1
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Červinková K, Vahalová P, Poplová M, Zakar T, Havelka D, Paidar M, Kolivoška V, Cifra M. Modulation of pulsed electric field induced oxidative processes in protein solutions by pro- and antioxidants sensed by biochemiluminescence. Sci Rep 2024; 14:22649. [PMID: 39349538 PMCID: PMC11442601 DOI: 10.1038/s41598-024-71626-6] [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: 06/26/2024] [Accepted: 08/29/2024] [Indexed: 10/02/2024] Open
Abstract
Technologies based on pulsed electric field (PEF) are increasingly pervasive in medical and industrial applications. However, the detailed understanding of how PEF acts on biosamples including proteins at the molecular level is missing. There are indications that PEF might act on biomolecules via electrogenerated reactive oxygen species (ROS). However, it is unclear how this action is modulated by the pro- and antioxidants, which are naturally present components of biosamples. This knowledge gap is often due to insufficient sensitivity of the conventionally utilized detection assays. To overcome this limitation, here we employed an endogenous (bio)chemiluminescence sensing platform, which enables sensitive detection of PEF-generated ROS and oxidative processes in proteins, to inspect effects of pro-and antioxidants. Taking bovine serum albumin (BSA) as a model protein, we found that the chemiluminescence signal arising from its solution is greatly enhanced in the presence ofH 2 O 2 as a prooxidant, especially during PEF treatment. In contrast, the chemiluminescence signal decreases in the presence of antioxidant enzymes (catalase, superoxide dismutase), indicating the involvement of bothH 2 O 2 and electrogenerated superoxide anion in oxidation-reporting chemiluminescence signal before, during, and after PEF treatment. We also performed additional biochemical and biophysical assays, which confirmed that BSA underwent structural changes afterH 2 O 2 treatment, with PEF having only a minor effect. We proposed a scheme describing the reactions leading from interfacial charge transfer at the anode by which ROS are generated to the actual photon emission. Results of our work help to elucidate the mechanisms of action of PEF on proteins via electrogenerated reactive oxygen species and open up new avenues for the application of PEF technology. The developed chemiluminescence technique enables label-free, in-situ and non-destructive sensing of interactions between ROS and proteins. The technique may be applied to study oxidative damage of other classes of biomolecules such as lipids, nucleic acids or carbohydrates.
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Affiliation(s)
- Kateřina Červinková
- Institute of Photonics and Electronics of the Czech Academy of Sciences, 18200, Prague, Czechia
| | - Petra Vahalová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, 18200, Prague, Czechia
| | - Michaela Poplová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, 18200, Prague, Czechia
| | - Tomáš Zakar
- Institute of Photonics and Electronics of the Czech Academy of Sciences, 18200, Prague, Czechia
| | - Daniel Havelka
- Institute of Photonics and Electronics of the Czech Academy of Sciences, 18200, Prague, Czechia
| | - Martin Paidar
- Department of Inorganic Technology, Faculty of Chemical Technology, University of Chemistry and Technology, Technická 5, 160 28, Prague, Czechia
| | - Viliam Kolivoška
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, 18200, Prague, Czechia.
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, 18200, Prague, Czechia.
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2
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Kristensen LG, Gupta S, Chen Y, Petzold CJ, Ralston CY. Residue-Specific Epitope Mapping of the PD-1/Nivolumab Interaction Using X-ray Footprinting Mass Spectrometry. Antibodies (Basel) 2024; 13:77. [PMID: 39311382 PMCID: PMC11417893 DOI: 10.3390/antib13030077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 07/02/2024] [Accepted: 08/23/2024] [Indexed: 09/26/2024] Open
Abstract
X-ray footprinting coupled with mass spectrometry (XFMS) presents a novel approach in structural biology, offering insights into protein conformation and dynamics in the solution state. The interaction of the cancer-immunotherapy monoclonal antibody nivolumab with its antigen target PD-1 was used to showcase the utility of XFMS against the previously published crystal structure of the complex. Changes in side-chain solvent accessibility, as determined by the oxidative footprint of free PD-1 versus PD-1 bound to nivolumab, agree with the binding interface side-chain interactions reported from the crystal structure of the complex. The N-linked glycosylation sites of PD-1 were confirmed through an LC-MS/MS-based deglycosylation analysis of asparagine deamidation. In addition, subtle changes in side-chain solvent accessibility were observed in the C'D loop region of PD-1 upon complex formation with nivolumab.
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Affiliation(s)
- Line G. Kristensen
- Lawrence Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging Division, Berkeley, CA 94720, USA; (L.G.K.); (S.G.)
| | - Sayan Gupta
- Lawrence Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging Division, Berkeley, CA 94720, USA; (L.G.K.); (S.G.)
| | - Yan Chen
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA; (Y.C.); (C.J.P.)
| | - Christopher J. Petzold
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA 94720, USA; (Y.C.); (C.J.P.)
| | - Corie Y. Ralston
- Lawrence Berkeley National Laboratory, Molecular Foundry Division, Berkeley, CA 94720, USA
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3
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Whalin J, Wu Y, Wang Y, Suman SP, Shohet JL, Richards MP. Use of plasma induced modification of biomolecules (PLIMB) to evaluate hemin dissociation from fish and bovine methemoglobins. Food Chem 2024; 452:139576. [PMID: 38735109 DOI: 10.1016/j.foodchem.2024.139576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/26/2024] [Accepted: 05/05/2024] [Indexed: 05/14/2024]
Abstract
Hemin dissociation occurs much faster from fish methemoglobin (metHb) compared to mammalian metHb yet the mechanism remains poorly understood. This may involve enhanced solvent access to His(E7) of fish metHbs by a protonation mechanism. Plasma induced modification of biomolecules (PLIMB) produces free radicals that covalently modify solvent accessible residues of proteins, and so can provide insight regarding accessibility of hydronium ions to protonate His(E7). PLIMB-induced modifications to heme crevice sites of trout IV and bovine metHb were determined using tandem mass spectrometry after generating peptides with Trypsin/Lys-C. αHis(CE3) was more modified in trout attributable to the more dynamic nature of bovine αHis(CE3) from available crystal structures. Although His(E7) was not found to be more modified in trout, aspects of trout peptides containing His(E7) hampered modification determinations. An existing computational structure-based approach was also used to estimate protonation tendencies, suggesting His(E7) of metHbs with low hemin affinity are more protonatable.
