DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins

Abstract

X-ray radiolytic labeling uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation. High flux density beams are essential to overcome radical scavengers. However, conventional sample delivery environments, such as capillary flow, limit the use of a fully unattenuated focused broadband beam. An alternative is to use a liquid jet, and we have previously demonstrated that use of this form of sample delivery can increase labeling by tenfold at an unfocused X-ray source. Here we report the first use of a liquid jet for automated inline quantitative fluorescence dosage characterization and sample exposure at a high flux density microfocused synchrotron beamline. Our approach enables exposure times in single-digit microseconds while retaining a high level of side-chain labeling. This development significantly boosts the method’s overall effectiveness and efficiency, generates high-quality data, and opens up the arena for high throughput and ultrafast time-resolved in situ hydroxyl radical labeling.

Authors:
 [1];  [1];  [2]; ORCiD logo [3]; ORCiD logo [3];  [3];  [3]; ORCiD logo [4];  [5];  [2]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [5];  [6];  [1]; ORCiD logo [2]; ORCiD logo [2]
  1. Sonoma State University, CA (United States)
  2. Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
  3. Case Western Reserve University, Cleveland, OH (United States)
  4. University of California, Berkeley, CA (United States)
  5. Michigan State University, East Lansing, MI (United States)
  6. SLAC National Accelerator Laboratory, Menlo Park, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); Case Western Reserve University; National Institutes of Health (NIH)
OSTI Identifier:
1907590
Grant/Contract Number:  
AC02-05CH11231; SC0012704; DBI-1228549; P30-EB-009998; 1R01GM126218; 1R21AG072478; SC0020606; GM050945
Resource Type:
Accepted Manuscript
Journal Name:
Communications Biology
Additional Journal Information:
Journal Volume: 5; Journal Issue: 1; Journal ID: ISSN 2399-3642
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; biological techniques; biophysical methods; structural biology

Citation Formats

Rosi, Matthew, Russell, Brandon, Kristensen, Line G., Farquhar, Erik R., Jain, Rohit, Abel, Donald, Sullivan, Michael, Costello, Shawn M., Dominguez-Martin, Maria Agustina, Chen, Yan, Marqusee, Susan, Petzold, Christopher J., Kerfeld, Cheryl A., DePonte, Daniel P., Farahmand, Farid, Gupta, Sayan, and Ralston, Corie Y. An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins. United States: N. p., 2022. Web. doi:10.1038/s42003-022-03775-1.
Rosi, Matthew, Russell, Brandon, Kristensen, Line G., Farquhar, Erik R., Jain, Rohit, Abel, Donald, Sullivan, Michael, Costello, Shawn M., Dominguez-Martin, Maria Agustina, Chen, Yan, Marqusee, Susan, Petzold, Christopher J., Kerfeld, Cheryl A., DePonte, Daniel P., Farahmand, Farid, Gupta, Sayan, & Ralston, Corie Y. An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins. United States. https://doi.org/10.1038/s42003-022-03775-1
Rosi, Matthew, Russell, Brandon, Kristensen, Line G., Farquhar, Erik R., Jain, Rohit, Abel, Donald, Sullivan, Michael, Costello, Shawn M., Dominguez-Martin, Maria Agustina, Chen, Yan, Marqusee, Susan, Petzold, Christopher J., Kerfeld, Cheryl A., DePonte, Daniel P., Farahmand, Farid, Gupta, Sayan, and Ralston, Corie Y. Thu . "An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins". United States. https://doi.org/10.1038/s42003-022-03775-1. https://www.osti.gov/servlets/purl/1907590.
@article{osti_1907590,
title = {An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins},
author = {Rosi, Matthew and Russell, Brandon and Kristensen, Line G. and Farquhar, Erik R. and Jain, Rohit and Abel, Donald and Sullivan, Michael and Costello, Shawn M. and Dominguez-Martin, Maria Agustina and Chen, Yan and Marqusee, Susan and Petzold, Christopher J. and Kerfeld, Cheryl A. and DePonte, Daniel P. and Farahmand, Farid and Gupta, Sayan and Ralston, Corie Y.},
abstractNote = {X-ray radiolytic labeling uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation. High flux density beams are essential to overcome radical scavengers. However, conventional sample delivery environments, such as capillary flow, limit the use of a fully unattenuated focused broadband beam. An alternative is to use a liquid jet, and we have previously demonstrated that use of this form of sample delivery can increase labeling by tenfold at an unfocused X-ray source. Here we report the first use of a liquid jet for automated inline quantitative fluorescence dosage characterization and sample exposure at a high flux density microfocused synchrotron beamline. Our approach enables exposure times in single-digit microseconds while retaining a high level of side-chain labeling. This development significantly boosts the method’s overall effectiveness and efficiency, generates high-quality data, and opens up the arena for high throughput and ultrafast time-resolved in situ hydroxyl radical labeling.},
doi = {10.1038/s42003-022-03775-1},
journal = {Communications Biology},
number = 1,
volume = 5,
place = {United States},
year = {Thu Aug 25 00:00:00 EDT 2022},
month = {Thu Aug 25 00:00:00 EDT 2022}
}

