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Larsen DN, Kaczmarek JZ, Palarasah Y, Graversen JH, Højrup P. Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141011. [PMID: 38499233 DOI: 10.1016/j.bbapap.2024.141011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024]
Abstract
Understanding protein-protein interactions is crucial for drug design and investigating biological processes. Various techniques, such as CryoEM, X-ray spectroscopy, linear epitope mapping, and mass spectrometry-based methods, can be employed to map binding regions on proteins. Commonly used mass spectrometry-based techniques are cross-linking and hydrogen‑deuterium exchange (HDX). Another approach, hydroxyl radical protein footprinting (HRPF), identifies binding residues on proteins but faces challenges due to high initial costs and complex setups. This study introduces a generally applicable method using Fenton chemistry for epitope mapping in a standard mass spectrometry laboratory. It emphasizes the importance of controls, particularly the inclusion of a negative antibody control, not widely utilized in HRPF epitope mapping. Quantification by TMT labelling is introduced to reduce false positives, enabling direct comparison between sample conditions and biological triplicates. Additionally, six technical replicates were incorporated to enhance the depth of analysis. Observations on the receptor-binding domain (RBD) of SARS-CoV-2 Spike Protein, Alpha and Delta variants, revealed both binding and opening regions. Significantly changed peptides upon mixing with a negative control antibody suggested structural alterations or nonspecific binding induced by the antibody alone. Integration of negative control antibody experiments and high overlap between biological triplicates led to the exclusion of 40% of significantly changed regions. The final identified binding region correlated with existing literature on neutralizing antibodies against RBD. The presented method offers a straightforward implementation for HRPF analysis in a generic mass spectrometry-based laboratory. Enhanced data reliability was achieved through increased technical and biological replicates alongside negative antibody controls.
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Affiliation(s)
- Daniel Nyberg Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark
| | | | - Yaseelan Palarasah
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Jonas Heilskov Graversen
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark.
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2
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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3
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Jain R, Dhillon NS, Kanchustambham VL, Lodowski DT, Farquhar ER, Kiselar J, Chance MR. Evaluating Mass Spectrometry-Based Hydroxyl Radical Protein Footprinting of a Benchtop Flash Oxidation System against a Synchrotron X-ray Beamline. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:476-486. [PMID: 38335063 DOI: 10.1021/jasms.3c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Hydroxyl radical protein footprinting (HRPF) using synchrotron X-ray radiation (XFP) and mass spectrometry is a well-validated structural biology method that provides critical insights into macromolecular structural dynamics, such as determining binding sites, measuring affinity, and mapping epitopes. Numerous alternative sources for generating the hydroxyl radicals (•OH) needed for HRPF, such as laser photolysis and plasma irradiation, complement synchrotron-based HRPF, and a recently developed commercially available instrument based on flash lamp photolysis, the FOX system, enables access to laboratory benchtop HRPF. Here, we evaluate performing HRPF experiments in-house with a benchtop FOX instrument compared to synchrotron-based X-ray footprinting at the NSLS-II XFP beamline. Using lactate oxidase (LOx) as a model system, we carried out •OH labeling experiments using both instruments, followed by nanoLC-MS/MS bottom-up peptide mass mapping. Experiments were performed under high glucose concentrations to mimic the highly scavenging conditions present in biological buffers and human clinical samples, where less •OH are available for reaction with the biomolecule(s) of interest. The performance of the FOX and XFP HRPF methods was compared, and we found that tuning the •OH dosage enabled optimal labeling coverage for both setups under physiologically relevant highly scavenging conditions. Our study demonstrates the complementarity of FOX and XFP labeling approaches, demonstrating that benchtop instruments such as the FOX photolysis system can increase both the throughput and the accessibility of the HRPF technique.
