Native top-down mass spectrometry for the structural characterization of human hemoglobin

Zhang, Jiang; Malmirchegini, G. Reza; Clubb, Robert T.; Loo, Joseph A.

doi:10.1255/ejms.1340

Title: Native top-down mass spectrometry for the structural characterization of human hemoglobin

Journal Article · Mon Jun 08 20:00:00 EDT 2015 · European Journal of Mass Spectrometry

DOI: https://doi.org/10.1255/ejms.1340 · OSTI ID:1345518

Zhang, Jiang ^[1]; Malmirchegini, G. Reza ^[2]; Clubb, Robert T. ^[2]; Loo, Joseph A. ^[2]

Univ. of California, Los Angeles, CA (United States); DOE Office of Scientific and Technical Information (OSTI)
Univ. of California, Los Angeles, CA (United States)

Native mass spectrometry (MS) has become an invaluable tool for the characterization of proteins and non-covalent protein complexes under near physiological solution conditions. Here we report the structural characterization of human hemoglobin (Hb), a 64 kDa oxygen-transporting protein complex, by high resolution native top-down mass spectrometry using electrospray ionization (ESI) and a 15-Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Native MS preserves the non-covalent interactions between the globin subunits, and electron capture dissociation (ECD) produces fragments directly from the intact Hb complex without dissociating the subunits. Using activated ion ECD, we observe the gradual unfolding process of the Hb complex in the gas phase. Without protein ion activation, the native Hb shows very limited ECD fragmentation from the N-termini, suggesting a tightly packed structure of the native complex and therefore low fragmentation efficiency. Precursor ion activation allows steady increase of N-terminal fragment ions, while the C-terminal fragments remain limited (38 c ions and 4 z ions on the α chain; 36 c ions and 2 z ions on the β chain). This ECD fragmentation pattern suggests that upon activation, the Hb complex starts to unfold from the N-termini of both subunits, whereas the C-terminal regions and therefore the potential regions involved in the subunit binding interactions remain intact. ECD-MS of the Hb dimer show similar fragmentation patterns as the Hb tetramer, providing further evidence for the hypothesized unfolding process of the Hb complex in the gas phase. Native top-down ECD-MS allows efficient probing of the Hb complex structure and the subunit binding interactions in the gas phase. Finally, it may provide a fast and effective means to probe the structure of novel protein complexes that are intractable to traditional structural characterization tools.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: FC03-02ER63421

OSTI ID:: 1345518

Journal Information:: European Journal of Mass Spectrometry, Journal Name: European Journal of Mass Spectrometry Journal Issue: 3 Vol. 21; ISSN 1469-0667

Publisher:: IM PublicationsCopyright Statement

Country of Publication:: United States

Language:: English

References (56)