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Affiliation(s)
- James Whalin
- University of Wisconsin-Madison, Department of Animal and Dairy Sciences, Meat Science and Animal Biologics Discovery, 1933 Observatory Dr, Madison, WI 53706, United States
| | - Yuting Wu
- University of Wisconsin-Madison, Department of Electrical and Computer Engineering, Engineering Hall, 1415 Engineering Dr, Madison, WI 53706, United States
| | - Yifei Wang
- Department of Animal and Food Sciences, University of Kentucky, Lexington, KY 40546, United States
| | - Surendranath P Suman
- Department of Animal and Food Sciences, University of Kentucky, Lexington, KY 40546, United States
| | - J Leon Shohet
- University of Wisconsin-Madison, Department of Electrical and Computer Engineering, Engineering Hall, 1415 Engineering Dr, Madison, WI 53706, United States
| | - Mark P Richards
- University of Wisconsin-Madison, Department of Animal and Dairy Sciences, Meat Science and Animal Biologics Discovery, 1933 Observatory Dr, Madison, WI 53706, United States.
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4
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Cai Y. Conjugation of primary amine groups in targeted proteomics. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39229771 DOI: 10.1002/mas.21906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/21/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024]
Abstract
Primary amines, in the form of unmodified N-terminus of peptide/protein and unmodified lysine residue, are perhaps the most important functional groups that can serve as the starting points in proteomic analysis, especially via mass spectrometry-based approaches. A variety of multifunctional probes that conjugate primary amine groups through covalent bonds have been developed and employed to facilitate protein/protein complex characterization, including identification, quantification, structure and localization elucidation, protein-protein interaction investigation, and so forth. As an integral part of more accurate peptide quantification in targeted proteomics, isobaric stable isotope-coded primary amine labeling approaches eventually facilitated protein/peptide characterization at the single-cell level, paving the way for single-cell proteomics. The development and advances in the field can be reviewed in terms of key components of a multifunctional probe: functional groups and chemistry for primary amine conjugation; hetero-bifunctional moiety for separation/enrichment of conjugated protein/protein complex; and functionalized linker/spacer. Perspectives are primarily focused on optimizing primary amine conjugation under physiological conditions to improve characterization of native proteins, especially those associated with the surface of living cells/microorganisms.
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Affiliation(s)
- Yang Cai
- Department of Chemistry, University of New Orleans, New Orleans, Louisiana, USA
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5
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Martinez M, Kiselar J, Wang B, Sadalge D, Zawadzke L, Taherbhoy A, Musser D, Davenport Y, Setser J, Chance MR, Bellon S. Mass Spectrometry-Based Protein Footprinting Defines the Binding Pocket of Crotonylated H3K14 in the PHD1 Domain of BAF45D within the BAF Chromatin Remodeling Complex. ACS BIO & MED CHEM AU 2024; 4:204-213. [PMID: 39184054 PMCID: PMC11342342 DOI: 10.1021/acsbiomedchemau.4c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 08/27/2024]
Abstract
The BRG-/BRM-associated factor (BAF) chromatin remodeling complex is a central actor in transcription. One mechanism by which BAF affects gene expression is via its various histone mark readers, including double plant homeodomains (DPF), located in the BAF45D subunit. DPF domains recognize lysine acetyl and acylations, including crotonylation, localized at promoters and enhancers. Despite a significant degree of conservation between DPF domains, attempts to crystallize BAF45D with a crotonylated histone 3 peptide (H3K14Cr) were unsuccessful. In addition, recent cryoEM and modeled structures failed to define the Req domain of BAF45D, which is responsible for reading lysine modifications. Thus, the precise mechanism of crotonyl group recognition and binding by BAF45D within the BAF complex remains unclear. We turned to protein footprinting mass spectrometry to map the binding interface between H3K14Cr and BAF45D. This technique is able to demarcate protein-binding interfaces by modifying surface-accessible residues and is not limited by protein size or composition. Experiments performed in the isolated DPF domain of BAF45D (BAF45DDPF)-delineated H3K14Cr peptide binding across the PHD1 and PHD2 pockets. We observed markedly similar effects on the BAF45D subunit when assessing H3K14Cr binding in the purified full BAF complex. The ATPase motor, BRM, also displayed H3K14Cr-protected peptides in two separate domains that were subsequently evaluated in direct binding assays. These data confirm the BAF45D-crotonylamide interaction within its obligate complex and are the first to demonstrate H3K14Cr direct binding to BRM.
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Affiliation(s)
- Marissa
R. Martinez
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Janna Kiselar
- NeoProteomics, Moreland Hills, Ohio 44022, United States
- Center
for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, 10009 Euclid Ave, Cleveland, Ohio 44106, United States
| | - Benlian Wang
- Center
for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, 10009 Euclid Ave, Cleveland, Ohio 44106, United States
| | - Dipti Sadalge
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Laura Zawadzke
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Asad Taherbhoy
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Derek Musser
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Yunji Davenport
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Jeremy Setser
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
| | - Mark R. Chance
- NeoProteomics, Moreland Hills, Ohio 44022, United States
- Center
for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, 10009 Euclid Ave, Cleveland, Ohio 44106, United States
| | - Steve Bellon
- Foghorn
Therapeutics, 500 Technology Square, Suite 700, Cambridge, Massachusetts 02139, United States
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6
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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7
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He L, McAndrew R, Barbu R, Gifford G, Halacoglu C, Drouin-Allaire C, Weber L, Kristensen LG, Gupta S, Chen Y, Petzold CJ, Allaire M, Li KH, Ralston CY, Gochin M. Structure and Interactions of HIV-1 gp41 CHR-NHR Reverse Hairpin Constructs Reveal Molecular Determinants of Antiviral Activity. J Mol Biol 2024; 436:168650. [PMID: 38866091 PMCID: PMC11297672 DOI: 10.1016/j.jmb.2024.168650] [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: 03/02/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
Engineered reverse hairpin constructs containing a partial C-heptad repeat (CHR) sequence followed by a short loop and full-length N-heptad repeat (NHR) were previously shown to form trimers in solution and to be nanomolar inhibitors of HIV-1 Env mediated fusion. Their target is the in situ gp41 fusion intermediate, and they have similar potency to other previously reported NHR trimers. However, their design implies that the NHR is partially covered by CHR, which would be expected to limit potency. An exposed hydrophobic pocket in the folded structure may be sufficient to confer the observed potency, or they may exist in a partially unfolded state exposing full length NHR. Here we examined their structure by crystallography, CD and fluorescence, establishing that the proteins are folded hairpins both in crystal form and in solution. We examined unfolding in the milieu of the fusion reaction by conducting experiments in the presence of a membrane mimetic solvent and by engineering a disulfide bond into the structure to prevent partial unfolding. We further examined the role of the hydrophobic pocket, using a hairpin-small molecule adduct that occluded the pocket, as confirmed by X-ray footprinting. The results demonstrated that the NHR region nominally covered by CHR in the engineered constructs and the hydrophobic pocket region that is exposed by design were both essential for nanomolar potency and that interaction with membrane is likely to play a role in promoting the required inhibitor structure. The design concepts can be applied to other Class 1 viral fusion proteins.
