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Zakopcanik M, Kavan D, Kukacka Z, Novak P, Loginov DS. Data-Independent Acquisition Represents a Promising Alternative for Fast Photochemical Oxidation of Proteins (FPOP) Samples Analysis. Anal Chem 2024; 96:11273-11279. [PMID: 38967040 PMCID: PMC11256011 DOI: 10.1021/acs.analchem.4c01084] [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: 02/27/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
Fast Photochemical Oxidation of Proteins (FPOP) is a protein footprinting method utilizing hydroxyl radicals to provide valuable information on the solvent-accessible surface area. The extensive number of oxidative modifications that are created by FPOP is both advantageous, leading to great spatial resolution, and challenging, increasing the complexity of data processing. The precise localization of the modification together with the appropriate reproducibility is crucial to obtain relevant structural information. In this paper, we propose a novel approach combining validated spectral libraries together with utilizing DIA data. First, the DDA data searched by FragPipe are subsequently validated using Skyline software to form a spectral library. This library is then matched against the DIA data to filter out nonrepresentative IDs. In comparison with FPOP data processing using only a search engine followed by generally applied filtration steps, the manually validated spectral library offers higher confidence in identifications and increased spatial resolution. Furthermore, the reproducibility of quantification was compared for DIA, DDA, and MS-only acquisition modes on timsTOF SCP. Comparison of coefficients of variation (CV) showed that the DIA and MS acquisition modes exhibit significantly better reproducibility in quantification (CV medians 0.1233 and 0.1494, respectively) compared to the DDA mode (CV median 0.2104).
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Affiliation(s)
- Marek Zakopcanik
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12820 Prague, Czech
Republic
| | - Daniel Kavan
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Zdenek Kukacka
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novak
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Dmitry S. Loginov
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
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2
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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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3
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Felčíková K, Hovan A, Polák M, Loginov DS, Holotová V, Díaz C, Kožár T, Lee O, Varhač R, Novák P, Bánó G, Sedlák E. Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer. Protein Sci 2024; 33:e4921. [PMID: 38501448 PMCID: PMC10949324 DOI: 10.1002/pro.4921] [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: 09/13/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 03/20/2024]
Abstract
Flavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1 O2 ). However, its 1 O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase 1 O2 production efficiency GEPS, but at the same time weakened native FMN-protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategically placed cysteines (oxidation-prone amino acids) in the isoalloxazine-binding site due to significantly increased volume of the cysteinyl side residue(s). As a proof of concept, in three variants of the LOV2 domain of Avena sativa (AsLOV2), namely V416C, T418C, and V416C/T418C, the effective 1 O2 production strongly correlated with the efficiency of irradiation-induced FMN dissociation (wild type (WT) < V416C < T418C < V416C/T418C). This alternative approach enables us: (i) to overcome the low 1 O2 production efficiency of flavin-based GEPSs without affecting native isoalloxazine ring-protein interactions and (ii) to utilize AsLOV2, due to its inherent binding propensity to FMN, as a PS vehicle, which is released at a target by light irradiation.
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Affiliation(s)
- Kristína Felčíková
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Andrej Hovan
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Marek Polák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Dmitry S. Loginov
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Veronika Holotová
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Carlos Díaz
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - One‐Sun Lee
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Petr Novák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Gregor Bánó
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
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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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Zakopcanik M, Kavan D, Novak P, Loginov DS. Quantifying the Impact of the Peptide Identification Framework on the Results of Fast Photochemical Oxidation of Protein Analysis. J Proteome Res 2024; 23:609-617. [PMID: 38158558 PMCID: PMC10845142 DOI: 10.1021/acs.jproteome.3c00390] [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: 06/30/2023] [Revised: 10/17/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
Fast Photochemical Oxidation of Proteins (FPOP) is a promising technique for studying protein structure and dynamics. The quality of insight provided by FPOP depends on the reliability of the determination of the modification site. This study investigates the performance of two search engines, Mascot and PEAKS, for the data processing of FPOP analyses. Comparison of Mascot and PEAKS of the hemoglobin--haptoglobin Bruker timsTOF data set (PXD021621) revealed greater consistency in the Mascot identification of modified peptides, with around 26% of the IDs being mutual for all three replicates, compared to approximately 22% for PEAKS. The intersection between Mascot and PEAKS results revealed a limited number (31%) of shared modified peptides. Principal Component Analysis (PCA) using the peptide-spectrum match (PSM) score, site probability, and peptide intensity was applied to evaluate the results, and the analyses revealed distinct clusters of modified peptides. Mascot showed the ability to assess confident site determination, even with lower PSM scores. However, high PSM scores from PEAKS did not guarantee a reliable determination of the modification site. Fragmentation coverage of the modification position played a crucial role in Mascot assignments, while the AScore localizations from PEAKS often become ambiguous because the software employs MS/MS merging.