Studying noncovalent protein complexes by electrospray ionization mass spectrometry Loo, Joseph A. Mass Spectrometry Reviews, Vol. 16, Issue 1 https://doi.org/10.1002/(SICI)1098-2787(1997)16:1<1::AID-MAS1>3.0.CO;2-L	journal	January 1997
Electrostatic Stabilization of a Native Protein Structure in the Gas Phase Breuker, Kathrin; Brüschweiler, Sven; Tollinger, Martin Angewandte Chemie, Vol. 123, Issue 4 https://doi.org/10.1002/ange.201005112	journal	November 2010
Electrostatic Stabilization of a Native Protein Structure in the Gas Phase Breuker, Kathrin; Brüschweiler, Sven; Tollinger, Martin Angewandte Chemie International Edition, Vol. 50, Issue 4 https://doi.org/10.1002/anie.201005112	journal	November 2010
Studying 18 MDa Virus Assemblies with Native Mass Spectrometry Snijder, Joost; Rose, Rebecca J.; Veesler, David Angewandte Chemie International Edition, Vol. 52, Issue 14 https://doi.org/10.1002/anie.201210197	journal	February 2013
Bioinformatics Keith, Jonathan M. Methods in Molecular Biology™ https://doi.org/10.1007/978-1-60327-159-2	book	January 2008
Protein Structure Determination by X-Ray Crystallography Ilari, Andrea; Savino, Carmelinda Bioinformatics https://doi.org/10.1007/978-1-60327-159-2_3	book	January 2008
Protein–Protein Binding Affinities in Solution Determined by Electrospray Mass Spectrometry Liu, Jiangjiang; Konermann, Lars Journal of The American Society for Mass Spectrometry, Vol. 22, Issue 3 https://doi.org/10.1007/s13361-010-0052-1	journal	February 2011
Mapping a Noncovalent Protein–Peptide Interface by Top-Down FTICR Mass Spectrometry Using Electron Capture Dissociation Clarke, David J.; Murray, Euan; Hupp, Ted Journal of The American Society for Mass Spectrometry, Vol. 22, Issue 8 https://doi.org/10.1007/s13361-011-0155-3	journal	May 2011
Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment Li, Huilin; Wongkongkathep, Piriya; Van Orden, Steve L. Journal of The American Society for Mass Spectrometry, Vol. 25, Issue 12 https://doi.org/10.1007/s13361-014-0928-6	journal	June 2014
Atomic resolution cryo electron microscopy of macromolecular complexes Zhou, Z. Hong Recent Advances in Electron Cryomicroscopy, Part B https://doi.org/10.1016/B978-0-12-386507-6.00001-4	book	April 2011
Protein structure determination in solution by NMR spectroscopy. Wüthrich, K. Journal of Biological Chemistry, Vol. 265, Issue 36 https://doi.org/10.1016/S0021-9258(18)45665-7	journal	December 1990
Unfolding of proteins monitored by electrospray ionization mass spectrometry: a comparison of positive and negative ion modes Konermann, Lars; Douglas, D. J. Journal of the American Society for Mass Spectrometry, Vol. 9, Issue 12 https://doi.org/10.1016/S1044-0305(98)00103-2	journal	December 1998
Systematic Interactome Mapping and Genetic Perturbation Analysis of a C. elegans TGF-β Signaling Network Tewari, Muneesh; Hu, Patrick J.; Ahn, Jin Sook Molecular Cell, Vol. 13, Issue 4 https://doi.org/10.1016/S1097-2765(04)00033-4	journal	February 2004
Electrospray ionization mass spectrometry: a technology for studying noncovalent macromolecular complexes Loo, Joseph A. International Journal of Mass Spectrometry, Vol. 200, Issue 1-3 https://doi.org/10.1016/S1387-3806(00)00298-0	journal	December 2000
Gas-phase dissociation of hemoglobin Versluis, Cees; Heck, Albert J. R. International Journal of Mass Spectrometry, Vol. 210-211 https://doi.org/10.1016/S1387-3806(01)00428-6	journal	September 2001
A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome Stelzl, Ulrich; Worm, Uwe; Lalowski, Maciej Cell, Vol. 122, Issue 6 https://doi.org/10.1016/j.cell.2005.08.029	journal	September 2005
A Protein–Protein Interaction Network for Human Inherited Ataxias and Disorders of Purkinje Cell Degeneration Lim, Janghoo; Hao, Tong; Shaw, Chad Cell, Vol. 125, Issue 4 https://doi.org/10.1016/j.cell.2006.03.032	journal	May 2006
Top-down mass spectrometry of supercharged native protein–ligand complexes Yin, Sheng; Loo, Joseph A. International Journal of Mass Spectrometry, Vol. 300, Issue 2-3 https://doi.org/10.1016/j.ijms.2010.06.032	journal	March 2011
Native electrospray ionization and electron-capture dissociation for comparison of protein structure in solution and the gas phase Zhang, Hao; Cui, Weidong; Gross, Michael L. International Journal of Mass Spectrometry, Vol. 354-355 https://doi.org/10.1016/j.ijms.2013.06.019	journal	November 2013
