.
  • Protein Science, Vol. 24, Issue 8
  • DOI: 10.1002/pro.2712

ETD Allows for Native Surface Mapping of a 150 kDa Noncovalent Complex on a Commercial Q-TWIMS-TOF Instrument
journal, January 2014

  • Lermyte, Frederik; Konijnenberg, Albert; Williams, Jonathan P.
  • Journal of The American Society for Mass Spectrometry, Vol. 25, Issue 3
  • DOI: 10.1007/s13361-013-0798-3

Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment
journal, June 2014

  • Li, Huilin; Wongkongkathep, Piriya; Van Orden, Steve L.
  • Journal of The American Society for Mass Spectrometry, Vol. 25, Issue 12
  • DOI: 10.1007/s13361-014-0928-6

Infrared Laser Activation of Soluble and Membrane Protein Assemblies in the Gas Phase
journal, July 2016

Ion Activation Methods for Peptides and Proteins
journal, December 2015

Activation of large lons in FT-ICR mass spectrometry
journal, January 2005

  • Laskin, Julia; Futrell, Jean H.
  • Mass Spectrometry Reviews, Vol. 24, Issue 2
  • DOI: 10.1002/mas.20012

Top-Down ESI-ECD-FT-ICR Mass Spectrometry Localizes Noncovalent Protein-Ligand Binding Sites
journal, November 2006

  • Xie, Yongming; Zhang, Jennifer; Yin, Sheng
  • Journal of the American Chemical Society, Vol. 128, Issue 45
  • DOI: 10.1021/ja063197p

Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure
journal, July 2004

  • Adams, Christopher M.; Kjeldsen, Frank; Zubarev, Roman A.
  • Journal of the American Society for Mass Spectrometry, Vol. 15, Issue 7
  • DOI: 10.1016/j.jasms.2004.04.026

Elucidating the site of protein-ATP binding by top-down mass spectrometry
journal, June 2010

Native Electrospray and Electron-Capture Dissociation FTICR Mass Spectrometry for Top-Down Studies of Protein Assemblies
journal, July 2011

  • Zhang, Hao; Cui, Weidong; Wen, Jianzhong
  • Analytical Chemistry, Vol. 83, Issue 14
  • DOI: 10.1021/ac200695d

Native Top-Down Electrospray Ionization-Mass Spectrometry of 158 kDa Protein Complex by High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
journal, December 2013

  • Li, Huilin; Wolff, Jeremy J.; Van Orden, Steve L.
  • Analytical Chemistry, Vol. 86, Issue 1
  • DOI: 10.1021/ac4033214

Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations
journal, February 2000

  • Zubarev, Roman A.; Horn, David M.; Fridriksson, Einar K.
  • Analytical Chemistry, Vol. 72, Issue 3
  • DOI: 10.1021/ac990811p

Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes
journal, April 2016

  • Loo, Rachel R. Ogorzalek; Loo, Joseph A.
  • Journal of The American Society for Mass Spectrometry, Vol. 27, Issue 6
  • DOI: 10.1007/s13361-016-1375-3

Complete Protein Characterization Using Top-Down Mass Spectrometry and Ultraviolet Photodissociation
journal, June 2013

  • Shaw, Jared B.; Li, Wenzong; Holden, Dustin D.
  • Journal of the American Chemical Society, Vol. 135, Issue 34
  • DOI: 10.1021/ja4029654

Characterization of Native Protein Complexes Using Ultraviolet Photodissociation Mass Spectrometry
journal, September 2014

  • O’Brien, John P.; Li, Wenzong; Zhang, Yan
  • Journal of the American Chemical Society, Vol. 136, Issue 37
  • DOI: 10.1021/ja505217w

Probing the Unfolding of Myoglobin and Domain C of PARP-1 with Covalent Labeling and Top-Down Ultraviolet Photodissociation Mass Spectrometry
journal, February 2014

  • Cammarata, Michael; Lin, Ke-Yi; Pruet, Jeff
  • Analytical Chemistry, Vol. 86, Issue 5
  • DOI: 10.1021/ac4036235

Structural characterization of holo- and apo-myoglobin in the gas phase by ultraviolet photodissociation mass spectrometry
journal, January 2015

  • Cammarata, Michael B.; Brodbelt, Jennifer S.
  • Chemical Science, Vol. 6, Issue 2
  • DOI: 10.1039/C4SC03200D

Top-Down 193-nm Ultraviolet Photodissociation Mass Spectrometry for Simultaneous Determination of Polyubiquitin Chain Length and Topology
journal, January 2015