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Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nanak S Dhillon
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Vijaya Lakshmi Kanchustambham
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - David T Lodowski
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Erik R Farquhar
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Janna Kiselar
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Mark R Chance
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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4
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Chapman J, Paukner M, Leser M, Teng KW, Koide S, Holder M, Armache KJ, Becker C, Ueberheide B, Brenowitz M. Systematic Fe(II)-EDTA Method of Dose-Dependent Hydroxyl Radical Generation for Protein Oxidative Footprinting. Anal Chem 2023; 95:18316-18325. [PMID: 38049117 PMCID: PMC10734636 DOI: 10.1021/acs.analchem.3c02319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
Correlating the structure and dynamics of proteins with biological function is critical to understanding normal and dysfunctional cellular mechanisms. We describe a quantitative method of hydroxyl radical generation via Fe(II)-ethylenediaminetetraacetic acid (EDTA)-catalyzed Fenton chemistry that provides ready access to protein oxidative footprinting using equipment commonly found in research and process control laboratories. Robust and reproducible dose-dependent oxidation of protein samples is observed and quantitated by mass spectrometry with as fine a single residue resolution. An oxidation analysis of lysozyme provides a readily accessible benchmark for our method. The efficacy of our oxidation method is demonstrated by mapping the interface of a RAS-monobody complex, the surface of the NIST mAb, and the interface between PRC2 complex components. These studies are executed using standard laboratory tools and a few pennies of reagents; the mass spectrometry analysis can be streamlined to map the protein structure with single amino acid residue resolution.
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Affiliation(s)
- Jessica
R. Chapman
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
| | - Max Paukner
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Micheal Leser
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Kai Wen Teng
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
| | - Shohei Koide
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Marlene Holder
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Karim-Jean Armache
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Chris Becker
- Protein
Metrics Inc., Cupertino, California 95014, United States
| | - Beatrix Ueberheide
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Michael Brenowitz
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department
of Molecular Pharmacology, Albert Einstein
College of Medicine, Bronx, New York 10461, United States
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5
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Ilmain JK, Perelman SS, Panepinto MC, Irnov I, Coudray N, Samhadaneh N, Pironti A, Ueberheide B, Ekiert DC, Bhabha G, Torres VJ. Unlatching of the stem domains in the Staphylococcus aureus pore-forming leukocidin LukAB influences toxin oligomerization. J Biol Chem 2023; 299:105321. [PMID: 37802313 PMCID: PMC10665946 DOI: 10.1016/j.jbc.2023.105321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is a serious global pathogen that causes a diverse range of invasive diseases. S. aureus utilizes a family of pore-forming toxins, known as bi-component leukocidins, to evade the host immune response and promote infection. Among these is LukAB (leukocidin A/leukocidin B), a toxin that assembles into an octameric β-barrel pore in the target cell membrane, resulting in host cell death. The established cellular receptor for LukAB is CD11b of the Mac-1 complex. Here, we show that hydrogen voltage-gated channel 1 is also required for the cytotoxicity of all major LukAB variants. We demonstrate that while each receptor is sufficient to recruit LukAB to the plasma membrane, both receptors are required for maximal lytic activity. Why LukAB requires two receptors, and how each of these receptors contributes to pore-formation remains unknown. To begin to resolve this, we performed an alanine scanning mutagenesis screen to identify mutations that allow LukAB to maintain cytotoxicity without CD11b. We discovered 30 mutations primarily localized in the stem domains of LukA and LukB that enable LukAB to exhibit full cytotoxicity in the absence of CD11b. Using crosslinking, electron microscopy, and hydroxyl radical protein footprinting, we show these mutations increase the solvent accessibility of the stem domain, priming LukAB for oligomerization. Together, our data support a model in which CD11b binding unlatches the membrane penetrating stem domains of LukAB, and this change in flexibility promotes toxin oligomerization.
