Advancements and Application of Microsecond Synchrotron X-ray Footprinting at the Advanced Light Source
Abstract
The method of synchrotron X-ray protein footprinting (XF-MS) is used to determine protein conformational changes, folding, protein-protein and protein-ligand interactions, providing information which is often difficult to obtain using X-ray crystallography and other common structural biology methods [1–3]. The technique uses comparative in situ labeling of solvent-accessible side chains by highly reactive hydroxyl radicals (•OH) in buffered aqueous solution under different assay conditions. In regions where a protein is folded or binds a partner, these •OH susceptible sites are inaccessible to solvent, and therefore protected from labeling. The •OH are generated by the ionization of water using high-flux-density X-rays. High-flux density is a key factor for XF-MS labeling because obtaining an adequate steady-state concentration of hydroxyl radical within a short irradiation time is necessary to minimize radiation-induced secondary damage and also to overcome various scavenging reactions that reduce the yield of labeled side chains.
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
- OSTI Identifier:
- 1576495
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Synchrotron Radiation News
- Additional Journal Information:
- Journal Volume: 29; Journal Issue: 1; Journal ID: ISSN 0894-0886
- Publisher:
- Taylor & Francis
- Country of Publication:
- United States
- Language:
- English
Citation Formats
Gupta, Sayan, Celestre, Rich, Feng, Jun, and Ralston, Corie. Advancements and Application of Microsecond Synchrotron X-ray Footprinting at the Advanced Light Source. United States: N. p., 2016.
Web. doi:10.1080/08940886.2016.1124684.
Gupta, Sayan, Celestre, Rich, Feng, Jun, & Ralston, Corie. Advancements and Application of Microsecond Synchrotron X-ray Footprinting at the Advanced Light Source. United States. doi:10.1080/08940886.2016.1124684.
Gupta, Sayan, Celestre, Rich, Feng, Jun, and Ralston, Corie. Sat .
"Advancements and Application of Microsecond Synchrotron X-ray Footprinting at the Advanced Light Source". United States. doi:10.1080/08940886.2016.1124684. https://www.osti.gov/servlets/purl/1576495.
@article{osti_1576495,
title = {Advancements and Application of Microsecond Synchrotron X-ray Footprinting at the Advanced Light Source},
author = {Gupta, Sayan and Celestre, Rich and Feng, Jun and Ralston, Corie},
abstractNote = {The method of synchrotron X-ray protein footprinting (XF-MS) is used to determine protein conformational changes, folding, protein-protein and protein-ligand interactions, providing information which is often difficult to obtain using X-ray crystallography and other common structural biology methods [1–3]. The technique uses comparative in situ labeling of solvent-accessible side chains by highly reactive hydroxyl radicals (•OH) in buffered aqueous solution under different assay conditions. In regions where a protein is folded or binds a partner, these •OH susceptible sites are inaccessible to solvent, and therefore protected from labeling. The •OH are generated by the ionization of water using high-flux-density X-rays. High-flux density is a key factor for XF-MS labeling because obtaining an adequate steady-state concentration of hydroxyl radical within a short irradiation time is necessary to minimize radiation-induced secondary damage and also to overcome various scavenging reactions that reduce the yield of labeled side chains.},
doi = {10.1080/08940886.2016.1124684},
journal = {Synchrotron Radiation News},
number = 1,
volume = 29,
place = {United States},
year = {2016},
month = {1}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
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:
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
Future directions of structural mass spectrometry using hydroxyl radical footprinting
journal, September 2010
- Kiselar, Janna G.; Chance, Mark R.
- Journal of Mass Spectrometry, Vol. 45, Issue 12
The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron Footprinting
journal, April 2007
- Gupta, Sayan; Sullivan, Michael; Toomey, John
- Journal of Synchrotron Radiation, Vol. 14, Issue 3
Installation and testing of a focusing mirror at beamline X28C for high flux x-ray radiolysis of biological macromolecules
journal, January 2008
- Sullivan, Michael R.; Rekhi, Sandeep; Bohon, Jen
- Review of Scientific Instruments, Vol. 79, Issue 2
Structural waters define a functional channel mediating activation of the GPCR, rhodopsin
journal, August 2009
- Angel, T. E.; Gupta, S.; Jastrzebska, B.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 34
Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop
journal, August 2008
- Bohon, Jen; Jennings, Laura D.; Phillips, Christine M.