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Affiliation(s)
- Li He
- Department of Foundational Biomedical Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Ryan McAndrew
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Razvan Barbu
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Grant Gifford
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Cari Halacoglu
- Master of Science in Medical Health Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA
| | - Camille Drouin-Allaire
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Lindsey Weber
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Line G Kristensen
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA
| | - Corie Y Ralston
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miriam Gochin
- Department of Foundational Biomedical Sciences, Touro University California College of Osteopathic Medicine, 1310 Club Drive, Mare Island, Vallejo, CA 94592, USA; Department of Pharmaceutical Chemistry, UCSF School of Pharmacy, San Francisco, CA 94143, USA.
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8
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Shah A, Batabyal D, Qiu D, Cui W, Harrahy J, Ivanov AR. Mapping conformational changes on bispecific antigen-binding biotherapeutic by covalent labeling and mass spectrometry. J Pharm Anal 2024; 14:100966. [PMID: 39263356 PMCID: PMC11388688 DOI: 10.1016/j.jpha.2024.100966] [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: 09/22/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 09/13/2024] Open
Abstract
Biotherapeutic's higher order structure (HOS) is a critical determinant of its functional properties and conformational relevance. Here, we evaluated two covalent labeling methods: diethylpyrocarbonate (DEPC)-labeling and fast photooxidation of proteins (FPOP), in conjunction with mass spectrometry (MS), to investigate structural modifications for the new class of immuno-oncological therapy known as bispecific antigen-binding biotherapeutics (BABB). The evaluated techniques unveiled subtle structural changes occurring at the amino acid residue level within the antigen-binding domain under both native and thermal stress conditions, which cannot be detected by conventional biophysical techniques, e.g., near-ultraviolet circular dichroism (NUV-CD). The determined variations in labeling uptake under native and stress conditions, corroborated by binding assays, shed light on the binding effect, and highlighted the potential of covalent-labeling methods to effectively monitor conformational changes that ultimately influence the product quality. Our study provides a foundation for implementing the developed techniques in elucidating the inherent structural characteristics of novel therapeutics and their conformational stability.
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Affiliation(s)
- Arnik Shah
- Amgen Inc., Cambridge, MA, 02141, USA
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
| | | | | | | | | | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115, USA
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9
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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: 7] [Impact Index Per Article: 7.0] [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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10
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Lopes FBTP, Schlatzer D, Li M, Yilmaz S, Wang R, Qi X, Ayati M, Koyutürk M, Chance MR. Methionine Sulfoxide Speciation in Mouse Hippocampus Revealed by Global Proteomics Exhibits Age- and Alzheimer's Disease-Dependent Changes Targeted to Mitochondrial and Glycolytic Pathways. Int J Mol Sci 2024; 25:6516. [PMID: 38928221 PMCID: PMC11203694 DOI: 10.3390/ijms25126516] [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: 04/30/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with non-specific chemical oxidation from reactive oxygen species (ROS), whose chemistries are linked to various disease pathologies, including neurodegeneration. Emerging evidence shows MSox site occupancy is, in some cases, under enzymatic regulatory control, mediating cellular signaling, including phosphorylation and/or calcium signaling, and raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer's and aging states. Using this model, we analyzed age-, sex-, and disease-dependent MSox speciation in the mouse hippocampus. In addition, we explored the chemical stability and statistical variance of oxidized peptide signals to understand the needed power for MSox-based proteome studies. Our results identify mitochondrial and glycolytic pathway targets with increases in MSox with age as well as neuroinflammatory targets accumulating MSox with AD in proteome studies of the mouse hippocampus. Further, this paper establishes a foundation for reproducible and rigorous experimental MSox-omics appropriate for novel target identification in biological discovery and for biomarker analysis in ROS and other oxidation-linked diseases.
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Affiliation(s)
- Filipa Blasco Tavares Pereira Lopes
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (F.B.T.P.L.); (D.S.); (M.K.)
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (F.B.T.P.L.); (D.S.); (M.K.)
| | - Mengzhen Li
- Department of Computer and Data Sciences, Case School of Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; (M.L.); (S.Y.)
| | - Serhan Yilmaz
- Department of Computer and Data Sciences, Case School of Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; (M.L.); (S.Y.)
| | - Rihua Wang
- Center for Mitochondrial Diseases, Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (R.W.); (X.Q.)
| | - Xin Qi
- Center for Mitochondrial Diseases, Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (R.W.); (X.Q.)
| | - Marzieh Ayati
- Department of Computer Science, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA;
| | - Mehmet Koyutürk
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (F.B.T.P.L.); (D.S.); (M.K.)
- Department of Computer and Data Sciences, Case School of Engineering, Case Western Reserve University, Cleveland, OH 44106, USA; (M.L.); (S.Y.)
| | - Mark R. Chance
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (F.B.T.P.L.); (D.S.); (M.K.)
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11
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Wu S, Zhu Q, Liu F, Pei C, Hong D, Zhang Y, Lai S. Multiphase reactions of proteins in the air: Oligomerization, nitration and degradation of bovine serum albumin upon ambient exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171617. [PMID: 38467257 DOI: 10.1016/j.scitotenv.2024.171617] [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: 12/30/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/13/2024]
Abstract
Proteins in atmospheric aerosol can react with atmospheric pollutants such as ozone (O3) and nitrogen dioxide (NO2) in the atmosphere via the reactions of oxidation, nitration, and cross-linking etc. Currently, the reactions have been more thoroughly studied in the laboratory but rarely investigated in the ambient environment. In this study, we used bovine serum albumin (BSA) as the model protein to conduct the exposure experiment in the ambient environment in southern China, an area with increasing oxidative capacity, to investigate the reactions of proteins in the atmosphere. We observed the occurrence of oligomerization, nitration and degradation of BSA upon exposure. The mass fraction of BSA monomer decreased by 5.86 ± 1.61% after exposure and those of dimers, trimers and higher oligomers increased by 1.04 ± 0.49%, 1.37 ± 0.74% and 3.40 ± 1.06%, respectively. Simultaneously, the nitration degrees of monomers, dimers, trimers and higher oligomers increased by 0.42 ± 0.15%, 0.53 ± 0.15%, 0.55 ± 0.28% and 2.15 ± 1.01%, respectively. The results show that oligomerization was significantly affected by O3 and temperature and nitration was jointly affected by O3, temperature and relative humidity, indicating the important role of atmospheric oxidants in the atmospheric reactions of protein. Atmospheric degradation of BSA was observed with the release of free amino acids (FAAs) such as glycine, alanine, serine and methionine. Glycine was the dominant FAA with a molar yield ranging from ∼8% to 33% for BSA. The estimated stoichiometric coefficient (α) of glycine is 10-7-10-6 for the degradation of BSA upon O3. Our observation suggests the occurrence of protein reactions in the oxidative ambient environment, leading to the production of nitrated products, oligomers and low molecular weight products such as peptides and FAAs. This study may deepen the current understanding of the atmospheric reaction mechanisms and reveal the influence of environmental factors in the atmosphere.