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Affiliation(s)
- Juliana K Ilmain
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Sofya S Perelman
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Maria C Panepinto
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA
| | - Irnov Irnov
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Nicolas Coudray
- Applied Bioinformatics Laboratories, New York University Grossman School of Medicine, New York, New York, USA; Department of Cell Biology, New York University Grossman School of Medicine, New York, New York, USA
| | - Nora Samhadaneh
- Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, USA
| | - Alejandro Pironti
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA; Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, New York, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA; Department of Neurology, Center for Cognitive Neurology, New York University Grossman School of Medicine, New York, New York, USA
| | - Damian C Ekiert
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA; Department of Cell Biology, New York University Grossman School of Medicine, New York, New York, USA; Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University Grossman School of Medicine, New York, New York, USA; Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, USA
| | - Victor J Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA; Department of Host-Microbe Interactions, St Jude Children's Research Hospital, Memphis, Tennessee, USA.
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6
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Qiu Y, Wang Y, Lu J, Zhu Q, Jia L, Lei F, Shen L, Jiang L, Wu A. Synthesis, spectroscopic analysis, DFT, docking, MD and antioxidant activity of tetrahydrocurcumin. J Biomol Struct Dyn 2023:1-13. [PMID: 37902569 DOI: 10.1080/07391102.2023.2275189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/20/2023] [Indexed: 10/31/2023]
Abstract
In recent years, numerous researchers have made local chemical modifications to the structure of curcumin while its basic structure remains unchanged, thus, producing curcumin derivatives. In this article, tetrahydrocurcumin was obtained by hydrogenation of curcumin, DFT calculation and characterization at the theoretical level of B3LYP/6 -311++G(d,p) were carried out. The observed IR and Raman spectra are in good agreement with the theoretical spectra. The FMO and ESP of tetrahydrocurcumin are predicted. The interaction in the system is shown graphically and analyzed by IGMH. Compared with curcumin, tetrahydrocurcumin lacks the unsaturated C = C bond, which makes it more stable and more bioavailable. Molecular docking with antioxidant targets elucidated the ligand-protein interaction and molecular dynamics simulation showed the antioxidant activity of tetrahydrocurcumin. The antioxidant activity of tetrahydrocurcumin was proved by DPPH• and •OH radical scavenging experiments. In essence, these derivatives exhibit enhanced physiological activity in certain aspects compared to the original curcumin. Moreover, the computational pharmacology techniques lay a theoretical groundwork for the development and modification of high-efficiency, low-toxicity drugs that interface with various targets of curcumin in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yingqi Qiu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Yuanmeng Wang
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Jiahao Lu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Qinghua Zhu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Li Jia
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Fuhou Lei
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Liqun Shen
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
| | - Lihe Jiang
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
- Medical College, Guangxi University, Nanning, China
| | - Aiqun Wu
- College of Chemistry and Chemical Engineering, GUANGXI MINZU UNIVERSITY, Key Laboratory of universities in Guangxi for Excavation and Development of ancient ethnomedicinal recipes, Nanning, China
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning, China
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7
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Oprica L, Vochita G, Grigore MN, Shvidkiy S, Molokanov A, Gherghel D, Les A, Creanga D. Cytogenetic and Biochemical Responses of Wheat Seeds to Proton Irradiation at the Bragg Peak. PLANTS (BASEL, SWITZERLAND) 2023; 12:842. [PMID: 36840190 PMCID: PMC9960546 DOI: 10.3390/plants12040842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The present study aimed to evaluate the morphological, cytogenetic and biochemical changes in wheat seedlings as affected by seed exposure to a proton beam at the Bragg peak. The average energy of the proton beam was of 171 MeV at the entrance into the irradiator room while at the point of sample irradiation the beam energy was of 150 MeV, with the average value of the Linear Energy Transfer of 0.539 keV/μm and the dose rate of 0.55 Gy/min, the radiation doses being of the order of tens of Gy. Cytogenetic investigation has revealed the remarkable diminution of the mitotic index as linear dose-response curve as well as the spectacular linear increase of the aberration index. Analyzing some biometric parameters, it was found that neither dry matter nor water content of wheat seedlings was influenced by proton beam exposure. Studying the biochemical parameters related to the antioxidant defense system, we found that the irradiation caused the slight increasing tendency of peroxidase activity as well as the decreasing trend in the activity of superoxidedismutase in the seedlings grown from the irradiated seeds. The level of malonedialdehyde (MDA) and total polyphenols showed an increasing tendency in all seedling variants corresponding to irradiated seeds, compared to the control. We conclude that the irradiation clearly induced dose-response curves at the level of cytogenetic parameters together with relatively slight variation tendency of some biochemical parameters related to the antioxidant defense system while imperceptible changes could be noticed in the biometric parameters.
