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Journal articles on the topic 'Hydroxyl radical footprinting (HRF)'

Author: Grafiati

Published: 14 March 2023

Last updated: 31 July 2025

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1

Chea, Emily E., and Lisa M. Jones. "Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting." Analyst 143, no. 4 (2018): 798–807. http://dx.doi.org/10.1039/c7an01323j.

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2

Kiselar, Janna, and Mark R. Chance. "High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery." Annual Review of Biophysics 47, no. 1 (2018): 315–33. http://dx.doi.org/10.1146/annurev-biophys-070317-033123.

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Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the l

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3

Carey, M., and S. T. Smale. "Hydroxyl-Radical Footprinting." Cold Spring Harbor Protocols 2007, no. 24 (2007): pdb.prot4810. http://dx.doi.org/10.1101/pdb.prot4810.

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4

Tullius, T. D. "DNA footprinting with hydroxyl radical." Nature 332, no. 6165 (1988): 663–64. http://dx.doi.org/10.1038/332663a0.

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5

Leser, Micheal, Jessica R. Chapman, Michelle Khine, et al. "Chemical Generation of Hydroxyl Radical for Oxidative ‘Footprinting’." Protein & Peptide Letters 26, no. 1 (2019): 61–69. http://dx.doi.org/10.2174/0929866526666181212164812.

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Background: For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative ‘footprinting’ of macromolecules. Objective: In this article, we start by reviewing the application of chemical generation of hydroxyl radical to the development of oxidative footprinting of DNA and RNA and the subsequent application of the method to oxidative footprinting of proteins. We next discuss a novel strategy for generating hydroxyl radicals by Fenton chemistry that immobilizes catalytic iron on a solid surface (Pyrite Shrink Wrap laminate) for the appli

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6

Tullius, Thomas D. "DNA Footprinting with the Hydroxyl Radical." Free Radical Research Communications 13, no. 1 (1991): 521–29. http://dx.doi.org/10.3109/10715769109145826.

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7

Gerasimova, N. S., and V. M. Studitsky. "Hydroxyl radical footprinting of fluorescently labeled DNA." Moscow University Biological Sciences Bulletin 71, no. 2 (2016): 93–96. http://dx.doi.org/10.3103/s0096392516020036.

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8

Jain, Swapan S., and Thomas D. Tullius. "Footprinting protein–DNA complexes using the hydroxyl radical." Nature Protocols 3, no. 6 (2008): 1092–100. http://dx.doi.org/10.1038/nprot.2008.72.

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9

Nilsen, Timothy W. "Mapping RNA–Protein Interactions Using Hydroxyl-Radical Footprinting." Cold Spring Harbor Protocols 2014, no. 12 (2014): pdb.prot080952. http://dx.doi.org/10.1101/pdb.prot080952.

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10

Leser, Micheal, Jonathan Pegan, Mohammed El Makkaoui, et al. "Protein footprinting by pyrite shrink-wrap laminate." Lab on a Chip 15, no. 7 (2015): 1646–50. http://dx.doi.org/10.1039/c4lc01288g.

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11

Shi, Liuqing, and Michael L. Gross. "Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry." Protein & Peptide Letters 26, no. 1 (2019): 27–34. http://dx.doi.org/10.2174/0929866526666181128124554.

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Background: Determination of the composition and some structural features of macromolecules can be achieved by using structural proteomics approaches coupled with mass spectrometry (MS). One approach is hydroxyl radical protein footprinting whereby amino-acid side chains are modified with reactive reagents to modify irreversibly a protein side chain. The outcomes, when deciphered with mass-spectrometry-based proteomics, can increase our knowledge of structure, assembly, and conformational dynamics of macromolecules in solution. Generating the hydroxyl radicals by laser irradiation, Hambly and

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12

Morton, Simon A., Sayan Gupta, Christopher J. Petzold, and Corie Y. Ralston. "Recent Advances in X-Ray Hydroxyl Radical Footprinting at the Advanced Light Source Synchrotron." Protein & Peptide Letters 26, no. 1 (2019): 70–75. http://dx.doi.org/10.2174/0929866526666181128125725.