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Affiliation(s)
- Shiyi Wu
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Qiaoze Zhu
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
| | - Fobang Liu
- Department of Environmental Science and Engineering, Xi'an Jiaotong University, Xi'an, Shanxi 710049, China
| | - Chenglei Pei
- Guangzhou Sub-branch of Guangdong Ecological and Environmental Monitoring Center, Guangzhou 510030, China
| | - Dachi Hong
- Guangzhou Sub-branch of Guangdong Ecological and Environmental Monitoring Center, Guangzhou 510030, China
| | - Yingyi Zhang
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China.
| | - Senchao Lai
- The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, School of Environment and Energy, South China University of Technology, Guangzhou 510006, China
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12
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Zheng Z, Zeng Y, Lai K, Liao B, Li P, Tan CSH. Protein painting for structural and binding site analysis via intracellular lysine reactivity profiling with o-phthalaldehyde. Chem Sci 2024; 15:6064-6075. [PMID: 38665522 PMCID: PMC11040650 DOI: 10.1039/d4sc00032c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
The three-dimensional structure and the molecular interaction of proteins determine their roles in many cellular processes. Chemical protein painting with protein mass spectrometry can identify changes in structural conformations and molecular interactions of proteins including their binding sites. Nevertheless, most current protein painting techniques identify protein targets and binding sites of drugs in vitro using a cell lysate or purified protein. Here, we tested 11 membrane-permeable lysine-reactive chemical probes for intracellular covalent labeling of endogenous proteins, which reveals ortho-phthalaldehyde (OPA) as the most reactive probe in the intracellular environment. An MS workflow and a new data analysis strategy termed RAPID (Reactive Amino acid Profiling by Inverse Detection) was developed to enhance detection sensitivity. RAPID with OPA successfully identified structural changes induced by the allosteric drug TEPP-46 on its target protein PKM2 and was applied to profile the conformation change of the proteome occurring in cells during thermal denaturation. The application of RAPID-OPA on cells treated with geldanamycin, selumetinib, and staurosporine successfully revealed their binding sites on target proteins. Thus, RAPID-OPA for cellular protein painting enables the identification of ligand-binding sites and detection of protein structural changes occurring in cells.
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Affiliation(s)
- Zhenxiang Zheng
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Ya Zeng
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
- Department of Chemistry, Hong Kong Baptist University Kowloon Hong Kong PR China
| | - Kunjia Lai
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Bin Liao
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Pengfei Li
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
| | - Chris Soon Heng Tan
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen Guangdong 518055 PR China
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13
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Mao L, Quan Z, Liu ZS, Huang CH, Wang ZH, Tang TS, Li PL, Shao J, Liu YJ, Zhu BZ. Molecular mechanism of the metal-independent production of hydroxyl radicals by thiourea dioxide and H 2O 2. Proc Natl Acad Sci U S A 2024; 121:e2302967120. [PMID: 38547063 PMCID: PMC10998598 DOI: 10.1073/pnas.2302967120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/12/2023] [Indexed: 04/08/2024] Open
Abstract
It is well-known that highly reactive hydroxyl radicals (HO•) can be produced by the classic Fenton system and our recently discovered haloquinone/H2O2 system, but rarely from thiol-derivatives. Here, we found, unexpectedly, that HO• can be generated from H2O2 and thiourea dioxide (TUO2), a widely used and environmentally friendly bleaching agent. A carbon-centered radical and sulfite were detected and identified as the transient intermediates, and urea and sulfate as the final products, with the complementary application of electron spin-trapping, oxygen-18 isotope labeling coupled with HPLC/MS analysis. Density functional theory calculations were conducted to further elucidate the detailed pathways for HO• production. Taken together, we proposed that the molecular mechanism for HO• generation by TUO2/H2O2: TUO2 tautomerizes from sulfinic acid into ketone isomer (TUO2-K) through proton transfer, then a nucleophilic addition of H2O2 on the S atom of TUO2-K, forming a S-hydroperoxide intermediate TUO2-OOH, which dissociates homolytically to produce HO•. Our findings represent the first experimental and computational study on an unprecedented new molecular mechanism of HO• production from simple thiol-derived sulfinic acids, which may have broad chemical, environmental, and biomedical significance for future research on the application of the well-known bleaching agent and its analogs.
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Affiliation(s)
- Li Mao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Zhuo Quan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing100875, China
| | - Zhi-Sheng Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Chun-Hua Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Zi-Han Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Tian-Shu Tang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Pei-Lin Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Jie Shao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing100875, China
- Center for Advanced Materials Research, College of Chemistry, Beijing Normal University, Zhuhai519087, China
| | - Ben-Zhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing100085, China
- College of Resources and Environment, University of the Chinese Academy of Sciences, Beijing100049, China
- State Key Laboratory of Chemical Resource Engineering, Department of Environmental Science and Engineering, Beijing University of Chemical Technology, Beijing100029, China
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14
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Adhikari J, Heffernan J, Edeling M, Fernandez E, Jethva PN, Diamond MS, Fremont DH, Gross ML. Epitope Mapping of Japanese Encephalitis Virus Neutralizing Antibodies by Native Mass Spectrometry and Hydrogen/Deuterium Exchange. Biomolecules 2024; 14:374. [PMID: 38540792 PMCID: PMC10967844 DOI: 10.3390/biom14030374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 06/27/2024] Open
Abstract
Japanese encephalitis virus (JEV) remains a global public health concern due to its epidemiological distribution and the existence of multiple strains. Neutralizing antibodies against this infection have shown efficacy in in vivo studies. Thus, elucidation of the epitopes of neutralizing antibodies can aid in the design and development of effective vaccines against different strains of JEV. Here, we describe a combination of native mass spectrometry (native-MS) and hydrogen/deuterium exchange mass spectrometry (HDX-MS) to complete screening of eight mouse monoclonal antibodies (MAbs) against JEV E-DIII to identify epitope regions. Native-MS was used as a first pass to identify the antibodies that formed a complex with the target antigen, and it revealed that seven of the eight monoclonal antibodies underwent binding. Native mass spectra of a MAb (JEV-27) known to be non-binding showed broad native-MS peaks and poor signal, suggesting the protein is a mixture or that there are impurities in the sample. We followed native-MS with HDX-MS to locate the binding sites for several of the complex-forming antibodies. This combination of two mass spectrometry-based approaches should be generally applicable and particularly suitable for screening of antigen-antibody and other protein-protein interactions when other traditional approaches give unclear results or are difficult, unavailable, or need to be validated.