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Affiliation(s)
- Lacramioara Oprica
- Biology Faculty, Alexandru Ioan Cuza University, 20A Carol I Bd., 700506 Iasi, Romania
| | - Gabriela Vochita
- Institute of Biological Research—Branch of NIRDBS, 47 Lascar Catargi Street, 700107 Iasi, Romania
| | - Marius-Nicușor Grigore
- Faculty of Medicine and Biological Sciences, Stefan cel Mare University of Suceava, 13 University Street, 720229 Suceava, Romania
| | - Sergey Shvidkiy
- Dzhelepov Laboratory, Joint Institute for Nuclear Research, 6 Joliot-Curie Street, 141980 Dubna, Russia
| | - Alexander Molokanov
- Dzhelepov Laboratory, Joint Institute for Nuclear Research, 6 Joliot-Curie Street, 141980 Dubna, Russia
| | - Daniela Gherghel
- Institute of Biological Research—Branch of NIRDBS, 47 Lascar Catargi Street, 700107 Iasi, Romania
| | - Anda Les
- Physic Faculty, Alexandru Ioan Cuza University, 20A Carol I Bd., 700506 Iasi, Romania
| | - Dorina Creanga
- Physic Faculty, Alexandru Ioan Cuza University, 20A Carol I Bd., 700506 Iasi, Romania
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8
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Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods. Antibodies (Basel) 2022; 11:antib11040071. [PMID: 36412837 PMCID: PMC9680451 DOI: 10.3390/antib11040071] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
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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9
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Fenton-Chemistry-Based Oxidative Modification of Proteins Reflects Their Conformation. Int J Mol Sci 2021; 22:ijms22189927. [PMID: 34576105 PMCID: PMC8469487 DOI: 10.3390/ijms22189927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 11/25/2022] Open
Abstract
In order to understand protein structure to a sufficient extent for, e.g., drug discovery, no single technique can provide satisfactory information on both the lowest-energy conformation and on dynamic changes over time (the ‘four-dimensional’ protein structure). Instead, a combination of complementary techniques is required. Mass spectrometry methods have shown promise in addressing protein dynamics, but often rely on the use of high-end commercial or custom instruments. Here, we apply well-established chemistry to conformation-sensitive oxidative protein labelling on a timescale of a few seconds, followed by analysis through a routine protein analysis workflow. For a set of model proteins, we show that site selectivity of labelling can indeed be rationalised in terms of known structural information, and that conformational changes induced by ligand binding are reflected in the modification pattern. In addition to conventional bottom-up analysis, further insights are obtained from intact mass measurement and native mass spectrometry. We believe that this method will provide a valuable and robust addition to the ‘toolbox’ of mass spectrometry researchers studying higher-order protein structure.