- Structure, Vol. 16, Issue 8
Development of a microsecond X-ray protein footprinting facility at the Advanced Light Source
journal, May 2014
- Gupta, Sayan; Celestre, Richard; Petzold, Christopher J.
- Journal of Synchrotron Radiation, Vol. 21, Issue 4
Visualizing the kinetic power stroke that drives proton-coupled zinc(ii) transport
journal, June 2014
- Gupta, Sayan; Chai, Jin; Cheng, Jie
- Nature, Vol. 512, Issue 7512
Modeling of protein binary complexes using structural mass spectrometry data
journal, November 2007
- Kamal, J. K. A.; Chance, M. R.
- Protein Science, Vol. 17, Issue 1
Quantitative Protein Topography Analysis and High-Resolution Structure Prediction Using Hydroxyl Radical Labeling and Tandem-Ion Mass Spectrometry (MS)
journal, February 2015
- Kaur, Parminder; Kiselar, Janna; Yang, Sichun
- Molecular & Cellular Proteomics, Vol. 14, Issue 4
On-plate deposition of oxidized proteins to facilitate protein footprinting studies by radical probe mass spectrometry: On-plate oxidation for protein footprinting by RP-MS
journal, August 2012
- Maleknia, Simin D.; Downard, Kevin M.
- Rapid Communications in Mass Spectrometry, Vol. 26, Issue 19
Laser flash photolysis of hydrogen peroxide to oxidize protein solvent-accessible residues on the microsecond timescale
journal, December 2005
- Hambly, David M.; Gross, Michael L.
- Journal of the American Society for Mass Spectrometry, Vol. 16, Issue 12
Pulsed Electron Beam Water Radiolysis for Submicrosecond Hydroxyl Radical Protein Footprinting
journal, April 2009
- Watson, Caroline; Janik, Ireneusz; Zhuang, Tiandi
- Analytical Chemistry, Vol. 81, Issue 7
Structure and dynamics of protein waters revealed by radiolysis and mass spectrometry
journal, August 2012
- Gupta, S.; D'Mello, R.; Chance, M. R.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 37
A 12 A carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection
journal, June 2015
- Leverenz, R. L.; Sutter, M.; Wilson, A.
- Science, Vol. 348, Issue 6242
Local and global structural drivers for the photoactivation of the orange carotenoid protein
journal, September 2015
- Gupta, Sayan; Guttman, Miklos; Leverenz, Ryan L.
- Proceedings of the National Academy of Sciences, Vol. 112, Issue 41
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
Crystal structure of the FRP and identification of the active site for modulation of OCP-mediated photoprotection in cyanobacteria
journal, May 2013
- Sutter, M.; Wilson, A.; Leverenz, R. L.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 24
Visualizing the Ca2+-dependent activation of gelsolin by using synchrotron footprinting
journal, March 2003
- Kiselar, J. G.; Janmey, P. A.; Almo, S. C.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 7
Methods for SAXS-Based Structure Determination of Biomolecular Complexes
journal, May 2014
- Yang, Sichun
- Advanced Materials, Vol. 26, Issue 46
In Vivo X-Ray Footprinting of Pre-30S Ribosomes Reveals Chaperone-Dependent Remodeling of Late Assembly Intermediates
journal, November 2013
- Clatterbuck Soper, Sarah F.; Dator, Romel P.; Limbach, Patrick A.
- Molecular Cell, Vol. 52, Issue 4
A Synchrotron-Based Hydroxyl Radical Footprinting Analysis of Amyloid Fibrils and Prefibrillar Intermediates with Residue-Specific Resolution
journal, December 2014
- Klinger, Alexandra L.; Kiselar, Janna; Ilchenko, Serguei
- Biochemistry, Vol. 53, Issue 49
CD4-Induced Activation in a Soluble HIV-1 Env Trimer
journal, July 2014
- Guttman, Miklos; Garcia, Natalie K.; Cupo, Albert
- Structure, Vol. 22, Issue 7