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Affiliation(s)
- Jagat Adhikari
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.A.); (P.N.J.)
| | - James Heffernan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
| | - Melissa Edeling
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
| | - Estefania Fernandez
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
| | - Prashant N. Jethva
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.A.); (P.N.J.)
| | - Michael S. Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63130, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63130, USA
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Daved H. Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63130, USA; (J.H.); (M.E.); (E.F.); (M.S.D.); (D.H.F.)
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63130, USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, Saint Louis, MO 63130, USA; (J.A.); (P.N.J.)
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15
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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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16
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Guo J, Fan Y, Dong X, Zeng H, Ma X, Fu Y. Study on preparation of UV-CDs/Zeolite-4A/TiO 2 composite photocatalyst coupled with ultraviolet-irradiation and their application of photocatalytic degradation of dyes. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 354:120342. [PMID: 38382431 DOI: 10.1016/j.jenvman.2024.120342] [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: 10/11/2023] [Revised: 01/11/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024]
Abstract
In this work, ultraviolet irradiation was employed to assist in the preparation of a novel photocatalyst composite in the form of carbon dots/zeolite-4A/TiO2, using coal tailings as the source of silicon-aluminum and carbon. The composite was designed for the degradation of methylene blue under 500 W of UV light irradiation. Zeolite-4A was used as a support for the well-dispersed carbon dots and TiO2 nanoparticles. The as-prepared composites were subjected to thorough characterization, confirming the successful formation of zeolite-4A with a cube structure, along with the loading of TiO2 and coal-based CDs in the composites. The experimental results demonstrated that the UV-CZTs nanocomposites exhibited a remarkable removal efficiency of 90.63% within 90 min for MB. The corresponding rate constant was exceptionally high at 0.0331 min-1, surpassing that of the Dark-CZTs and pure TiO2. This significant enhancement was possibly due to the synergistic effect of adsorption photocatalysis of the UV-CZTs, combined with the excellent electron-accepting capabilities of the coal-based CDs, which led to highly improved charge separation. An investigation of the spent photocatalyst's recyclability revealed that it retained a remarkable 82.94% MB removal efficiency after five consecutive cycles, signifying the stability of the composite. Trapping experiments also elucidated the primary reactive species responsible for MB degradation, which were identified as photo-generated holes and ⸱O2- species. By this process, the hydroxyl radicals generated in the system successfully promoted the transformation of coal tailings to coal-based zeolite and coal-based CDs. Coal-based zeolite served as an excellent carrier of titanium dioxide, which improved its dispersibility. The inhibition of e--h+ recombination of titanium dioxide by introducing coal-based CDs improved the photocatalytic ability of titanium dioxide. Through this study, coal tailings, as a coal processing waste, were transformed into high-value materials, and relevant photocatalytic composite materials could be prepared with broad application prospects.
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Affiliation(s)
- Jiaqi Guo
- College of Mining Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China; Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada
| | - Yuping Fan
- College of Mining Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
| | - Xianshu Dong
- College of Mining Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China.
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada.
| | - Xiaomin Ma
- College of Mining Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
| | - Yuanpeng Fu
- College of Mining Engineering, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
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17
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Liu SH, Dong ZC, Zang ZL, Zhou CH, Cai GX. Selective α-oxidation of amides via visible-light-driven iron catalysis. Org Biomol Chem 2024; 22:1205-1212. [PMID: 38224270 DOI: 10.1039/d3ob01984e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Hydroxyl radicals (˙OH) as one of the highly reactive species can react unselectively with a wide range of chemicals. The ˙OH radicals are typically generated under harsh conditions. Herein, we report hydroxyl radical-induced selective N-α C(sp3)-H bond oxidation of amides under greener and mild conditions via an Fe(NO3)3·9H2O catalyst inner sphere pathway upon irradiation with a 30 W blue LED light strip (λ = 455 nm) using NaBrO3 as the oxidant. This protocol exhibited high chemoselectivity and excellent functional group tolerance. A preliminary mechanism investigation demonstrated that the iron catalyst afforded hydroxyl radicals via the visible-light-induced homolysis (VLIH) of iron complexes followed by a hydrogen atom transfer (HAT) process to realize this transformation.
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Affiliation(s)
- Shu-Hong Liu
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Zhi-Chao Dong
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Zhong-Lin Zang
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
| | - Gui-Xin Cai
- Institute of Bioorganic & Medicinal Chemistry, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China.
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18
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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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19
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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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20
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Gao Y, Wang P, Chu Y, Kang F, Cheng Y, Repo E, Feng M, Yu X, Zeng H. Redox property of coordinated iron ion enables activation of O 2 via in-situ generated H 2O 2 and additionally added H 2O 2 in EDTA-chelated Fenton reaction. WATER RESEARCH 2024; 248:120826. [PMID: 37976952 DOI: 10.1016/j.watres.2023.120826] [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: 07/05/2023] [Revised: 10/20/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
The Fenton system was a generation system of reactive oxygen species via the chain reactions, which employed H2O2 and O2 as radical precursors and Fe2+/Fe3+ as electron-donor/acceptor for triggering or terminating the generation of radicals. Recent work mainly emphasized the Fe2+- activated H2O2 and the application of in-situ generated •OH, while neglecting other side-reactions. In this work, EDTA (Ethylene diamine tetraacetic acid) was employed as a chelating agent of iron ions, which simultaneously changed the redox property of coordinated iron. The Fe2+-EDTA complexes in the presence of dissolved oxygen enabled the two-electron transfer from Fe2+ to O2 and the in-situ production of H2O2, which further activate H2O2 for yielding •OH. Meanwhile, coordinated Fe3+ exhibited non-negligible reactivity toward H2O2, which was higher than that of free Fe3+ in the traditional Fenton system. The complexation of EDTA with Fe3+ could enhance the Fe2+ generation reaction by the H2O2, accompanied by the O2•- formation. The enhancement of O2•- formation and Fe2+-EDTA regeneration induced the subsequent H2O2 activation by Fe2+-EDTA, thus accelerating the Fe3+-EDTA/Fe2+-EDTA cycle for simultaneously producing O2•- and •OH. To sum up, the EDTA-chelated Fenton system extended the applicable pH range to circumneutral/alkaline level and tuned the redox property of coordinated iron for diversifying the •OH production routes. The research reinterpreted the chain reactions in the Fenton system, revealing another way to enhance the radical production or other property of the Fenton/Fenton-like system.