Folding and assembly of hemoglobin monitored by electrospray mass spectrometry using an on-line dialysis system Boys, Brian L.; Konermann, Lars Journal of the American Society for Mass Spectrometry, Vol. 18, Issue 1 https://doi.org/10.1016/j.jasms.2006.08.013	journal	January 2007
Analysis of protein mixtures by electrospray mass spectrometry: Effects of conformation and desolvation behavior on the signal intensities of hemoglobin subunits Kuprowski, Mark C.; Boys, Brian L.; Konermann, Lars Journal of the American Society for Mass Spectrometry, Vol. 18, Issue 7 https://doi.org/10.1016/j.jasms.2007.04.002	journal	July 2007
Collisional activation of protein complexes: Picking up the pieces Benesch, Justin L. P. Journal of the American Society for Mass Spectrometry, Vol. 20, Issue 3 https://doi.org/10.1016/j.jasms.2008.11.014	journal	March 2009
Elucidating the site of protein-ATP binding by top-down mass spectrometry Yin, Sheng; Loo, Joseph A. Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 6 https://doi.org/10.1016/j.jasms.2010.01.002	journal	June 2010
Deciphering modifications in swine cardiac troponin I by top-down high-resolution tandem mass spectrometry Zhang, Jiang; Dong, Xintong; Hacker, Timothy A. Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 6 https://doi.org/10.1016/j.jasms.2010.02.005	journal	June 2010
Native Electrospray and Electron-Capture Dissociation in FTICR Mass Spectrometry Provide Top-Down Sequencing of a Protein Component in an Intact Protein Assembly Zhang, Hao; Cui, Weidong; Wen, Jianzhong Journal of the American Society for Mass Spectrometry, Vol. 21, Issue 12 https://doi.org/10.1016/j.jasms.2010.08.006	journal	December 2010
Molecular dynamics of protein complexes from four-dimensional cryo-electron microscopy Heymann, J. Bernard; Conway, James F.; Steven, Alasdair C. Journal of Structural Biology, Vol. 147, Issue 3 https://doi.org/10.1016/j.jsb.2004.02.006	journal	September 2004
A Protein Interaction Network Links GIT1, an Enhancer of Huntingtin Aggregation, to Huntington's Disease Goehler, Heike; Lalowski, Maciej; Stelzl, Ulrich Molecular Cell, Vol. 15, Issue 6 https://doi.org/10.1016/j.molcel.2004.09.016	journal	September 2004
A Protein Interaction Network Links GIT1, an Enhancer of Huntingtin Aggregation, to Huntington’s Disease Goehler, Heike; Lalowski, Maciej; Stelzl, Ulrich Molecular Cell, Vol. 19, Issue 2 https://doi.org/10.1016/j.molcel.2005.06.031	journal	July 2005
Protein–protein interactions in human disease Ryan, D.; Matthews, J. Current Opinion in Structural Biology, Vol. 15, Issue 4 https://doi.org/10.1016/j.sbi.2005.06.001	journal	August 2005
The Nitty-Gritty of Protein Interactions Schreiber, Gideon Structure, Vol. 13, Issue 12 https://doi.org/10.1016/j.str.2005.11.001	journal	December 2005
Huntingtin–protein interactions and the pathogenesis of Huntington's disease Li, Shi-Hua; Li, Xiao-Jiang Trends in Genetics, Vol. 20, Issue 3 https://doi.org/10.1016/j.tig.2004.01.008	journal	March 2004
Activated Ion Electron Capture Dissociation for Mass Spectral Sequencing of Larger (42 kDa) Proteins Horn, David M.; Ge, Ying; McLafferty, Fred W. Analytical Chemistry, Vol. 72, Issue 20 https://doi.org/10.1021/ac000494i	journal	October 2000
Combined Electron Capture and Infrared Multiphoton Dissociation for Multistage MS/MS in a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Håkansson, Kristina; Chalmers, Michael J.; Quinn, John P. Analytical Chemistry, Vol. 75, Issue 13 https://doi.org/10.1021/ac030015q	journal	July 2003
Native Electrospray and Electron-Capture Dissociation FTICR Mass Spectrometry for Top-Down Studies of Protein Assemblies Zhang, Hao; Cui, Weidong; Wen, Jianzhong Analytical Chemistry, Vol. 83, Issue 14 https://doi.org/10.1021/ac200695d	journal	July 2011
Native Top-Down Electrospray Ionization-Mass Spectrometry of 158 kDa Protein Complex by High-Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Li, Huilin; Wolff, Jeremy J.; Van Orden, Steve L. Analytical Chemistry, Vol. 86, Issue 1 https://doi.org/10.1021/ac4033214	journal	December 2013
Highly Asymmetric Interactions between Globin Chains during Hemoglobin Assembly Revealed by Electrospray Ionization Mass Spectrometry ^† Griffith, Wendell P.; Kaltashov, Igor A. Biochemistry, Vol. 42, Issue 33 https://doi.org/10.1021/bi034035y	journal	August 2003
