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McKenzie-Coe A, Montes NS, Jones LM. Hydroxyl Radical Protein Footprinting: A Mass Spectrometry-Based Structural Method for Studying the Higher Order Structure of Proteins. Chem Rev 2021; 122:7532-7561. [PMID: 34633178 DOI: 10.1021/acs.chemrev.1c00432] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been successfully used to investigate a plethora of protein-related questions. The method, which utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids, can inform on protein interaction sites and regions of conformational change. Hydroxyl radical-based footprinting was originally developed to study nucleic acids, but coupling the method with mass spectrometry has enabled the study of proteins. The method has undergone several advancements since its inception that have increased its utility for more varied applications such as protein folding and the study of biotherapeutics. In addition, recent innovations have led to the study of increasingly complex systems including cell lysates and intact cells. Technological advances have also increased throughput and allowed for better control of experimental conditions. In this review, we provide a brief history of the field of HRPF and detail recent innovations and applications in the field.
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Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicholas S Montes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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Maleknia SD, Downard KM. Protein Footprinting with Radical Probe Mass Spectrometry- Two Decades of Achievement. Protein Pept Lett 2019; 26:4-15. [PMID: 30484400 DOI: 10.2174/0929866526666181128124241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/31/2018] [Accepted: 09/11/2018] [Indexed: 01/19/2023]
Abstract
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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Affiliation(s)
- Simin D Maleknia
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, University of New South Wales-Medicine, Sydney, NSW, Australia
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Downard KM, Maleknia SD. Mass spectrometry in structural proteomics: The case for radical probe protein footprinting. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Saikusa K, Shimoyama S, Asano Y, Nagadoi A, Sato M, Kurumizaka H, Nishimura Y, Akashi S. Charge-neutralization effect of the tail regions on the histone H2A/H2B dimer structure. Protein Sci 2015; 24:1224-31. [PMID: 25752661 PMCID: PMC4534173 DOI: 10.1002/pro.2673] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/18/2015] [Accepted: 03/03/2015] [Indexed: 12/18/2022]
Abstract
It is well known that various modifications of histone tails play important roles in the regulation of transcription initiation. In this study, some lysine (Lys) and arginine (Arg) residues were acetylated and deiminated, respectively, in the histone H2A/H2B dimer, and charge-neutralization effects on the dimer structure were studied by native mass spectrometry. Given that both acetylation and deimination neutralize the positive charges of basic amino acid residues, it had been expected that these modifications would correspondingly affect the gas-phase behavior of the histone H2A/H2B dimer. Contrary to this expectation, it was found that Arg deimination led to greater difficulty of dissociation of the dimer by gas-phase collision, whereas acetylation of Lys residues did not cause such a drastic change in the dimer stability. In contrast, ion mobility-mass spectrometry (IM-MS) experiments showed that arrival times in the mobility cell both of acetylated and of deiminated dimer ions changed little from those of the unmodified dimer ions, indicating that the sizes of the dimer ions did not change by modification. Charge neutralization of Arg, basicity of which is higher than Lys, might have triggered some alteration of the dimer structure that cannot be found in IM-MS but can be detected by collision in the gas phase.