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Affiliation(s)
- Yuan Gao
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Pengyi Wang
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Yu Chu
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Fan Kang
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Yue Cheng
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China
| | - Eveliina Repo
- Department of Separation Science, School of Engineering Science, Lappeenranta-Lahti University of Technology (LUT), Lappeenranta FI-53850, Finland
| | - Mingbao Feng
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361102, PR China
| | - Xin Yu
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361102, PR China
| | - Huabin Zeng
- College of the Environment & Ecology, Xiamen University, Xiamen 361102, PR China; Fujian Key Laboratory of Coastal Pollution Prevention and Control, Xiamen University, Xiamen 361102, PR China.
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21
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Rezaei M, Ghasemitarei M, Razzokov J, Yusupov M, Ghorbanalilu M, Ejtehadi MR. In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel. Arch Biochem Biophys 2024; 751:109835. [PMID: 38000492 DOI: 10.1016/j.abb.2023.109835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 ± 0.7 kJ mol-1 and 10.8 ± 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake.
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Affiliation(s)
- Mahsa Rezaei
- Department of Physics, Shahid Beheshti University, Tehran, 19839-69411, Iran
| | - Maryam Ghasemitarei
- Department of Physics, Sharif University of Technology, 14588-89694, Tehran, Iran; Research Group PLASMANT, Department of Chemistry, University of Antwerp, 2610, Antwerp, Belgium.
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, 100000, Tashkent, Uzbekistan; School of Engineering, Central Asian University, Tashkent, 111221, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, 100174, Tashkent, Uzbekistan; Department of Chemistry, Termez State University, 190111, Termez, Uzbekistan
| | - Maksudbek Yusupov
- School of Engineering, New Uzbekistan University, 100000, Tashkent, Uzbekistan; Department of Information Technologies, Tashkent International University of Education, 100207, Tashkent, Uzbekistan; Laboratory of Thermal Physics of Multiphase Systems, Arifov Institute of Ion-Plasma and Laser Technologies, Academy of Sciences of Uzbekistan, 100125, Tashkent, Uzbekistan; Department of Power Supply and Renewable Energy Sources, National Research University TIIAME, 100000, Tashkent, Uzbekistan
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22
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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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23
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Gupta S, Inman JL, De Chant J, Obst-Huebl L, Nakamura K, Costello SM, Marqusee S, Mao JH, Kunz L, Paisley R, Vozenin MC, Snijders AM, Ralston CY. A Novel Platform for Evaluating Dose Rate Effects on Oxidative Damage to Peptides: Toward a High-Throughput Method to Characterize the Mechanisms Underlying the FLASH Effect. Radiat Res 2023; 200:523-530. [PMID: 38014573 PMCID: PMC10754258 DOI: 10.1667/rade-23-00131.1] [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: 07/06/2023] [Accepted: 10/05/2023] [Indexed: 11/29/2023]
Abstract
High dose rate radiation has gained considerable interest recently as a possible avenue for increasing the therapeutic window in cancer radiation treatment. The sparing of healthy tissue at high dose rates relative to conventional dose rates, while maintaining tumor control, has been termed the FLASH effect. Although the effect has been validated in animal models using multiple radiation sources, it is not yet well understood. Here, we demonstrate a new experimental platform for quantifying oxidative damage to protein sidechains in solution as a function of radiation dose rate and oxygen availability using liquid chromatography mass spectrometry. Using this reductionist approach, we show that for both X-ray and electron sources, isolated peptides in solution are oxidatively modified to different extents as a function of both dose rate and oxygen availability. Our method provides an experimental platform for exploring the parameter space of the dose rate effect on oxidative changes to proteins in solution.
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Affiliation(s)
- Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Jamie L. Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Jared De Chant
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Lieselotte Obst-Huebl
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Kei Nakamura
- Accelerator Technology and Applied Physics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Shawn M. Costello
- Biophysics Graduate Program, Department of Chemistry; California Institute for Quantitative Biosciences, University of California, Berkeley, Califormia; Chan Zuckerberg Biohub, San Francisco, California
| | - Susan Marqusee
- Department of Molecular and Cell Biology, Department of Chemistry; California Institute for Quantitative Biosciences, University of California, Berkeley, Califormia; Chan Zuckerberg Biohub, San Francisco, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Louis Kunz
- University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ryan Paisley
- University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
| | - Corie Y. Ralston
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720
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24
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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25
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Rojas Ramírez C, Espino JA, Jones LM, Polasky DA, Nesvizhskii AI. Efficient Analysis of Proteome-Wide FPOP Data by FragPipe. Anal Chem 2023; 95:16131-16137. [PMID: 37878603 DOI: 10.1021/acs.analchem.3c02388] [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] [Indexed: 10/27/2023]
Abstract
Monitoring protein structure before and after environmental alterations (e.g., different cell states) can give insights into the role and function of proteins. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry (MS) allows for monitoring of structural rearrangements by exposing proteins to OH radicals that oxidize solvent-accessible residues, indicating protein regions undergoing movement. Some of the benefits of FPOP include high throughput and a lack of scrambling due to label irreversibility. However, the challenges of processing FPOP data have thus far limited its proteome-scale uses. Here, we present a computational workflow for fast and sensitive analysis of FPOP data sets. Our workflow, implemented as part of the FragPipe computational platform, combines the speed of the MSFragger search with a unique hybrid search method to restrict the large search space of FPOP modifications. Together, these features enable more than 10-fold faster FPOP searches that identify 150% more modified peptide spectra than previous methods. We hope this new workflow will increase the accessibility of FPOP to enable more protein structure and function relationships to be explored.
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Affiliation(s)
- Carolina Rojas Ramírez
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jessica A Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States
| | - Lisa M Jones
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, California 92093, United States
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
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26
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Liu W, Berge-Lefranc D, Chaspoul F, Slaveykova VI. Cytochrome c - silver nanoparticle interactions: Spectroscopy, thermodynamic and enzymatic activity studies. Chem Biol Interact 2023; 382:110647. [PMID: 37499996 DOI: 10.1016/j.cbi.2023.110647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023]
Abstract
Cytochrome c, an iron containing metalloprotein in the mitochondria of the cells with an oxide/redox property, plays key role in the cell apoptotic pathway. In this study, the interaction of silver nanoparticles (AgNPs) with cytochrome c (Cyt c) was investigated by using a combination of spectroscopic, imaging and thermodynamic techniques, including dynamic light scattering (DLS), ultraviolet-visible (UV-vis) spectroscopy, transmission electron microscopy (TEM), fluorescence spectroscopy, near and far circular dichroism (CD) spectroscopy, and isothermal titration calorimetry (ITC). DLS and UV-vis analysis evidenced the formation of surface complexes of Cyt c on AgNPs. The saturation of surface coverage of AgNPs was observed at 4.36 Cyt c molecules per nm2 of AgNPs. The surface complexation resulted in a promotion of the Ag dissolution overtime. The negative sign of enthalpic (ΔH) contribution suggested that electrostatic forces are indicative forces in the interaction between protein and AgNPs. Moreover, the fluorescence spectra revealed that the conformation of protein was altered around tryptophan (Trp) and tyrosine (Tyr) residues indicating the alteration of the tertiary structure of Cyt c. CD analysis evidenced that the secondary structure of Cyt c was modified under AgNPs-Cyt c interactions and the binding of Cyt c onto AgNPs resulted in remarkable structural perturbation around the active site heme, which in turn alter the protein enzymatic activity. The results of the present study contributed to a deeper insight on the mechanisms of interaction between NPs and biomacromolecules and could help establish the in vivo fate of AgNPs on cellular redox homeostasis.
