skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies

Abstract

Here, we report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded “heavy” and “light” GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the “heavy” and “light” peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.

Authors:
 [1];  [1];  [1];  [1]
  1. Washington Univ., St. Louis, MO (United States)
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC), Washington, D.C. (United States). Photosynthetic Antenna Research Center (PARC)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1371148
Grant/Contract Number:  
SC0001035
Resource Type:
Accepted Manuscript
Journal Name:
Journal of the American Society for Mass Spectrometry
Additional Journal Information:
Journal Volume: 27; Journal Issue: 1; Related Information: PARC partners with Washington University in St. Louis (lead); University of California, Riverside; University of Glasgow, UK; Los Alamos National Laboratory; University of New Mexico; New Mexico Corsortium; North Carolina State University; Northwestern University; Oak Ridge National Laboratory; University of Pennsylvania; Sandia National Laboratories; University of Sheffield, UK; Journal ID: ISSN 1044-0305
Publisher:
American Society for Mass Spectrometry
Country of Publication:
United States
Language:
English
Subject:
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEAR CHEMISTRY; solar (fuels); photosynthesis (natural and artificial); biofuels (including algae and biomass); bio-inspired; charge transport; membrane; synthesis (novel materials); synthesis (self-assembly)

Citation Formats

Zhang, Hao, Liu, Haijun, Blankenship, Robert E., and Gross, Michael L. Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies. United States: N. p., 2015. Web. doi:10.1007/s13361-015-1260-5.
Zhang, Hao, Liu, Haijun, Blankenship, Robert E., & Gross, Michael L. Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies. United States. doi:10.1007/s13361-015-1260-5.
Zhang, Hao, Liu, Haijun, Blankenship, Robert E., and Gross, Michael L. Fri . "Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies". United States. doi:10.1007/s13361-015-1260-5. https://www.osti.gov/servlets/purl/1371148.
@article{osti_1371148,
title = {Isotope-Encoded Carboxyl Group Footprinting for Mass Spectrometry-Based Protein Conformational Studies},
author = {Zhang, Hao and Liu, Haijun and Blankenship, Robert E. and Gross, Michael L.},
abstractNote = {Here, we report an isotope-encoding method coupled with carboxyl-group footprinting to monitor protein conformational changes. The carboxyl groups of aspartic/glutamic acids and of the C-terminus of proteins can serve as reporters for protein conformational changes when labeled with glycine ethyl ester (GEE) mediated by carbodiimide. In the new development, isotope-encoded “heavy” and “light” GEE are used to label separately the two states of the orange carotenoid protein (OCP) from cyanobacteria. Two samples are mixed (1:1 ratio) and analyzed by a single LC-MS/MS experiment. The differences in labeling extent between the two states are represented by the ratio of the “heavy” and “light” peptides, providing information about protein conformational changes. Combining isotope-encoded MS quantitative analysis and carboxyl-group footprinting reduces the time of MS analysis and improves the sensitivity of GEE and other footprinting.},
doi = {10.1007/s13361-015-1260-5},
journal = {Journal of the American Society for Mass Spectrometry},
number = 1,
volume = 27,
place = {United States},
year = {2015},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 6 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

The role of the 6 lysines and the terminal amine of escherichia coli single-strand binding protein in its binding of single-stranded DNA
journal, August 1998


Isotope-Coded Affinity Tags with Tunable Reactivities for Protein Footprinting
journal, December 2008

  • Underbakke, Eric S.; Zhu, Yimin; Kiessling, Laura L.
  • Angewandte Chemie International Edition, Vol. 47, Issue 50
  • DOI: 10.1002/anie.200803378

The Orange Carotenoid Protein: a blue-green light photoactive protein
journal, January 2013

  • Kirilovsky, Diana; Kerfeld, Cheryl A.
  • Photochemical & Photobiological Sciences, Vol. 12, Issue 7
  • DOI: 10.1039/c3pp25406b

Mass Spectrometry-Based Protein Footprinting Characterizes the Structures of Oligomeric Apolipoprotein E2, E3, and E4
journal, September 2011

  • Gau, Brian; Garai, Kanchan; Frieden, Carl
  • Biochemistry, Vol. 50, Issue 38
  • DOI: 10.1021/bi200911c

Monitoring protein conformational changes and dynamics using stable-isotope labeling and mass spectrometry
journal, May 2014

  • Kahsai, Alem W.; Rajagopal, Sudarshan; Sun, Jinpeng
  • Nature Protocols, Vol. 9, Issue 6
  • DOI: 10.1038/nprot.2014.075

Membrane orientation of the FMO antenna protein from Chlorobaculum tepidum as determined by mass spectrometry-based footprinting
journal, April 2009

  • Wen, J.; Zhang, H.; Gross, M. L.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 15
  • DOI: 10.1073/pnas.0901691106

Protein Footprinting in a Complex Milieu: Identifying the Interaction Surfaces of the Chemotaxis Adaptor Protein CheW
journal, June 2011