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Affiliation(s)
- Kazumi Saikusa
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City UniversityTsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Singo Shimoyama
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City UniversityTsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuuki Asano
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City UniversityTsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Aritaka Nagadoi
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City UniversityTsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mamoru Sato
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City UniversityTsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hitoshi Kurumizaka
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda UniversityShinjuku-ku, Tokyo, 162-8480, Japan
| | - Yoshifumi Nishimura
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City UniversityTsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoko Akashi
- Department of Medical Life Science, Graduate School of Medical Life Science, Yokohama City UniversityTsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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Saikusa K, Nagadoi A, Hara K, Fuchigami S, Kurumizaka H, Nishimura Y, Akashi S. Mass Spectrometric Approach for Characterizing the Disordered Tail Regions of the Histone H2A/H2B Dimer. Anal Chem 2015; 87:2220-7. [DOI: 10.1021/ac503689w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Kazumi Saikusa
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Aritaka Nagadoi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kana Hara
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Sotaro Fuchigami
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hitoshi Kurumizaka
- Graduate
School of Advanced Science and Engineering, Waseda University, 2-2
Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoshifumi Nishimura
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Satoko Akashi
- Graduate
School of Medical Life Science, Yokohama City University, 1-7-29
Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Akashi S, Maleknia SD, Saikusa K, Downard KM. Stability of the βB2B3 crystallin heterodimer to increased oxidation by radical probe and ion mobility mass spectrometry. J Struct Biol 2014; 189:20-7. [PMID: 25478970 DOI: 10.1016/j.jsb.2014.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 11/11/2014] [Accepted: 11/24/2014] [Indexed: 10/24/2022]
Abstract
Ion mobility mass spectrometry was employed to study the structure of the βB2B3-crystallin heterodimer following oxidation through its increased exposure to hydroxyl radicals. The results demonstrate that the heterodimer can withstand limited oxidation through the incorporation of up to some 10 oxygen atoms per subunit protein without any appreciable change to its average collision cross section and thus conformation. These results are in accord with the oxidation levels and timescales applicable to radical probe mass spectrometry (RP-MS) based protein footprinting experiments. Following prolonged exposure, the heterodimer is increasingly degraded through cleavage of the backbone of the subunit crystallins rather than denaturation such that heterodimeric structures with altered conformations and ion mobilities were not detected. However, evidence from measurements of oxidation levels within peptide segments, suggest the presence of some aggregated structure involving C-terminal domain segments of βB3 crystallin across residues 115-126 and 152-166. The results demonstrate, for the first time, the ability of ion mobility in conjunction with RP-MS to investigate the stability of protein complexes to, and the onset of, free radical based oxidative damage that has important implications in cataractogenesis.
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Affiliation(s)
- Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Simin D Maleknia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Kazumi Saikusa
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kevin M Downard
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia.
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Slingsby C, Wistow GJ. Functions of crystallins in and out of lens: roles in elongated and post-mitotic cells. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 115:52-67. [PMID: 24582830 PMCID: PMC4104235 DOI: 10.1016/j.pbiomolbio.2014.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 02/18/2014] [Indexed: 12/25/2022]
Abstract
The vertebrate lens evolved to collect light and focus it onto the retina. In development, the lens grows through massive elongation of epithelial cells possibly recapitulating the evolutionary origins of the lens. The refractive index of the lens is largely dependent on high concentrations of soluble proteins called crystallins. All vertebrate lenses share a common set of crystallins from two superfamilies (although other lineage specific crystallins exist). The α-crystallins are small heat shock proteins while the β- and γ-crystallins belong to a superfamily that contains structural proteins of uncertain function. The crystallins are expressed at very high levels in lens but are also found at lower levels in other cells, particularly in retina and brain. All these proteins have plausible connections to maintenance of cytoplasmic order and chaperoning of the complex molecular machines involved in the architecture and function of cells, particularly elongated and post-mitotic cells. They may represent a suite of proteins that help maintain homeostasis in such cells that are at risk from stress or from the accumulated insults of aging.
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Affiliation(s)
- Christine Slingsby
- Department of Biological Sciences, Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, UK.
| | - Graeme J Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, Bg 6, Rm 106, National Institutes of Health, Bethesda, MD 20892-0608, USA
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Maleknia SD, Downard KM. Advances in radical probe mass spectrometry for protein footprinting in chemical biology applications. Chem Soc Rev 2014; 43:3244-58. [PMID: 24590115 DOI: 10.1039/c3cs60432b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Radical Probe Mass Spectrometry (RP-MS), first introduced in 1999, utilizes hydroxyl radicals generated directly within aqueous solutions using synchrotron radiolysis, electrical discharge, and photochemical laser sources to probe protein structures and their interactions. It achieves this on millisecond and submillisecond timescales that can be used to capture protein dynamics and folding events. Hydroxyl radicals are ideal probes of solvent accessibility as their size approximates a water molecule. Their high reactivity results in oxidation at a multitude of amino acid side chains providing greater structural information than a chemical cross-linker that reacts with only one or few residues. The oxidation of amino acid side chains occurs at rates in accord with the solvent accessibility of the residue so that the extent of oxidation can be quantified to reveal a three-dimensional map or footprint of the protein's surface. Mass spectrometry is central to this analysis of chemical oxidative labelling. This tutorial review, some 15 years on from the first reports, highlights the development and significant growth of the application of RP-MS including its validation and utility with ion-mobility mass spectrometry (IM-MS), the use of RP-MS data to help model protein complexes, studies of the onset of oxidative damage, and more recent advances that enable high throughput applications through simultaneous protein oxidation and on-plate deposition. The accessibility of the RP-MS technology, by means of a modified electrospray ionization source, enables the approach to be implemented in many laboratories to address a wide range of applications in chemical biology.