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Affiliation(s)
- Wei Liu
- University of Geneva, Faculty of Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Switzerland.
| | - David Berge-Lefranc
- ICR UMR Aix Marseille Université - CNRS 7273, IMBE UMR Aix Marseille Université - CNRS - IRD - AUPV 7263, France
| | - Florence Chaspoul
- ICR UMR Aix Marseille Université - CNRS 7273, IMBE UMR Aix Marseille Université - CNRS - IRD - AUPV 7263, France
| | - Vera I Slaveykova
- University of Geneva, Faculty of Sciences, Department F.-A. Forel for Environmental and Aquatic Sciences, Switzerland
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27
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Ramírez CR, Espino JA, Jones LM, Polasky DA, Nesvizhskii AI. Efficient Analysis of Proteome-wide FPOP Data by FragPipe. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543263. [PMID: 37333157 PMCID: PMC10274679 DOI: 10.1101/2023.06.01.543263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Monitoring protein structure before and after perturbations can give insights into the role and function of proteins. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry (MS) allows monitoring of structural rearrangements by exposing proteins to OH radicals that oxidize solvent accessible residues, indicating protein regions undergoing movement. Some of the benefits of FPOP include high throughput and lack of scrambling due to label irreversibility. However, the challenges of processing FPOP data have thus far limited its proteome-scale uses. Here, we present a computational workflow for fast and sensitive analysis of FPOP datasets. Our workflow combines the speed of MSFragger search with a unique hybrid search method to restrict the large search space of FPOP modifications. Together, these features enable more than 10-fold faster FPOP searches that identify 50% more modified peptide spectra than previous methods. We hope this new workflow will increase the accessibility of FPOP to enable more protein structure and function relationships to be explored.
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Affiliation(s)
| | - Jessica Arlett Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, USA
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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28
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Son A, Kim H, Diedrich JK, Bamberger C, McClatchy DB, Yates JR. In vivo Protein Footprinting Reveals the Dynamic Conformational Changes of Proteome of Multiple Tissues in Progressing Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542496. [PMID: 37397995 PMCID: PMC10312442 DOI: 10.1101/2023.05.29.542496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Numerous studies have investigated changes in protein expression at the system level using proteomic mass spectrometry, but only recently have studies explored the structure of proteins at the proteome level. We developed covalent protein painting (CPP), a protein footprinting method that quantitatively labels exposed lysine, and have now extended the method to whole intact animals to measure surface accessibility as a surrogate of in vivo protein conformations. We investigated how protein structure and protein expression change as Alzheimer's disease (AD) progresses by conducting in vivo whole animal labeling of AD mice. This allowed us to analyze broadly protein accessibility in various organs over the course of AD. We observed that structural changes of proteins related to 'energy generation,' 'carbon metabolism,' and 'metal ion homeostasis' preceded expression changes in the brain. We found that proteins in certain pathways undergoing structural changes were significantly co-regulated in the brain, kidney, muscle, and spleen.
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29
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Ding YH, Wang XL, Li SR, Li QX, Xu TA, Zhang YT. The crosslink between the hyaluronic acid and drugs treated by reactive oxygen species produced in plasma based on the molecular dynamics simulation. Int J Biol Macromol 2023; 242:124944. [PMID: 37210061 DOI: 10.1016/j.ijbiomac.2023.124944] [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: 03/23/2023] [Revised: 04/29/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
Hyaluronic Acid (HA)-based pre-drugs can enable targeted drug delivery to cancer cells with CD44-high expressing, thus, it is essential to design an efficient, target specific drug delivery system based on HA. Plasma, as a simple and clean tool, has been widely used in the modification and crosslinking of biological materials in recent years. In this paper, we used the Reactive Molecular Dynamic (RMD) to explore the reaction between reactive oxygen species (ROS) in plasma and HA with drugs (PTX, SN-38, and DOX), in order to examine possible drug-coupled systems. The simulation results indicated the acetylamino groups in HA could be oxidized to unsaturated acyl groups, which offers the possibility of crosslinking. Three drugs also exposed the unsaturated atoms under the impact of ROS, which can cross-link directly to HA through CO and CN bonds, forming a drug coupling system with better release. This study revealed the exposure of active sites on HA and drugs by ROS impact in plasma, allowing us to study the crosslinking mechanism between HA and drugs at molecular level deeply, and also provided a new light for establishment of HA-based targeted drug delivery system.
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Affiliation(s)
- Yun-Han Ding
- School of Electrical Engineeringe, Shandong University, Jinan, Shandong Province 250061, China
| | - Xiao-Long Wang
- School of Electrical Engineeringe, Shandong University, Jinan, Shandong Province 250061, China.
| | - Shan-Rui Li
- School of Electrical Engineeringe, Shandong University, Jinan, Shandong Province 250061, China
| | - Quan-Xin Li
- The Second Hospital of Shandong University, Shandong University, Jinan, Shandong 250033, China
| | - Tian-Ao Xu
- School of Electrical Engineeringe, Shandong University, Jinan, Shandong Province 250061, China
| | - Yuan-Tao Zhang
- School of Electrical Engineeringe, Shandong University, Jinan, Shandong Province 250061, China
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30
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Yang HC, Li W, Sun J, Gross ML. Advances in Mass Spectrometry on Membrane Proteins. MEMBRANES 2023; 13:457. [PMID: 37233518 PMCID: PMC10220746 DOI: 10.3390/membranes13050457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023]
Abstract
Understanding the higher-order structure of membrane proteins (MPs), which are vital for numerous biological processes, is crucial for comprehending their function. Although several biophysical approaches have been used to study the structure of MPs, limitations exist owing to the proteins' dynamic nature and heterogeneity. Mass spectrometry (MS) is emerging as a powerful tool for investigating membrane protein structure and dynamics. Studying MPs using MS, however, must meet several challenges including the lack of stability and solubility of MPs, the complexity of the protein-membrane system, and the difficulty of digestion and detection. To meet these challenges, recent advances in MS have engendered opportunities in resolving the dynamics and structures of MP. This article reviews achievements over the past few years that enable the study of MPs by MS. We first introduce recent advances in hydrogen deuterium exchange and native mass spectrometry for MPs and then focus on those footprinting methods that report on protein structure.