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10
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Nuszkiewicz J, Woźniak A, Szewczyk-Golec K. Ionizing Radiation as a Source of Oxidative Stress-The Protective Role of Melatonin and Vitamin D. Int J Mol Sci 2020; 21:E5804. [PMID: 32823530 PMCID: PMC7460937 DOI: 10.3390/ijms21165804] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/31/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Ionizing radiation (IR) has found widespread application in modern medicine, including medical imaging and radiotherapy. As a result, both patients and healthcare professionals are exposed to various IR doses. To minimize the negative side effects of radiation associated with oxidative imbalance, antioxidant therapy has been considered. In this review, studies on the effects of melatonin and vitamin D on radiation-induced oxidative stress are discussed. According to the research data, both substances meet the conditions for use as agents that protect humans against IR-induced tissue damage. Numerous studies have confirmed that melatonin, a hydro- and lipophilic hormone with strong antioxidant properties, can potentially be used as a radioprotectant in humans. Less is known about the radioprotective effects of vitamin D, but the results to date have been promising. Deficiencies in melatonin and vitamin D are common in modern societies and may contribute to the severity of adverse side effects of medical IR exposure. Hence, supporting supplementation with both substances seems to be of first importance. Interestingly, both melatonin and vitamin D have been found to selectively radiosensitise cancer cells, which makes them promising adjuvants in radiotherapy. More research is needed in this area, especially in humans.
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Affiliation(s)
- Jarosław Nuszkiewicz
- Department of Medical Biology and Biochemistry, Faculty of Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 24 Karłowicza St, 85-092 Bydgoszcz, Poland;
| | | | - Karolina Szewczyk-Golec
- Department of Medical Biology and Biochemistry, Faculty of Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 24 Karłowicza St, 85-092 Bydgoszcz, Poland;
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11
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Espino JA, Zhang Z, Jones LM. Chemical Penetration Enhancers Increase Hydrogen Peroxide Uptake in C. elegans for In Vivo Fast Photochemical Oxidation of Proteins. J Proteome Res 2020; 19:3708-3715. [PMID: 32506919 PMCID: PMC7861136 DOI: 10.1021/acs.jproteome.0c00245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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Fast photochemical oxidation of proteins (FPOP) is a hydroxyl radical protein
footprinting method that covalently labels solvent-accessible amino acids by photolysis
of hydrogen peroxide. Recently, we expanded the use of FPOP for in vivo
(IV-FPOP) covalent labeling in C. elegans. In initial IV-FPOP studies,
545 proteins were oxidatively modified in all body systems within the worm. Here, with
the use of chemical penetration enhancers (CPEs), we increased the number of modified
proteins as well as the number of modifications per protein to gain more structural
information. CPEs aid in the delivery of hydrogen peroxide inside C.
elegans by disturbing the highly ordered lipid bilayer of the worm cuticle
without affecting worm viability. IV-FPOP experiments performed using the CPE azone
showed an increase in oxidatively modified proteins and peptides. This increase
correlated with greater hydrogen peroxide uptake by C. elegans
quantified using a chemical fluorophore demonstrating the efficacy of using CPEs with
IV-FPOP. Mass spectrometry proteomics data are available via ProteomeXchange with
identifier PXD019290.
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Affiliation(s)
- Jessica A Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States
| | - Zhihui Zhang
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States
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12
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Espino JA, King CD, Jones LM, Robinson RAS. In Vivo Fast Photochemical Oxidation of Proteins Using Enhanced Multiplexing Proteomics. Anal Chem 2020; 92:7596-7603. [PMID: 32383586 PMCID: PMC7815197 DOI: 10.1021/acs.analchem.0c00174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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In vivo fast photochemical oxidation of proteins
(IV-FPOP) is a hydroxyl radical protein footprinting method used to
study protein structure and protein–protein interactions. Oxidatively
modified proteins by IV-FPOP are analyzed by mass spectrometry (MS),
and the extent of oxidation is quantified by label-free MS. Peptide
oxidation changes yield useful information about protein structure,
due to changes in solvent accessibility. However, the sample size
necessary for animal studies requires increased sample preparation
and instrument time. Here, we report the combined application of IV-FPOP
and the enhanced multiplexing strategy combined precursor isotopic
labeling and isobaric tagging (cPILOT) for higher-throughput analysis
of oxidative modifications in C. elegans. Key differences
in the performance of label-free MS and cPILOT were identified. The
addition of oxygen (+16) was the most abundant modification identified
among all known possible FPOP modifications. This study presents IV-FPOP
coupled with enhanced multiplexing strategies such as cPILOT to increase
throughput of studies seeking to examine oxidative protein modifications.