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Affiliation(s)
- Simin D Maleknia
- School of Civil and Environmental Engineering, University of New South Wales, Sydney, Australia
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Saikusa K, Fuchigami S, Takahashi K, Asano Y, Nagadoi A, Tachiwana H, Kurumizaka H, Ikeguchi M, Nishimura Y, Akashi S. Gas-Phase Structure of the Histone Multimers Characterized by Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation. Anal Chem 2013; 85:4165-71. [DOI: 10.1021/ac400395j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Kazumi Saikusa
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Sotaro Fuchigami
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Kyohei Takahashi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Yuuki Asano
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Aritaka Nagadoi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Hiroaki Tachiwana
- Graduate School of Advanced
Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hitoshi Kurumizaka
- Graduate School of Advanced
Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Mitsunori Ikeguchi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Yoshifumi Nishimura
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
| | - Satoko Akashi
- Department of Supramolecular
Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama,
Kanagawa 230-0045, Japan
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Maleknia SD, Downard KM. On-plate deposition of oxidized proteins to facilitate protein footprinting studies by radical probe mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:2311-2318. [PMID: 22956323 DOI: 10.1002/rcm.6358] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The on-plate deposition of oxidized proteins is described to advance footprinting applications by radical probe mass spectrometry (RP-MS). An electrospray ionization (ESI) needle assembly mounted vertically over a 384-target matrix-assisted laser desorption/ionization (MALDI) plate enabled the limited oxidation of proteins as they were released in the charged droplets ahead of their deposition on the plate. This method combined with on-plate proteolytic digestion protocols expedites the analysis of proteins oxidized by RP-MS, and avoids the need to collect and reconstitute samples prior to analysis by MALDI mass spectrometry. Oxidation of peptides from solutions in water as well as an ammonium bicarbonate solution was investigated to test the optimal conditions required for on-plate oxidation of proteins. These comprised of peptides with a wide range of reactive amino acids including Phe, Tyr, Pro, His, Leu, Met and Lys that were previously shown to oxidize in both electrospray discharge and synchrotron radiolysis based footprinting experiments. The on-plate deposition of lysozyme oxidized at electrospray needle voltages of 6 and 9 kV were carried out to demonstrate conditions suitable for footprinting experiments as well as those that induce the onset of protein damage.
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Affiliation(s)
- Simin D Maleknia
- School of Molecular Bioscience, University of Sydney, Sydney, Australia.
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Downard KM, Maleknia SD, Akashi S. Impact of limited oxidation on protein ion mobility and structure of importance to footprinting by radical probe mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:226-230. [PMID: 22223306 DOI: 10.1002/rcm.5320] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The effect of hydroxyl radical induced oxidation on the collision cross-sections of hen egg lysozyme and bovine ubiquitin was investigated by travelling wave ion mobility mass spectrometry for the first time. The oxidized ions of lysozyme and ubiquitin share common collision cross-sections with their unoxidized counterparts suggesting that they share common structures that were unaffected by limited oxidation. In the case of bovine ubiquitin, two distinct conformers were detected for the protein in its unoxidized and oxidized states though no change in the levels of each was observed upon oxidation. This supports the validity of Radical Probe Mass Spectrometry (RP-MS) using an electrical discharge source for protein footprinting experiments. Travelling wave ion mobility mass spectrometry has been used for the first time to confirm that limited oxidation does not have an impact on the global structure of proteins.
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Affiliation(s)
- Kevin M Downard
- School of Molecular Bioscience, University of Sydney, Sydney, Australia.
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