Works referenced in this record:

Thorough small-angle X-ray scattering analysis of the instability of liquid micro-jets in air
journal, December 2013

  • Marmiroli, Benedetta; Cacho-Nerin, Fernando; Sartori, Barbara
  • Journal of Synchrotron Radiation, Vol. 21, Issue 1
  • DOI: 10.1107/S1600577513027951

Fluorescent approaches for understanding interactions of ligands with G protein coupled receptors
journal, January 2014

  • Sridharan, Rajashri; Zuber, Jeffrey; Connelly, Sara M.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1838, Issue 1
  • DOI: 10.1016/j.bbamem.2013.09.005

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
  • DOI: 10.1107/S0909049507013118

Lysozyme Modification by the Fenton Reaction and Gamma Radiation
journal, January 2002


New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting
journal, July 2021

  • Jain, Rohit; Abel, Donald; Rakitin, Maksim
  • Journal of Synchrotron Radiation, Vol. 28, Issue 5
  • DOI: 10.1107/S1600577521005026

Fluorescence Polarization/Anisotropy in Diagnostics and Imaging
journal, March 2010

  • Jameson, David M.; Ross, Justin A.
  • Chemical Reviews, Vol. 110, Issue 5
  • DOI: 10.1021/cr900267p

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
  • DOI: 10.1073/pnas.1209060109

Investigation of the conformational flexibility of DGAT1 peptides using tryptophan fluorescence
journal, March 2015

  • Lopes, Jose L. S.; Araujo, Ana P. U.; Jameson, David M.
  • Methods and Applications in Fluorescence, Vol. 3, Issue 2
  • DOI: 10.1088/2050-6120/3/2/025003

Conformational Changes During the Gating of a Potassium Channel Revealed by Structural Mass Spectrometry
journal, July 2010


Characterization of Förster resonance energy transfer in a botulinum neurotoxin protease assay
journal, June 2011

  • Ross, Justin A.; Gilmore, Marcella A.; Williams, Dudley
  • Analytical Biochemistry, Vol. 413, Issue 1
  • DOI: 10.1016/j.ab.2011.01.045

Visualizing the kinetic power stroke that drives proton-coupled zinc(ii) transport
journal, June 2014


Elucidating in Vivo Structural Dynamics in Integral Membrane Protein by Hydroxyl Radical Footprinting
journal, May 2009


Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry
journal, October 2018


Cyanobacterial photoprotection by the orange carotenoid protein
journal, December 2016


Ultraviolet Resonance Raman Examination of the Light-Induced Protein Structural Changes in Rhodopsin Activation
journal, October 1997

  • Kochendoerfer, Gerd G.; Kaminaka, Shoji; Mathies, Richard A.
  • Biochemistry, Vol. 36, Issue 43
  • DOI: 10.1021/bi971541c

Critical Review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals (⋅OH/⋅O in Aqueous Solution
journal, April 1988

  • Buxton, George V.; Greenstock, Clive L.; Helman, W. Phillips
  • Journal of Physical and Chemical Reference Data, Vol. 17, Issue 2
  • DOI: 10.1063/1.555805

Microfluidic polyimide gas dynamic virtual nozzles for serial crystallography
journal, August 2020

  • Vakili, Mohammad; Vasireddi, Ramakrishna; Gwozdz, Paul V.
  • Review of Scientific Instruments, Vol. 91, Issue 8
  • DOI: 10.1063/5.0012806

Raman Spectroscopy for Protein Analysis
journal, December 2014

  • Bunaciu, Andrei A.; Aboul-Enein, Hassan Y.; Hoang, Vu Dang
  • Applied Spectroscopy Reviews, Vol. 50, Issue 5
  • DOI: 10.1080/05704928.2014.990463

Development of Container Free Sample Exposure for Synchrotron X-ray Footprinting
journal, December 2019


Nanosecond Laser-Induced Photochemical Oxidation Method for Protein Surface Mapping with Mass Spectrometry
journal, September 2005

  • Aye, Thin Thin; Low, Teck Yew; Sze, Siu Kwan
  • Analytical Chemistry, Vol. 77, Issue 18
  • DOI: 10.1021/ac050353m