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Affiliation(s)
- Jessica A Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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13
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Huang G, Lin Y, Zhang L, Yan Z, Wang Y, Liu Y. Synthesis of Sulfur-Selenium Doped Carbon Quantum Dots for Biological Imaging and Scavenging Reactive Oxygen Species. Sci Rep 2019; 9:19651. [PMID: 31873130 PMCID: PMC6928214 DOI: 10.1038/s41598-019-55996-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
The sulfur-selenium doped carbon quantum dots (S,Se-CQDs) were synthesized by one-step through hydrothermal method in this study, which have high fluorescence quantum yield (43%) and advanced ability to scavenge reactive oxygen species (ROS). They were characterized by transmission electron microscope (TEM), nuclear magnetic resonance (NMR), X-ray photoelectron spectroscopy (XPS), fourier transform infrared spectroscopy (FTIR). The results showed that the clearance rate of free radical reached to 40% with 200 μg/mL of S,Se-CQDs. The antioxidant activity of S,Se-CQDs is related to -SH and Se-SH on carbon quantum dots. S,Se-CQDs were able to access to cells which is beneficial to enhance the removal efficiency to ROS. In the biocompatibility experiment, the cell survival rate exceeded 95%, there was little effect on hatching rate, survival rate and heart rate of zebrafish which demonstrated that S,Se-CQDs have an excellent biocompatibility. It prompts that S,Se-CQDs will has proud application prospects in the field of biomedicine.
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Affiliation(s)
- Guojie Huang
- College of Pharmacy, Guangdong Pharmaceutical University, Guangdong, China
| | - Yaqi Lin
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong, China
| | - Linxiu Zhang
- School of Chemistry and Chemical Engineering,Guangdong Pharmaceutical University, Guangdong, China
| | - Zhihong Yan
- College of Pharmacy, Guangdong Pharmaceutical University, Guangdong, China.
| | - Yudong Wang
- The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangdong, China.
| | - Yi Liu
- School of Chemistry and Chemical Engineering,Guangdong Pharmaceutical University, Guangdong, China
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14
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Johnson DT, Di Stefano LH, Jones LM. Fast photochemical oxidation of proteins (FPOP): A powerful mass spectrometry-based structural proteomics tool. J Biol Chem 2019; 294:11969-11979. [PMID: 31262727 DOI: 10.1074/jbc.rev119.006218] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fast photochemical oxidation of proteins (FPOP) is a MS-based method that has proved useful in studies of protein structures, interactions, conformations, and protein folding. The success of this method relies on the irreversible labeling of solvent-exposed amino acid side chains by hydroxyl radicals. FPOP generates these radicals through laser-induced photolysis of hydrogen peroxide. The data obtained provide residue-level resolution of protein structures and interactions on the microsecond timescale, enabling investigations of fast processes such as protein folding and weak protein-protein interactions. An extensive comparison between FPOP and other footprinting techniques gives insight on their complementarity as well as the robustness of FPOP to provide unique structural information once unattainable. The versatility of this method is evidenced by both the heterogeneity of samples that can be analyzed by FPOP and the myriad of applications for which the method has been successfully used: from proteins of varying size to intact cells. This review discusses the wide applications of this technique and highlights its high potential. Applications including, but not limited to, protein folding, membrane proteins, structure elucidation, and epitope mapping are showcased. Furthermore, the use of FPOP has been extended to probing proteins in cells and in vivo These promising developments are also presented herein.
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Affiliation(s)
- Danté T Johnson
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Luciano H Di Stefano
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201.
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