  • Cannon, Joe R.; Martinez-Fonts, Kirby; Robotham, Scott A.
  • Analytical Chemistry, Vol. 87, Issue 3
  • DOI: 10.1021/ac5038363

Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry
journal, July 2015

  • Cammarata, Michael B.; Thyer, Ross; Rosenberg, Jake
  • Journal of the American Chemical Society, Vol. 137, Issue 28
  • DOI: 10.1021/jacs.5b04628

SPECIAL FEATURE:TUTORIAL Slow Heating Methods in Tandem Mass Spectrometry
journal, May 1997

Electron Ionization Dissociation of Singly and Multiply Charged Peptides
journal, July 2009

  • Fung, Y. M. Eva; Adams, Christopher M.; Zubarev, Roman A.
  • Journal of the American Chemical Society, Vol. 131, Issue 29
  • DOI: 10.1021/ja8087407

Dimer destabilization in superoxide dismutase may result in disease-causing properties: Structures of motor neuron disease mutants
journal, March 2004

  • Hough, M. A.; Grossmann, J. G.; Antonyuk, S. V.
  • Proceedings of the National Academy of Sciences, Vol. 101, Issue 16
  • DOI: 10.1073/pnas.0305143101

Folding and Stability of the N-Terminus of Human Carbonic Anhydrase II
journal, February 1995

  • Aronsson, Goeran; Mrtensson, Lars-Goeran; Carlsson, Uno
  • Biochemistry, Vol. 34, Issue 7
  • DOI: 10.1021/bi00007a008

Folding around the C-terminus of human carbonic anhydrase II Kinetic characterization by use of a chemically reactive SH-group introduced by protein engineering
journal, September 1991

Reshaping the folding energy landscape of human carbonic anhydrase II by a single point genetic mutation Pro237His
journal, January 2008

  • Jiang, Yan; Su, Jing-Tan; Zhang, Jun
  • The International Journal of Biochemistry & Cell Biology, Vol. 40, Issue 4
  • DOI: 10.1016/j.biocel.2007.10.022

Characterization of a folding intermediate of human carbonic anhydrase II: probing local mobility by electron paramagnetic resonance
journal, July 1995

Trigger factor-assisted folding of bovine carbonic anhydrase II
journal, January 2004

  • Liu, Chuan-Peng; Zhou, Jun-Mei
  • Biochemical and Biophysical Research Communications, Vol. 313, Issue 3
  • DOI: 10.1016/j.bbrc.2003.11.142

Denaturation and reactivation of human carbonic anhydrases in guanidine hydrochloride and urea
journal, June 1973

  • Carlsson, Uno; Henderson, Louis E.; Lindskog, Sven
  • Biochimica et Biophysica Acta (BBA) - Protein Structure, Vol. 310, Issue 2
  • DOI: 10.1016/0005-2795(73)90119-0

Partially Folded Conformations in the Folding Pathway of Bovine Carbonic Anhydrase II: A Fluorescence Spectroscopic Analysis
journal, November 2001

Solution Structure of Apo Cu,Zn Superoxide Dismutase:  Role of Metal Ions in Protein Folding †
journal, August 2003

  • Banci, Lucia; Bertini, Ivano; Cramaro, Fiorenza
  • Biochemistry, Vol. 42, Issue 32
  • DOI: 10.1021/bi034324m

Functional features cause misfolding of the ALS-provoking enzyme SOD1
journal, June 2009

  • Nordlund, A.; Leinartaite, L.; Saraboji, K.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 24
  • DOI: 10.1073/pnas.0812046106

Structure, folding, and misfolding of Cu,Zn superoxide dismutase in amyotrophic lateral sclerosis
journal, November 2006

  • Rakhit, Rishi; Chakrabartty, Avijit
  • Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1762, Issue 11-12
  • DOI: 10.1016/j.bbadis.2006.05.004

Structural similarity of wild-type and ALS-mutant superoxide dismutase-1 fibrils using limited proteolysis and atomic force microscopy
journal, June 2013

  • Chan, P. K.; Chattopadhyay, M.; Sharma, S.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 27
  • DOI: 10.1073/pnas.1309613110

193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology
journal, August 2016

  • Morrison, Lindsay J.; Brodbelt, Jennifer S.
  • Journal of the American Chemical Society, Vol. 138, Issue 34
  • DOI: 10.1021/jacs.6b03905

Fragmentation of Singly Charged Peptide Ions by Photodissociation atλ=157 nm
journal, January 2004