  • Underbakke, Eric S.; Zhu, Yimin; Kiessling, Laura L.
  • Journal of Molecular Biology, Vol. 409, Issue 4
  • DOI: 10.1016/j.jmb.2011.03.040

A Mass Spectrometric Approach to the Study of DNA-Binding Proteins:  Interaction of Human TRF2 with Telomeric DNA
journal, February 2008

  • Sperry, Justin B.; Shi, Xiangguo; Rempel, Don L.
  • Biochemistry, Vol. 47, Issue 6
  • DOI: 10.1021/bi702037p

Advances in quantitative proteomics via stable isotope tagging and mass spectrometry
journal, February 2003


Covalent Labeling with Isotopically Encoded Reagents for Faster Structural Analysis of Proteins by Mass Spectrometry
journal, September 2013

  • Zhou, Yuping; Vachet, Richard W.
  • Analytical Chemistry, Vol. 85, Issue 20
  • DOI: 10.1021/ac401978w

Probing Conformational Changes in Human DNA Topoisomerase IIα by Pulsed Alkylation Mass Spectrometry
journal, June 2012

  • Chen, Yu-tsung; Collins, Tammy R. L.; Guan, Ziqiang
  • Journal of Biological Chemistry, Vol. 287, Issue 30
  • DOI: 10.1074/jbc.M112.377606

A photoactive carotenoid protein acting as light intensity sensor
journal, August 2008

  • Wilson, A.; Punginelli, C.; Gall, A.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 33
  • DOI: 10.1073/pnas.0804636105

Mass spectrometry-based carboxyl footprinting of proteins: Method evaluation
journal, February 2012

  • Zhang, Hao; Wen, Jianzhong; Huang, Richard Y-C.
  • International Journal of Mass Spectrometry, Vol. 312
  • DOI: 10.1016/j.ijms.2011.07.015

Probing protein structure by amino acid-specific covalent labeling and mass spectrometry
journal, September 2009

  • Mendoza, Vanessa Leah; Vachet, Richard W.
  • Mass Spectrometry Reviews, Vol. 28, Issue 5
  • DOI: 10.1002/mas.20203

Mass spectrometry footprinting reveals the structural rearrangements of cyanobacterial orange carotenoid protein upon light activation
journal, December 2014

  • Liu, Haijun; Zhang, Hao; King, Jeremy D.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837, Issue 12
  • DOI: 10.1016/j.bbabio.2014.09.004

Analytical Aspects of Hydrogen Exchange Mass Spectrometry
journal, July 2015


Carboxyl Group Footprinting Mass Spectrometry and Molecular Dynamics Identify Key Interactions in the HER2-HER3 Receptor Tyrosine Kinase Interface
journal, July 2013

  • Collier, Timothy S.; Diraviyam, Karthikeyan; Monsey, John
  • Journal of Biological Chemistry, Vol. 288, Issue 35
  • DOI: 10.1074/jbc.M113.474882

Hydroxyl Radical-Mediated Modification of Proteins as Probes for Structural Proteomics
journal, August 2007

  • Xu, Guozhong; Chance, Mark R.
  • Chemical Reviews, Vol. 107, Issue 8
  • DOI: 10.1021/cr0682047

Mass spectrometric-based approaches in quantitative proteomics
journal, February 2003


Protein footprinting by the combined use of reversible and irreversible lysine modifications.
journal, December 1994

  • Hanai, R.; Wang, J. C.
  • Proceedings of the National Academy of Sciences, Vol. 91, Issue 25
  • DOI: 10.1073/pnas.91.25.11904

The Crystal Structure of a Cyanobacterial Water-Soluble Carotenoid Binding Protein
journal, January 2003


Type I Antifreeze Proteins Enhance Ice Nucleation above Certain Concentrations
journal, September 2010

  • Wilson, Peter W.; Osterday, Katie E.; Heneghan, Aaron F.
  • Journal of Biological Chemistry, Vol. 285, Issue 45
  • DOI: 10.1074/jbc.M110.171983

Characterizing monoclonal antibody structure by carboxyl group footprinting
journal, March 2015


Biosynthesis of soluble carotenoid holoproteins in Escherichia coli
journal, March 2015

  • de Carbon, Céline Bourcier; Thurotte, Adrien; Wilson, Adjélé
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep09085

Molecular Mechanism of Photoactivation and Structural Location of the Cyanobacterial Orange Carotenoid Protein
journal, December 2013

  • Zhang, Hao; Liu, Haijun; Niedzwiedzki, Dariusz M.
  • Biochemistry, Vol. 53, Issue 1
  • DOI: 10.1021/bi401539w

Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules
journal, December 2013

  • Konermann, Lars; Vahidi, Siavash; Sowole, Modupeola A.
  • Analytical Chemistry, Vol. 86, Issue 1
  • DOI: 10.1021/ac4039306