Observation of the heme-globin complex in native myoglobin by electrospray-ionization mass spectrometry Katta, Viswanatham; Chait, Brian T. Journal of the American Chemical Society, Vol. 113, Issue 22 https://doi.org/10.1021/ja00022a058	journal	October 1991
Top-Down ESI-ECD-FT-ICR Mass Spectrometry Localizes Noncovalent Protein-Ligand Binding Sites Xie, Yongming; Zhang, Jennifer; Yin, Sheng Journal of the American Chemical Society, Vol. 128, Issue 45 https://doi.org/10.1021/ja063197p	journal	November 2006
Top-Down Quantitative Proteomics Identified Phosphorylation of Cardiac Troponin I as a Candidate Biomarker for Chronic Heart Failure Zhang, Jiang; Guy, Moltu J.; Norman, Holly S. Journal of Proteome Research, Vol. 10, Issue 9 https://doi.org/10.1021/pr200258m	journal	September 2011
Structure of Hæmoglobin: A Three-Dimensional Fourier Synthesis at 5.5-Å. Resolution, Obtained by X-Ray Analysis Perutz, M. F.; Rossmann, M. G.; Cullis, Ann F. Nature, Vol. 185, Issue 4711 https://doi.org/10.1038/185416a0	journal	February 1960
Stereochemistry of Cooperative Effects in Haemoglobin: Haem–Haem Interaction and the Problem of Allostery Perutz, M. F. Nature, Vol. 228, Issue 5273 https://doi.org/10.1038/228726a0	journal	November 1970
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Ho, Yuen; Gruhler, Albrecht; Heilbut, Adrian Nature, Vol. 415, Issue 6868 https://doi.org/10.1038/415180a	journal	January 2002
Towards a proteome-scale map of the human protein–protein interaction network Rual, Jean-François; Venkatesan, Kavitha; Hao, Tong Nature, Vol. 437, Issue 7062 https://doi.org/10.1038/nature04209	journal	September 2005
Proteome survey reveals modularity of the yeast cell machinery Gavin, Anne-Claude; Aloy, Patrick; Grandi, Paola Nature, Vol. 440, Issue 7084 https://doi.org/10.1038/nature04532	journal	January 2006
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae Krogan, Nevan J.; Cagney, Gerard; Yu, Haiyuan Nature, Vol. 440, Issue 7084 https://doi.org/10.1038/nature04670	journal	March 2006
Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets Gandhi, T. K. B.; Zhong, Jun; Mathivanan, Suresh Nature Genetics, Vol. 38, Issue 3 https://doi.org/10.1038/ng1747	journal	February 2006
The way to NMR structures of proteins Wüthrich, Kurt Nature Structural Biology, Vol. 8, Issue 11, p. 923-925 https://doi.org/10.1038/nsb1101-923	journal	November 2001
Interaction between amyloid precursor protein and presenilins in mammalian cells: Implications for the pathogenesis of Alzheimer disease Xia, W.; Zhang, J.; Perez, R. Proceedings of the National Academy of Sciences, Vol. 94, Issue 15 https://doi.org/10.1073/pnas.94.15.8208	journal	July 1997
Staphylococcus aureus Uses a Novel Multidomain Receptor to Break Apart Human Hemoglobin and Steal Its Heme Spirig, Thomas; Malmirchegini, G. Reza; Zhang, Jiang Journal of Biological Chemistry, Vol. 288, Issue 2 https://doi.org/10.1074/jbc.M112.419119	journal	November 2012
Aberrant Interactions of Transcriptional Repressor Proteins with the Huntington's Disease Gene Product, Huntingtin Boutell, J. M.; Thomas, P.; Neal, J. W. Human Molecular Genetics, Vol. 8, Issue 9 https://doi.org/10.1093/hmg/8.9.1647	journal	September 1999
Protein interaction mapping: A Drosophila case study Formstecher, E. Genome Research, Vol. 15, Issue 3 https://doi.org/10.1101/gr.2659105	journal	February 2005
A Protein Interaction Map of Drosophila melanogaster Giot, L. Science, Vol. 302, Issue 5651 https://doi.org/10.1126/science.1090289	journal	December 2003
A Map of the Interactome Network of the Metazoan C. elegans Li, S. Science, Vol. 303, Issue 5657 https://doi.org/10.1126/science.1091403	journal	January 2004
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network Yu, H.; Braun, P.; Yildirim, M. A. Science, Vol. 322, Issue 5898 https://doi.org/10.1126/science.1158684	journal	October 2008
The Role of Mass Spectrometry in Structure Elucidation of Dynamic Protein Complexes Sharon, Michal; Robinson, Carol V. Annual Review of Biochemistry, Vol. 76, Issue 1 https://doi.org/10.1146/annurev.biochem.76.061005.090816	journal	June 2007
Mass Spectrometry in the Study of Hemoglobin: from Covalent Structure to Higher Order Assembly Griffith, Wendell; Kaltashov, Igor Current Organic Chemistry, Vol. 10, Issue 5 https://doi.org/10.2174/138527206776055303	journal	March 2006

