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Title: Plasma-Generated OH Radical Production for Analyzing Three-Dimensional Structure in Protein Therapeutics

Abstract

Protein three-dimensional structure dynamically changes in solution depending on the presence of ligands and interacting proteins. Methods for detecting these changes in protein conformation include ‘protein footprinting,’ using mass spectrometry. We describe herein a new technique, PLIMB (Plasma Induced Modification of Biomolecules), that generates µs bursts of hydroxyl radicals from water, to measure changes in protein structure via altered solvent accessibility of amino acid side chains. PLIMB was first benchmarked with model compounds, and then applied to a biological problem, i.e., ligand (EGF) induced changes in the conformation of the external (ecto) domain of Epidermal Growth Factor Receptor (EGFR). Regions in which oxidation decreased upon adding EGF fall along the dimerization interface, consistent with models derived from crystal structures. Furthermore these results demonstrate that plasma-generated hydroxyl radicals from water can be used to map protein conformational changes, and provide a readily accessible means of studying protein structure in solution.

Authors:
 [1];  [1];  [1];  [1];  [1];  [1]
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  1. Univ. of Wisconsin-Madison, Madison, WI (United States)
Publication Date:
Research Org.:
Univ. of Wisconsin, Madison, WI (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1500095
Grant/Contract Number:  
FG02-88ER13938
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Minkoff, Benjamin B., Blatz, Joshua M., Choudhury, Faraz A., Benjamin, Daniel, Shohet, J. Leon, and Sussman, Michael R. Plasma-Generated OH Radical Production for Analyzing Three-Dimensional Structure in Protein Therapeutics. United States: N. p., 2017. Web. doi:10.1038/s41598-017-13371-7.
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Minkoff, Benjamin B., Blatz, Joshua M., Choudhury, Faraz A., Benjamin, Daniel, Shohet, J. Leon, & Sussman, Michael R. Plasma-Generated OH Radical Production for Analyzing Three-Dimensional Structure in Protein Therapeutics. United States. https://doi.org/10.1038/s41598-017-13371-7
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Minkoff, Benjamin B., Blatz, Joshua M., Choudhury, Faraz A., Benjamin, Daniel, Shohet, J. Leon, and Sussman, Michael R. Wed . "Plasma-Generated OH Radical Production for Analyzing Three-Dimensional Structure in Protein Therapeutics". United States. https://doi.org/10.1038/s41598-017-13371-7. https://www.osti.gov/servlets/purl/1500095.
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@article{osti_1500095,
title = {Plasma-Generated OH Radical Production for Analyzing Three-Dimensional Structure in Protein Therapeutics},
author = {Minkoff, Benjamin B. and Blatz, Joshua M. and Choudhury, Faraz A. and Benjamin, Daniel and Shohet, J. Leon and Sussman, Michael R.},
abstractNote = {Protein three-dimensional structure dynamically changes in solution depending on the presence of ligands and interacting proteins. Methods for detecting these changes in protein conformation include ‘protein footprinting,’ using mass spectrometry. We describe herein a new technique, PLIMB (Plasma Induced Modification of Biomolecules), that generates µs bursts of hydroxyl radicals from water, to measure changes in protein structure via altered solvent accessibility of amino acid side chains. PLIMB was first benchmarked with model compounds, and then applied to a biological problem, i.e., ligand (EGF) induced changes in the conformation of the external (ecto) domain of Epidermal Growth Factor Receptor (EGFR). Regions in which oxidation decreased upon adding EGF fall along the dimerization interface, consistent with models derived from crystal structures. Furthermore these results demonstrate that plasma-generated hydroxyl radicals from water can be used to map protein conformational changes, and provide a readily accessible means of studying protein structure in solution.},
doi = {10.1038/s41598-017-13371-7},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {Wed Oct 11 00:00:00 EDT 2017},
month = {Wed Oct 11 00:00:00 EDT 2017}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1038/s41598-017-13371-7
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Cited by: 25 works
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Figures / Tables:

Figure 1 Figure 1: Microsecond bursts of radicals modify free methionine and BSA in a dose dependent fashion. (A) Left, schematic of sample and instrument. Right, photograph demonstrating treatment in progress. (B) Graph demonstrating μs breakdowns to produce μs bursts of hydroxyl radicals. (C) Production of oxidized methionine with increasing plasma treatmentmore » time. For each data point, n = 3 and error bars are ± standard deviation. (D) Modification observed on native (above) and digested (below) BSA with increasing plasma treatment times. Regions shown for comparison have been selected; full data in Fig. S3. For each bar, n = 3 and error bars are ± standard deviation.« less
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Works referenced in this record:

Study of the Ribonuclease−S-Protein−Peptide Complex Using a Radical Probe and Electrospray Ionization Mass Spectrometry
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A Structural Perspective on the Regulation of the Epidermal Growth Factor Receptor
journal, June 2015

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

Generation mechanism of hydroxyl radical species and its lifetime prediction during the plasma-initiated ultraviolet (UV) photolysis
journal, March 2015

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Novel mutant-selective EGFR kinase inhibitors against EGFR T790M
journal, December 2009

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  • Nature, Vol. 462, Issue 7276
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Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment
journal, March 2017

Probing the Time Scale of FPOP (Fast Photochemical Oxidation of Proteins): Radical Reactions Extend Over Tens of Milliseconds
journal, April 2016

  • Vahidi, Siavash; Konermann, Lars
  • Journal of The American Society for Mass Spectrometry, Vol. 27, Issue 7
  • DOI: 10.1007/s13361-016-1389-x

Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains
journal, September 2002

Study of the Ribonuclease−S-Protein−Peptide Complex Using a Radical Probe and Electrospray Ionization Mass Spectrometry
journal, April 2003

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Generation mechanism of hydroxyl radical species and its lifetime prediction during the plasma-initiated ultraviolet (UV) photolysis
journal, March 2015

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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
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    Works referencing / citing this record:

    Fluorierte Reagenzien in der Strukturproteomik
    journal, January 2020

    • Cheng, Ming; Guo, Chunyang; Gross, Michael L.
    • Angewandte Chemie, Vol. 132, Issue 15
    • DOI: 10.1002/ange.201907662

    The Application of Fluorine‐Containing Reagents in Structural Proteomics
    journal, January 2020

    • Cheng, Ming; Guo, Chunyang; Gross, Michael L.
    • Angewandte Chemie International Edition, Vol. 59, Issue 15
    • DOI: 10.1002/anie.201907662
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