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Background: Synchrotron hydroxyl radical footprinting is a relatively new structural method used to investigate structural features and conformational changes of nucleic acids and proteins in the solution state. It was originally developed at the National Synchrotron Light Source at Brookhaven National Laboratory in the late nineties, and more recently, has been established at the Advanced Light Source at Lawrence Berkeley National Laboratory. The instrumentation for this method is an active area of development, and includes methods to increase dose to the samples while implementing high-throu

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13

Ralston, Corie Y., and Joshua S. Sharp. "Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods." Antibodies 11, no. 4 (2022): 71. http://dx.doi.org/10.3390/antib11040071.

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Commercial monoclonal antibodies are growing and important components of modern therapies against a multitude of human diseases. Well-known high-resolution structural methods such as protein crystallography are often used to characterize antibody structures and to determine paratope and/or epitope binding regions in order to refine antibody design. However, many standard structural techniques require specialized sample preparation that may perturb antibody structure or require high concentrations or other conditions that are far from the conditions conducive to the accurate determination of an

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14

Maleknia, Simin D., and Kevin M. Downard. "Protein Footprinting with Radical Probe Mass Spectrometry- Two Decades of Achievement." Protein & Peptide Letters 26, no. 1 (2019): 4–15. http://dx.doi.org/10.2174/0929866526666181128124241.

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Background: Radical Probe Mass Spectrometry (RP-MS) describes a pioneering methodology in structural biology that enables the study of protein structures, their interactions, and dynamics on fast timescales (down to sub-milliseconds). Hydroxyl radicals (•OH) generated directly from water within aqueous solutions induce the oxidation of reactive, solvent accessible amino acid side chains that are then analyzed by mass spectrometry. Introduced in 1998 at the American Society for Mass Spectrometry annual conference, RP-MS was first published on in 1999. Objective: This review article describes de

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15

Loginov, Dmitry S., Jan Fiala, Peter Brechlin, Gary Kruppa, and Petr Novak. "Hydroxyl radical footprinting analysis of a human haptoglobin-hemoglobin complex." Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1870, no. 2 (2022): 140735. http://dx.doi.org/10.1016/j.bbapap.2021.140735.

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16

Watson, Caroline, and Joshua S. Sharp. "Conformational Analysis of Therapeutic Proteins by Hydroxyl Radical Protein Footprinting." AAPS Journal 14, no. 2 (2012): 206–17. http://dx.doi.org/10.1208/s12248-012-9336-7.

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17

Sclavi, B. "RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting." Science 279, no. 5358 (1998): 1940–43. http://dx.doi.org/10.1126/science.279.5358.1940.

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18

Hao, Yumeng, Jen Bohon, Ryan Hulscher, et al. "Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays." Current Protocols in Nucleic Acid Chemistry 73, no. 1 (2018): e52. http://dx.doi.org/10.1002/cpnc.52.

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19

Kiselar, Janna G., and Mark R. Chance. "Future directions of structural mass spectrometry using hydroxyl radical footprinting." Journal of Mass Spectrometry 45, no. 12 (2010): 1373–82. http://dx.doi.org/10.1002/jms.1808.

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20

Xie, Boer, and Joshua S. Sharp. "Hydroxyl Radical Dosimetry for High Flux Hydroxyl Radical Protein Footprinting Applications Using a Simple Optical Detection Method." Analytical Chemistry 87, no. 21 (2015): 10719–23. http://dx.doi.org/10.1021/acs.analchem.5b02865.

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21

BROWN, Philip M., and Keith R. FOX. "DNA triple-helix formation on nucleosome-bound poly(dA)·poly(dT) tracts." Biochemical Journal 333, no. 2 (1998): 259–67. http://dx.doi.org/10.1042/bj3330259.

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We have used DNase I and hydroxyl-radical footprinting to examine the formation of intermolecular DNA triple helices on nucleosome-bound DNA fragments containing An·Tn tracts. We found that it is possible to form triplexes on these nucleosome-bound DNAs, but the stability of the complexes depends on the orientation of the A tract with respect to the protein surface. Hydroxyl-radical cleavage of these complexes suggests that the DNA fragments are still associated with the nucleosome. However, the phased cleavage pattern is lost in the vicinity of the triplex, suggesting that the DNA has locally

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22

Zhu, Yi, Tiannan Guo, Jung Eun Park, et al. "Elucidatingin VivoStructural Dynamics in Integral Membrane Protein by Hydroxyl Radical Footprinting." Molecular & Cellular Proteomics 8, no. 8 (2009): 1999–2010. http://dx.doi.org/10.1074/mcp.m900081-mcp200.

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23

Garcia, Natalie K., Alavattam Sreedhara, Galahad Deperalta, and Aaron T. Wecksler. "Optimizing Hydroxyl Radical Footprinting Analysis of Biotherapeutics Using Internal Standard Dosimetry." Journal of the American Society for Mass Spectrometry 31, no. 7 (2020): 1563–71. http://dx.doi.org/10.1021/jasms.0c00146.

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24

Mah, Stanley C., Craig A. Townsend, and Thomas D. Tullius. "Hydroxyl radical footprinting of calicheamicin. Relationship of DNA binding to cleavage." Biochemistry 33, no. 2 (1994): 614–21. http://dx.doi.org/10.1021/bi00168a029.

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25

Wang, Liwen, and Mark R. Chance. "Structural Mass Spectrometry of Proteins Using Hydroxyl Radical Based Protein Footprinting." Analytical Chemistry 83, no. 19 (2011): 7234–41. http://dx.doi.org/10.1021/ac200567u.

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26

Watson, Caroline, Ireneusz Janik, Tiandi Zhuang, Olga Charvátová, Robert J. Woods, and Joshua S. Sharp. "Pulsed Electron Beam Water Radiolysis for Submicrosecond Hydroxyl Radical Protein Footprinting." Analytical Chemistry 81, no. 7 (2009): 2496–505. http://dx.doi.org/10.1021/ac802252y.

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27

Adilakshmi, T. "Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation." Nucleic Acids Research 34, no. 8 (2006): e64-e64. http://dx.doi.org/10.1093/nar/gkl291.

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28

Wang, X. D., and R. A. Padgett. "Hydroxyl radical "footprinting" of RNA: application to pre-mRNA splicing complexes." Proceedings of the National Academy of Sciences 86, no. 20 (1989): 7795–99. http://dx.doi.org/10.1073/pnas.86.20.7795.

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29

Hulscher, Ryan. "Using Hydroxyl Radical Footprinting to Observe Ribosome Assembly Intermediates in vivo." Biophysical Journal 108, no. 2 (2015): 391a. http://dx.doi.org/10.1016/j.bpj.2014.11.2143.

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30

Hampel, Ken J., and John M. Burke. "Time-Resolved Hydroxyl-Radical Footprinting of RNA Using Fe(II)-EDTA." Methods 23, no. 3 (2001): 233–39. http://dx.doi.org/10.1006/meth.2000.1134.

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31

Aprahamian, Melanie L., Emily E. Chea, Lisa M. Jones, and Steffen Lindert. "Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data." Analytical Chemistry 90, no. 12 (2018): 7721–29. http://dx.doi.org/10.1021/acs.analchem.8b01624.

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32

Deperalta, Galahad, Melissa Alvarez, Charity Bechtel, Ken Dong, Ross McDonald, and Victor Ling. "Structural analysis of a therapeutic monoclonal antibody dimer by hydroxyl radical footprinting." mAbs 5, no. 1 (2013): 86–101. http://dx.doi.org/10.4161/mabs.22964.

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33

Kimball, A. S., G. Milman, and T. D. Tullius. "High-resolution footprints of the DNA-binding domain of Epstein-Barr virus nuclear antigen 1." Molecular and Cellular Biology 9, no. 6 (1989): 2738–42. http://dx.doi.org/10.1128/mcb.9.6.2738-2742.1989.

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The DNA-binding domain of Epstein-Barr virus nuclear antigen 1 was found by hydroxyl radical footprinting to protect backbone positions on one side of its DNA-binding site. The guanines contacted in the major groove by the DNA-binding domain of Epstein-Barr virus nuclear antigen 1 were identified by methylation protection. No difference was found in the interaction of the DNA-binding domain of Epstein-Barr virus nuclear antigen 1 with tandemly repeated and overlapping binding sites.

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34

Kimball, A. S., G. Milman, and T. D. Tullius. "High-resolution footprints of the DNA-binding domain of Epstein-Barr virus nuclear antigen 1." Molecular and Cellular Biology 9, no. 6 (1989): 2738–42. http://dx.doi.org/10.1128/mcb.9.6.2738.

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The DNA-binding domain of Epstein-Barr virus nuclear antigen 1 was found by hydroxyl radical footprinting to protect backbone positions on one side of its DNA-binding site. The guanines contacted in the major groove by the DNA-binding domain of Epstein-Barr virus nuclear antigen 1 were identified by methylation protection. No difference was found in the interaction of the DNA-binding domain of Epstein-Barr virus nuclear antigen 1 with tandemly repeated and overlapping binding sites.

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35

Kiselar, Janna G., Manish Datt, Mark R. Chance, and Michael A. Weiss. "Structural Analysis of Proinsulin Hexamer Assembly by Hydroxyl Radical Footprinting and Computational Modeling." Journal of Biological Chemistry 286, no. 51 (2011): 43710–16. http://dx.doi.org/10.1074/jbc.m111.297853.

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36

Calabrese, Antonio N., James R. Ault, Sheena E. Radford, and Alison E. Ashcroft. "Using hydroxyl radical footprinting to explore the free energy landscape of protein folding." Methods 89 (November 2015): 38–44. http://dx.doi.org/10.1016/j.ymeth.2015.02.018.

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37

Rinas, Aimee, Jessica A. Espino, and Lisa M. Jones. "An efficient quantitation strategy for hydroxyl radical-mediated protein footprinting using Proteome Discoverer." Analytical and Bioanalytical Chemistry 408, no. 11 (2016): 3021–31. http://dx.doi.org/10.1007/s00216-016-9369-3.

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38

Li, Xiaoyan, Zixuan Li, Boer Xie, and Joshua S. Sharp. "Supercharging by m-NBA Improves ETD-Based Quantification of Hydroxyl Radical Protein Footprinting." Journal of The American Society for Mass Spectrometry 26, no. 8 (2015): 1424–27. http://dx.doi.org/10.1007/s13361-015-1129-7.

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39

Ogundairo, Oluwatosin, Oluwatoyin Ayo-Farai, Chinedu Paschal Maduka, Chiamaka Chinaemelum Okongwu, Abdulraheem Olaide Babarinde, and Olamide Sodamade. "REVIEW ON PROTEIN FOOTPRINTING AS A TOOL IN STRUCTURAL BIOLOGY." Science Heritage Journal 7, no. 2 (2023): 83–90. http://dx.doi.org/10.26480/gws.02.2023.83.90.

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Structural characterization of proteins is fundamental for understanding their functions and interactions within cellular environments. Protein footprinting has emerged as a powerful and versatile technique in structural biology, providing valuable insights into protein structure, dynamics, and conformational changes. This study comprehensively explores the principles, methodologies, and applications of protein footprinting as an indispensable tool in structural biology. Protein footprinting encompasses a range of innovative techniques, including hydroxyl radical footprinting, mass spectrometr

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40

Elliot, Marie A., and Brenda K. Leskiw. "The BldD Protein from Streptomyces coelicolor Is a DNA-Binding Protein." Journal of Bacteriology 181, no. 21 (1999): 6832–35. http://dx.doi.org/10.1128/jb.181.21.6832-6835.1999.

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ABSTRACT Gel mobility shift assays with His-tagged BldD isolated fromEscherichia coli have illustrated that BldD is capable of specifically recognizing its own promoter region. DNase I and hydroxyl radical footprinting assays have served to delimit the BldD binding site, revealing that BldD recognizes and binds to a site just upstream from, and overlapping with, the −10 region of the promoter. How BldD binds to its promoter and the effect this binding has on the expression of BldD are discussed.

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41

Jain, Rohit, Donald Abel, Maksim Rakitin, et al. "New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting." Journal of Synchrotron Radiation 28, no. 5 (2021): 1321–32. http://dx.doi.org/10.1107/s1600577521005026.

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Synchrotron X-ray footprinting (XF) is a growing structural biology technique that leverages radiation-induced chemical modifications via X-ray radiolysis of water to produce hydroxyl radicals that probe changes in macromolecular structure and dynamics in solution states of interest. The X-ray Footprinting of Biological Materials (XFP) beamline at the National Synchrotron Light Source II provides the structural biology community with access to instrumentation and expert support in the XF method, and is also a platform for development of new technological capabilities in this field. The design

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42

Shaytan, Alexey K., Hua Xiao, Grigoriy A. Armeev, et al. "Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID." Nature Protocols 13, no. 11 (2018): 2535–56. http://dx.doi.org/10.1038/s41596-018-0048-z.

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43

Portugal, J., and M. J. Waring. "Hydroxyl radical footprinting of the sequence-selective binding of netropsin and distamycin to DNA." FEBS Letters 225, no. 1-2 (1987): 195–200. http://dx.doi.org/10.1016/0014-5793(87)81156-0.

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44

He, Gaofei, Elena Vasilieva, James K. Bashkin, and Cynthia M. Dupureur. "Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis." Analytical Biochemistry 439, no. 2 (2013): 99–101. http://dx.doi.org/10.1016/j.ab.2013.04.011.

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45

Li, Zixuan, Heather Moniz, Shuo Wang, et al. "High Structural Resolution Hydroxyl Radical Protein Footprinting Reveals an Extended Robo1-Heparin Binding Interface." Journal of Biological Chemistry 290, no. 17 (2015): 10729–40. http://dx.doi.org/10.1074/jbc.m115.648410.

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46

Saladino, Jessica, Mian Liu, David Live, and Joshua S. Sharp. "Aliphatic peptidyl hydroperoxides as a source of secondary oxidation in hydroxyl radical protein footprinting." Journal of the American Society for Mass Spectrometry 20, no. 6 (2009): 1123–26. http://dx.doi.org/10.1016/j.jasms.2009.02.004.

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47

Oztug Durer, Zeynep A., J. K. Amisha Kamal, Sabrina Benchaar, Mark R. Chance, and Emil Reisler. "Myosin Binding Surface on Actin Probed by Hydroxyl Radical Footprinting and Site-Directed Labels." Journal of Molecular Biology 414, no. 2 (2011): 204–16. http://dx.doi.org/10.1016/j.jmb.2011.09.035.

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48

Garcia, Natalie K., Galahad Deperalta, and Aaron T. Wecksler. "Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry." Protein & Peptide Letters 26, no. 1 (2019): 35–43. http://dx.doi.org/10.2174/0929866526666181128141953.

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Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry

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49

Baud, Anna, Florence Gonnet, Isabelle Salard, et al. "Probing the solution structure of Factor H using hydroxyl radical protein footprinting and cross-linking." Biochemical Journal 473, no. 12 (2016): 1805–19. http://dx.doi.org/10.1042/bcj20160225.

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The control protein Factor H (FH) is a crucial regulator of the innate immune complement system, where it is active on host cell membranes and in the fluid phase. Mutations impairing the binding capacity of FH lead to severe autoimmune diseases. Here, we studied the solution structure of full-length FH, in its free state and bound to the C3b complement protein. To do so, we used two powerful techniques, hydroxyl radical protein footprinting (HRPF) and chemical cross-linking coupled with mass spectrometry (MS), to probe the structural rearrangements and to identify protein interfaces. The footp

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50

Woger, Johannes Wolfgang, and Günther Koraimann. "Hydroxyl radical footprinting using PCR-generated fluorescent-labelled DNA fragments and the ALFexpres DNA sequencer." Technical Tips Online 2, no. 1 (1997): 167–68. http://dx.doi.org/10.1016/s1366-2120(08)70074-6.

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