  • Thompson, Matthew S.; Cui, Weidong; Reilly, James P.
  • Angewandte Chemie International Edition
  • DOI: 10.1002/anie.200460788

157 nm Photodissociation of Dipeptide Ions Containing N-Terminal Arginine
journal, December 2013

  • Webber, Nathaniel; He, Yi; Reilly, James P.
  • Journal of The American Society for Mass Spectrometry, Vol. 25, Issue 2
  • DOI: 10.1007/s13361-013-0762-2

New Insights into the Vacuum UV Photodissociation of Peptides
journal, January 2010

  • Parthasarathi, Ramakrishnan; He, Yi; Reilly, James P.
  • Journal of the American Chemical Society, Vol. 132, Issue 5
  • DOI: 10.1021/ja907975v

Peptide Radical Cations: Gender Determines Dissociation Chemistry
journal, January 2013

Multiple Soft Ionization of Gas-Phase Proteins and Swift Backbone Dissociation in Collisions with ≤99 eV Electrons
journal, January 2010

  • Zubarev, Roman A.; Yang, Hongqian
  • Angewandte Chemie International Edition, Vol. 49, Issue 8
  • DOI: 10.1002/anie.200905977

Fragmentation of Positively-Charged Biological Ions Activated with a Beam of High-Energy Cations
journal, December 2013

  • Chingin, Konstantin; Makarov, Alexander; Denisov, Eduard
  • Analytical Chemistry, Vol. 86, Issue 1
  • DOI: 10.1021/ac403193k

Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase: ION ACTIVATION BY SYNCHROTRON RADIATION
journal, December 2013

  • Giuliani, Alexandre; Milosavljević, Aleksandar R.; Canon, Francis
  • Mass Spectrometry Reviews, Vol. 33, Issue 6
  • DOI: 10.1002/mas.21398
    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure
    journal, February 2018

    • Lermyte, Frederik; Valkenborg, Dirk; Loo, Joseph A.
    • Mass Spectrometry Reviews, Vol. 37, Issue 6
    • DOI: 10.1002/mas.21560

    An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes
    journal, January 2018

    • Li, Huilin; Nguyen, Hong Hanh; Ogorzalek Loo, Rachel R.
    • Nature Chemistry, Vol. 10, Issue 2
    • DOI: 10.1038/nchem.2908

    Native Top-Down Mass Spectrometry and Ion Mobility MS for Characterizing the Cobalt and Manganese Metal Binding of α-Synuclein Protein
    journal, June 2018

    • Wongkongkathep, Piriya; Han, Jong Yoon; Choi, Tae Su
    • Journal of The American Society for Mass Spectrometry, Vol. 29, Issue 9
    • DOI: 10.1007/s13361-018-2002-2

    Surface Induced Dissociation Coupled with High Resolution Mass Spectrometry Unveils Heterogeneity of a 211 kDa Multicopper Oxidase Protein Complex
    journal, January 2018

    • Zhou, Mowei; Yan, Jing; Romano, Christine A.
    • Journal of The American Society for Mass Spectrometry, Vol. 29, Issue 4
    • DOI: 10.1007/s13361-017-1882-x

    Structural and functional consequences of age-related isomerization in α-crystallins
    journal, February 2019

    • Lyon, Yana A.; Collier, Miranda P.; Riggs, Dylan L.
    • Journal of Biological Chemistry, Vol. 294, Issue 19
    • DOI: 10.1074/jbc.ra118.007052

    Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics
    journal, December 2019

    • Fornelli, Luca; Srzentić, Kristina; Toby, Timothy K.
    • Molecular & Cellular Proteomics, Vol. 19, Issue 2
    • DOI: 10.1074/mcp.tir119.001638

    Structural mass spectrometry comes of age: new insight into protein structure, function and interactions
    journal, January 2019

    • Allison, Timothy M.; Bechara, Cherine
    • Biochemical Society Transactions, Vol. 47, Issue 1
    • DOI: 10.1042/bst20180356

    In situ mass spectrometry analysis of intact proteins and protein complexes from biological substrates
    journal, February 2020

    • Hale, Oliver J.; Cooper, Helen J.
    • Biochemical Society Transactions, Vol. 48, Issue 1
    • DOI: 10.1042/bst20190793

    Structural and Functional Consequences of Age-Related Isomerization in α-Crystallins
    journal, July 2018

    • Lyon, Yana A.; Riggs, Dylan L.; Collier, Miranda P.
    • Journal of Biological Chemistry
    • DOI: 10.1101/364497
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: