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

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Author: Grafiati

Published: 14 March 2023

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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 (May 20, 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 labeling of individual residues, transforming the approach to high resolution. Lastly, advances in understanding of the chemistry of the approach have led to the determination of absolute protein topologies from HRF data. Overall, the technology can provide precise and accurate measures of side-chain solvent accessibility in a wide range of interesting and useful contexts for the study of protein structure and dynamics in both academia and industry.

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3

Carey, M., and S. T. Smale. "Hydroxyl-Radical Footprinting." Cold Spring Harbor Protocols 2007, no. 24 (December 1, 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 (April 1988): 663–64. http://dx.doi.org/10.1038/332663a0.

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5

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

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6

Leser, Micheal, Jessica R. Chapman, Michelle Khine, Jonathan Pegan, Matt Law, Mohammed El Makkaoui, Beatrix M. Ueberheide, and Michael Brenowitz. "Chemical Generation of Hydroxyl Radical for Oxidative ‘Footprinting’." Protein & Peptide Letters 26, no. 1 (February 13, 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 application of nucleic acid and protein footprinting. Method: Pyrite Shrink-Wrap Laminate is fabricated by depositing pyrite (Fe-S2, aka ‘fool’s gold’) nanocrystals onto thermolabile plastic (Shrinky Dink). The laminate can be thermoformed into a microtiter plate format into which samples are deposited for oxidation. Results: We demonstrate the utility of the Pyrite Shrink-Wrap Laminate for the chemical generation of hydroxyl radicals by mapping the surface of the T-cell co-stimulatory protein Programmed Death – 1 (PD-1) and the interface of the complex with its ligand PD-L1. Conclusion: We have developed and validated an affordable and reliable benchtop method of hydroxyl radical generation that will broaden the application of protein oxidative footprinting. Due to the minimal equipment required to implement this method, it should be easily adaptable by many laboratories with access to mass spectrometry.

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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 (April 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 (June 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 (December 2014): pdb.prot080952. http://dx.doi.org/10.1101/pdb.prot080952.

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10

Leser, Micheal, Jonathan Pegan, Mohammed El Makkaoui, Joerg C. Schlatterer, Michelle Khine, Matt Law, and Michael Brenowitz. "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

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 (February 2022): 140735. http://dx.doi.org/10.1016/j.bbapap.2021.140735.

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12

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

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13

Sclavi, B. "RNA Folding at Millisecond Intervals by Synchrotron Hydroxyl Radical Footprinting." Science 279, no. 5358 (March 20, 1998): 1940–43. http://dx.doi.org/10.1126/science.279.5358.1940.

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14

Kiselar, Janna G., and Mark R. Chance. "Future directions of structural mass spectrometry using hydroxyl radical footprinting." Journal of Mass Spectrometry 45, no. 12 (September 1, 2010): 1373–82. http://dx.doi.org/10.1002/jms.1808.

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15

Hao, Yumeng, Jen Bohon, Ryan Hulscher, Mollie C. Rappé, Sayan Gupta, Tadepalli Adilakshmi, and Sarah A. Woodson. "Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays." Current Protocols in Nucleic Acid Chemistry 73, no. 1 (June 2018): e52. http://dx.doi.org/10.1002/cpnc.52.

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16

Ralston, Corie Y., and Joshua S. Sharp. "Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods." Antibodies 11, no. 4 (November 14, 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 antigen binding or kinetics. We describe here in this minireview the relatively new method of hydroxyl radical protein footprinting, a solution-state method that can provide structural and kinetic information on antibodies or antibody–antigen interactions useful for therapeutic antibody design. We provide a brief history of hydroxyl radical footprinting, examples of current implementations, and recent advances in throughput and accessibility.

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17

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 (October 15, 2015): 10719–23. http://dx.doi.org/10.1021/acs.analchem.5b02865.

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18

Shi, Liuqing, and Michael L. Gross. "Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry." Protein & Peptide Letters 26, no. 1 (February 13, 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 Gross developed the approach of Fast Photochemical Oxidation of Proteins (FPOP), which labels proteins on the sub millisecond time scale and provides, with MS analysis, deeper understanding of protein structure and protein-ligand and protein- protein interactions. This review highlights the fundamentals of FPOP and provides descriptions of hydroxyl-radical and other radical and carbene generation, of the hydroxyl labeling of proteins, and of determination of protein modification sites. We also summarize some recent applications of FPOP coupled with MS in protein footprinting. Conclusion: We survey results that show the capability of FPOP for qualitatively measuring protein solvent accessibility on the residue level. To make these approaches more valuable, we describe recent method developments that increase FPOP’s quantitative capacity and increase the spatial protein sequence coverage. To improve FPOP further, several new labeling reagents including carbenes and other radicals have been developed. These growing improvements will allow oxidative- footprinting methods coupled with MS to play an increasingly significant role in determining the structure and dynamics of macromolecules and their assemblies.

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19

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 (February 13, 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-throughput sample delivery methods. Conclusion: Improving instrumentation to irradiate biological samples in real time using a sample droplet generator and inline fluorescence monitoring to rapidly determine dose response curves for samples will significantly increase the range of biological problems that can be investigated using synchrotron hydroxyl radical footprinting.

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20

Maleknia, Simin D., and Kevin M. Downard. "Protein Footprinting with Radical Probe Mass Spectrometry- Two Decades of Achievement." Protein & Peptide Letters 26, no. 1 (February 13, 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 developments and applications of the RP-MS methodology over the past two decades. Methods: The RP-MS method has been variously referred to as synchrotron X-ray radiolysis footprinting, Hydroxyl Radical Protein Footprinting (HRPF), X-ray Footprinting with Mass Spectrometry (XF-MS), Fast Photochemical Oxidation of Proteins (FPOP), oxidative labelling, covalent oxidative labelling, and even the Stability of Proteins from Rates of Oxidation (SPROX). Results: The article describes the utility of hydroxyl radicals as a protein structural probe, the advantages of RP-MS in comparison to other MS-based approaches, its proof of concept using ion mobility mass spectrometry, its application to protein structure, folding, complex and aggregation studies, its extension to study the onset of protein damage, its implementation using a high throughput sample loading approach, and the development of protein docking algorithms to aid with data analysis and visualization. Conclusion: RP-MS represents a powerful new structural approach that can aid in our understanding of the structure and functions of proteins, and the impact of sustained oxidation on proteins in disease pathogenesis.

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21

Zhu, Yi, Tiannan Guo, Jung Eun Park, Xin Li, Wei Meng, Arnab Datta, Marshall Bern, Sai Kiang Lim, and Siu Kwan Sze. "Elucidatingin VivoStructural Dynamics in Integral Membrane Protein by Hydroxyl Radical Footprinting." Molecular & Cellular Proteomics 8, no. 8 (May 26, 2009): 1999–2010. http://dx.doi.org/10.1074/mcp.m900081-mcp200.

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22

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 (May 14, 2020): 1563–71. http://dx.doi.org/10.1021/jasms.0c00146.

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23

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 (January 1994): 614–21. http://dx.doi.org/10.1021/bi00168a029.

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24

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

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25

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 (April 2009): 2496–505. http://dx.doi.org/10.1021/ac802252y.

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26

Adilakshmi, T. "Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation." Nucleic Acids Research 34, no. 8 (April 28, 2006): e64-e64. http://dx.doi.org/10.1093/nar/gkl291.

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27

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 (October 1, 1989): 7795–99. http://dx.doi.org/10.1073/pnas.86.20.7795.

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28

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

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29

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

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30

BROWN, Philip M., and Keith R. FOX. "DNA triple-helix formation on nucleosome-bound poly(dA)·poly(dT) tracts." Biochemical Journal 333, no. 2 (July 15, 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 moved away from the protein surface.

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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 (June 6, 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 (January 2013): 86–101. http://dx.doi.org/10.4161/mabs.22964.

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33

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 (October 26, 2011): 43710–16. http://dx.doi.org/10.1074/jbc.m111.297853.

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34

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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35

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 (April 28, 2015): 1424–27. http://dx.doi.org/10.1007/s13361-015-1129-7.

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36

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 (February 12, 2016): 3021–31. http://dx.doi.org/10.1007/s00216-016-9369-3.

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37

Shaytan, Alexey K., Hua Xiao, Grigoriy A. Armeev, Daria A. Gaykalova, Galina A. Komarova, Carl Wu, Vasily M. Studitsky, David Landsman, and Anna R. Panchenko. "Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID." Nature Protocols 13, no. 11 (October 19, 2018): 2535–56. http://dx.doi.org/10.1038/s41596-018-0048-z.

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38

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 (December 10, 1987): 195–200. http://dx.doi.org/10.1016/0014-5793(87)81156-0.

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39

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 (August 2013): 99–101. http://dx.doi.org/10.1016/j.ab.2013.04.011.

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40

Li, Zixuan, Heather Moniz, Shuo Wang, Annapoorani Ramiah, Fuming Zhang, Kelley W. Moremen, Robert J. Linhardt, and Joshua S. Sharp. "High Structural Resolution Hydroxyl Radical Protein Footprinting Reveals an Extended Robo1-Heparin Binding Interface." Journal of Biological Chemistry 290, no. 17 (March 9, 2015): 10729–40. http://dx.doi.org/10.1074/jbc.m115.648410.

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41

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 (June 2009): 1123–26. http://dx.doi.org/10.1016/j.jasms.2009.02.004.

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42

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 (November 2011): 204–16. http://dx.doi.org/10.1016/j.jmb.2011.09.035.

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43

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 (June 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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44

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 (June 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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45

Elliot, Marie A., and Brenda K. Leskiw. "The BldD Protein from Streptomyces coelicolor Is a DNA-Binding Protein." Journal of Bacteriology 181, no. 21 (November 1, 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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46

Jain, Rohit, Donald Abel, Maksim Rakitin, Michael Sullivan, David T. Lodowski, Mark R. Chance, and Erik R. Farquhar. "New high-throughput endstation to accelerate the experimental optimization pipeline for synchrotron X-ray footprinting." Journal of Synchrotron Radiation 28, no. 5 (July 20, 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 and implementation of a new high-throughput endstation device based around use of a 96-well PCR plate form factor and supporting diagnostic instrumentation for synchrotron XF is described. This development enables a pipeline for rapid comprehensive screening of the influence of sample chemistry on hydroxyl radical dose using a convenient fluorescent assay, illustrated here with a study of 26 organic compounds. The new high-throughput endstation device and sample evaluation pipeline now available at the XFP beamline provide the worldwide structural biology community with a robust resource for carrying out well optimized synchrotron XF studies of challenging biological systems with complex sample compositions.

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47

Baud, Anna, Florence Gonnet, Isabelle Salard, Maxime Le Mignon, Alexandre Giuliani, Pascal Mercère, Bianca Sclavi, and Régis Daniel. "Probing the solution structure of Factor H using hydroxyl radical protein footprinting and cross-linking." Biochemical Journal 473, no. 12 (June 10, 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 footprint of C3b on the FH surface matches existing crystal structures of C3b complexed with the N- and C-terminal fragments of FH. In addition, we revealed the position of the central portion of FH in the protein complex. Moreover, cross-linking studies confirmed the involvement of the C-terminus in the dimerization of FH.

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48

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 (January 1997): 167–68. http://dx.doi.org/10.1016/s1366-2120(08)70074-6.

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49

Hulscher, Ryan M., Jen Bohon, Mollie C. Rappé, Sayan Gupta, Rhijuta D’Mello, Michael Sullivan, Corie Y. Ralston, Mark R. Chance, and Sarah A. Woodson. "Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting." Methods 103 (July 2016): 49–56. http://dx.doi.org/10.1016/j.ymeth.2016.03.012.

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50

Orphanides, George, and Anthony Maxwell. "Evidence for a conformational change in the DNA gyrase–DNA complex from hydroxyl radical footprinting." Nucleic Acids Research 22, no. 9 (1994): 1567–75. http://dx.doi.org/10.1093/nar/22.9.1567.

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