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Affiliation(s)
- Marek Zakopcanik
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12820 Prague, Czech Republic
| | - Daniel Kavan
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novak
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Dmitry S. Loginov
- Institute
of Microbiology, The Czech Academy of Sciences, 14220 Prague, Czech Republic
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6
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Polák M, Černý J, Novák P. Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis. Anal Chem 2024; 96:1478-1487. [PMID: 38226459 PMCID: PMC10831798 DOI: 10.1021/acs.analchem.3c03759] [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: 08/22/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/17/2024]
Abstract
Protein radical labeling, like fast photochemical oxidation of proteins (FPOP), coupled to a top-down mass spectrometry (MS) analysis offers an alternative analytical method for probing protein structure or protein interaction with other biomolecules, for instance, proteins and DNA. However, with the increasing mass of studied analytes, the MS/MS spectra become complex and exhibit a low signal-to-noise ratio. Nevertheless, these difficulties may be overcome by protein isotope depletion. Thus, we aimed to use protein isotope depletion to analyze FPOP-oxidized samples by top-down MS analysis. For this purpose, we prepared isotopically natural (IN) and depleted (ID) forms of the FOXO4 DNA binding domain (FOXO4-DBD) and studied the protein-DNA interaction interface with double-stranded DNA, the insulin response element (IRE), after exposing the complex to hydroxyl radicals. As shown by comparing tandem mass spectra of natural and depleted proteins, the ID form increased the signal-to-noise ratio of useful fragment ions, thereby enhancing the sequence coverage by more than 19%. This improvement in the detection of fragment ions enabled us to detect 22 more oxidized residues in the ID samples than in the IN sample. Moreover, less common modifications were detected in the ID sample, including the formation of ketones and lysine carbonylation. Given the higher quality of ID top-down MSMS data set, these results provide more detailed information on the complex formation between transcription factors and DNA-response elements. Therefore, our study highlights the benefits of isotopic depletion for quantitative top-down proteomics. Data are available via ProteomeXchange with the identifier PXD044447.
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Affiliation(s)
- Marek Polák
- Institute
of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12843 Prague, Czech Republic
| | - Jiří Černý
- Laboratory
of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novák
- Institute
of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12843 Prague, Czech Republic
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7
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High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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8
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Yassaghi G, Kukačka Z, Fiala J, Kavan D, Halada P, Volný M, Novák P. Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation. Anal Chem 2022; 94:9993-10002. [PMID: 35797180 DOI: 10.1021/acs.analchem.1c05476] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein conformation, structural dynamics, and interactions. Bottom-up mass spectrometry is an established standard method to analyze FPOP samples. In the bottom-up approach, all forms of the protein are digested together by a protease of choice, which results in a mixture of peptides from various subpopulations of proteins with varying degrees of photochemical oxidation. Here, we investigate the possibility to analyze a specifically selected population of only singly oxidized proteins. This requires utilization of more specific top-down mass spectrometry approaches. The key element of any top-down experiment is the selection of a suitable method of ion isolation, excitation, and fragmentation. Here, we employ and compare collision-induced dissociation, electron-transfer dissociation, and electron-capture dissociation combined with multi-continuous accumulation of selected ions. A singly oxidized subpopulation of FPOP-labeled ubiquitin was used to optimize the method. The top-down approach in FPOP is limited to smaller proteins, but its usefulness was demonstrated by using it to visualize structural changes induced by co-factor removal from the holo/apo myoglobin system. The top-down data were compared with the literature and with the bottom-up data set obtained on the same samples. The top-down results were found to be in good agreement, which indicates that monitoring a singly oxidized FPOP ion population by the top-down approach is a functional workflow for oxidative protein footprinting.
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Affiliation(s)
- Ghazaleh Yassaghi
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Jan Fiala
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic.,Faculty of Science, Charles University, Albertov 6, Prague 2 128 00, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Michael Volný
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, Prague 4 142 20, Czech Republic
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