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins
journal, March 2006


A 12 A carotenoid translocation in a photoswitch associated with cyanobacterial photoprotection
journal, June 2015


Hydroxyl radical probe of protein surfaces using synchrotron X-ray radiolysis and mass spectrometry
journal, January 2002

  • Kiselar, J. G.; Maleknia, S. D.; Sullivan, M.
  • International Journal of Radiation Biology, Vol. 78, Issue 2
  • DOI: 10.1080/09553000110094805

Phycobilisomes from Blue-Green and Red Algae: Isolation Criteria and Dissociation Characteristics
journal, April 1979

  • Gantt, Elisabeth; Lipschultz, Claudia A.; Grabowski, Joseph
  • Plant Physiology, Vol. 63, Issue 4
  • DOI: 10.1104/pp.63.4.615

Synchrotron X-ray footprinting as a method to visualize water in proteins
journal, July 2016

  • Gupta, Sayan; Feng, Jun; Chan, Leanne Jade G.
  • Journal of Synchrotron Radiation, Vol. 23, Issue 5
  • DOI: 10.1107/S1600577516009024

Structure, function and evolution of the cyanobacterial orange carotenoid protein and its homologs
journal, July 2017

  • Kerfeld, Cheryl A.; Melnicki, Matthew R.; Sutter, Markus
  • New Phytologist, Vol. 215, Issue 3
  • DOI: 10.1111/nph.14670

Double-focusing mixing jet for XFEL study of chemical kinetics
journal, October 2014

  • Wang, Dingjie; Weierstall, Uwe; Pollack, Lois
  • Journal of Synchrotron Radiation, Vol. 21, Issue 6
  • DOI: 10.1107/S160057751401858X

Protein surface mapping by chemical oxidation: Structural analysis by mass spectrometry
journal, February 2003


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
  • DOI: 10.1016/j.jasms.2005.09.008

The amazing phycobilisome
journal, April 2020

  • Adir, Noam; Bar-Zvi, Shira; Harris, Dvir
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1861, Issue 4
  • DOI: 10.1016/j.bbabio.2019.07.002

Echinenone vibrational properties: From solvents to the orange carotenoid protein
journal, October 2015

  • Kish, Elizabeth; Pinto, Maria Manuela Mendes; Kirilovsky, Diana
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1847, Issue 10
  • DOI: 10.1016/j.bbabio.2015.05.010

Millisecond Radiolytic Modification of Peptides by Synchrotron X-rays Identified by Mass Spectrometry
journal, September 1999

  • Maleknia, Simin D.; Brenowitz, Michael; Chance, Mark R.
  • Analytical Chemistry, Vol. 71, Issue 18
  • DOI: 10.1021/ac990500e

Transient Resonance Raman Spectroscopy of a Light-Driven Sodium-Ion-Pump Rhodopsin from Indibacter alkaliphilus
journal, April 2017

  • Kajimoto, Kousuke; Kikukawa, Takashi; Nakashima, Hiroki
  • The Journal of Physical Chemistry B, Vol. 121, Issue 17
  • DOI: 10.1021/acs.jpcb.7b02421

X-ray phase-contrast tomography with a compact laser-driven synchrotron source
journal, April 2015

  • Eggl, Elena; Schleede, Simone; Bech, Martin
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 18
  • DOI: 10.1073/pnas.1500938112

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
  • DOI: 10.1063/1.2839027

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

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
  • DOI: 10.1021/ac802252y

Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry
journal, July 2021

  • Kristensen, Line G.; Holton, James M.; Rad, Behzad
  • Journal of Synchrotron Radiation, Vol. 28, Issue 5
  • DOI: 10.1107/S1600577521004744

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
  • DOI: 10.1107/S1600577514007000

Recent Advances in X-Ray Hydroxyl Radical Footprinting at the Advanced Light Source Synchrotron
journal, February 2019


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
  • DOI: 10.1073/pnas.0901074106

Gas dynamic virtual nozzle for generation of microscopic droplet streams
journal, September 2008

  • DePonte, D. P.; Weierstall, U.; Schmidt, K.
  • Journal of Physics D: Applied Physics, Vol. 41, Issue 19, Article No. 195505
  • DOI: 10.1088/0022-3727/41/19/195505

UV Resonance Raman Investigations of Peptide and Protein Structure and Dynamics
journal, February 2012

  • Oladepo, Sulayman A.; Xiong, Kan; Hong, Zhenmin
  • Chemical Reviews, Vol. 112, Issue 5
  • DOI: 10.1021/cr200198a

Protein Aggregation Caused by Aminoglycoside Action Is Prevented by a Hydrogen Peroxide Scavenger
journal, December 2012