Cited By (6)

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31 Dyachenko, Andrey; Tamara, Sem; Heck, Albert J. R. Journal of the American Society for Mass Spectrometry, Vol. 30, Issue 1 https://doi.org/10.1007/s13361-018-1910-5	journal	May 2018
Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses Coorssen, Jens; Yergey, Alfred Proteomes, Vol. 3, Issue 4 https://doi.org/10.3390/proteomes3040440	journal	December 2015
Radical solutions: Principles and application of electron-based dissociation in mass spectrometry-based analysis of protein structure Lermyte, Frederik; Valkenborg, Dirk; Loo, Joseph A. Mass Spectrometry Reviews, Vol. 37, Issue 6 https://doi.org/10.1002/mas.21560	journal	February 2018
Structural mass spectrometry comes of age: new insight into protein structure, function and interactions Allison, Timothy M.; Bechara, Cherine Biochemical Society Transactions, Vol. 47, Issue 1 https://doi.org/10.1042/bst20180356	journal	January 2019
Diagnosis of Hemoglobinopathy and β-Thalassemia by 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry of Hemoglobin from Blood He, Lidong; Rockwood, Alan L.; Agarwal, Archana M. Clinical Chemistry, Vol. 65, Issue 8 https://doi.org/10.1373/clinchem.2018.295766	journal	August 2019
Proteomics Is Analytical Chemistry: Fitness-for-Purpose in the Application of Top-Down and Bottom-Up Analyses Coorssen, Jens; Yergey, Alfred Proteomes, Vol. 3, Issue 4 https://doi.org/10.3390/proteomes3040440	journal	December 2015

Similar Records

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

Journal Article · Mon Feb 06 19:00:00 EST 2017 · Analytical Chemistry · OSTI ID:1463126

Li, Huilin; Sheng, Yuewei; McGee, William; +3 more

Charge Movement and Structural Changes in the Gas-Phase Unfolding of Multimeric Protein Complexes Captured by Native Top-Down Mass Spectrometry

Journal Article · Sun Dec 22 19:00:00 EST 2019 · Analytical Chemistry · OSTI ID:1597653

Zhou, Mowei; Liu, Weijing; Shaw, Jared B.

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

Journal Article · Sat Sep 15 00:00:00 EDT 2018 · Journal of the American Society for Mass Spectrometry · OSTI ID:22776840

Wongkongkathep, Piriya; Han, Jong Yoon; Choi, Tae Su; +2 more

Related Subjects

47 OTHER INSTRUMENTATION
binding interface
electron capture dissociation
gas phase structure
hemoglobin
native mass spectrometry
protein complex

Title: Native top-down mass spectrometry for the structural characterization of human hemoglobin

Citation Formats

References (56)

Cited By (6)

Similar Records

Related Subjects