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Affiliation(s)
- Hsin-Chieh Yang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Jie Sun
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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31
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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [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: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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32
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Shortt R, Wang Y, Hummon AB, Jones LM. Development of Spheroid-FPOP: An In-Cell Protein Footprinting Method for 3D Tumor Spheroids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:417-425. [PMID: 36700916 PMCID: PMC9983004 DOI: 10.1021/jasms.2c00307] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Many cancer drugs fail at treating solid epithelial tumors with hypoxia and insufficient drug penetration thought to be contributing factors to the observed chemoresistance. Owing to this, it is imperative to evaluate potential cancer drugs in conditions as close to in vivo as possible, which is not always done. To address this, we developed a mass spectrometry-based protein footprinting method for exploring the impact of hypoxia on protein in 3D colorectal cancer cells. Our group has previously extended the protein footprinting method fast photochemical oxidation of proteins (FPOP) for live cell analysis (IC-FPOP); however, this is the first application of IC-FPOP in a 3D cancer model. In this study, we perform IC-FPOP on intact spheroids (Spheroid-FPOP) using a modified version of the static platform incubator with an XY movable stage (PIXY) FPOP platform. We detected modification in each of three spheroid layers, even the hypoxic core. Pathway analysis revealed protein modifications in over 10 distinct protein pathways, including some involved in protein ubiquitination; a process modulated in cancer pathologies. These results demonstrate the feasibility of Spheroid-FPOP to be utilized as a tool to interrogate protein interactions within a native tumor microenvironment.
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Affiliation(s)
- Raquel
L. Shortt
- Department
of Pharmaceutical Sciences, University of
Maryland, Baltimore, Maryland 21201, United States
| | - Yijia Wang
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Amanda B. Hummon
- Department
of Chemistry and Biochemistry, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Lisa M. Jones
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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33
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Souris JS, Leoni L, Zhang HJ, Pan A, Tanios E, Tsai HM, Balyasnikova IV, Bissonnette M, Chen CT. X-ray Activated Nanoplatforms for Deep Tissue Photodynamic Therapy. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:673. [PMID: 36839041 PMCID: PMC9962876 DOI: 10.3390/nano13040673] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 05/10/2023]
Abstract
Photodynamic therapy (PDT), the use of light to excite photosensitive molecules whose electronic relaxation drives the production of highly cytotoxic reactive oxygen species (ROS), has proven an effective means of oncotherapy. However, its application has been severely constrained to superficial tissues and those readily accessed either endoscopically or laparoscopically, due to the intrinsic scattering and absorption of photons by intervening tissues. Recent advances in the design of nanoparticle-based X-ray scintillators and photosensitizers have enabled hybridization of these moieties into single nanocomposite particles. These nanoplatforms, when irradiated with diagnostic doses and energies of X-rays, produce large quantities of ROS and permit, for the first time, non-invasive deep tissue PDT of tumors with few of the therapeutic limitations or side effects of conventional PDT. In this review we examine the underlying principles and evolution of PDT: from its initial and still dominant use of light-activated, small molecule photosensitizers that passively accumulate in tumors, to its latest development of X-ray-activated, scintillator-photosensitizer hybrid nanoplatforms that actively target cancer biomarkers. Challenges and potential remedies for the clinical translation of these hybrid nanoplatforms and X-ray PDT are also presented.
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Affiliation(s)
- Jeffrey S. Souris
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA
- Integrated Small Animal Imaging Research Resource, Office of Shared Research Facilities, The University of Chicago, Chicago, IL 60637, USA
| | - Lara Leoni
- Integrated Small Animal Imaging Research Resource, Office of Shared Research Facilities, The University of Chicago, Chicago, IL 60637, USA
| | - Hannah J. Zhang
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA
- Integrated Small Animal Imaging Research Resource, Office of Shared Research Facilities, The University of Chicago, Chicago, IL 60637, USA
| | - Ariel Pan
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY 10065, USA
| | - Eve Tanios
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA
| | - Hsiu-Ming Tsai
- Integrated Small Animal Imaging Research Resource, Office of Shared Research Facilities, The University of Chicago, Chicago, IL 60637, USA
| | | | - Marc Bissonnette
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Chin-Tu Chen
- Department of Radiology, The University of Chicago, Chicago, IL 60637, USA
- Integrated Small Animal Imaging Research Resource, Office of Shared Research Facilities, The University of Chicago, Chicago, IL 60637, USA
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Vagkidis N, Li L, Marsh J, Chechik V. Synergy of UV light and heat in peptide degradation. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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35
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Pan X, Tran T, Kirsch ZJ, Thompson LK, Vachet RW. Diethylpyrocarbonate-Based Covalent Labeling Mass Spectrometry of Protein Interactions in a Membrane Complex System. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:82-91. [PMID: 36475668 PMCID: PMC9812933 DOI: 10.1021/jasms.2c00262] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Membrane-associated proteins are important because they mediate interactions between a cell's external and internal environment and they are often targets of therapeutics. Characterizing their structures and binding interactions, however, is challenging because they typically must be solubilized using artificial membrane systems that can make measurements difficult. Mass spectrometry (MS) is emerging as a valuable tool for studying membrane-associated proteins, and covalent labeling MS has unique potential to provide higher order structure and binding information for these proteins in complicated membrane systems. Here, we demonstrate that diethylpyrocarbonate (DEPC) can be effectively used as a labeling reagent to characterize the binding interactions between a membrane-associated protein and its binding partners in an artificial membrane system. Using chemotaxis histidine kinase (CheA) as a model system, we demonstrate that DEPC-based covalent labeling MS can provide structural and binding information about the ternary complex of CheA with two other proteins that is consistent with structural models of this membrane-associated chemoreceptor system. Despite the moderate hydrophobicity of DEPC, we find that its reactivity with proteins is not substantially influenced by the presence of the artificial membranes. However, correct structural information for this multiprotein chemoreceptor system requires measurements of DEPC labeling at multiple reagent concentrations to enable an accurate comparison between CheA and its ternary complex in the chemoreceptor system. In addition to providing structural information that is consistent with the model of this complex system, the labeling data supplements structural information that is not sufficiently refined in the chemoreceptor model.
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Affiliation(s)
- Xiao Pan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Thomas Tran
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
| | - Zachary J. Kirsch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
| | - Lynmarie K. Thompson
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, MA 01003
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36
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Gupta S, Raskatov JA, Ralston CY. A Hybrid Structural Method for Investigating Low Molecular Weight Oligomeric Structures of Amyloid Beta. Chembiochem 2022; 23:e202200333. [PMID: 35980391 PMCID: PMC9729406 DOI: 10.1002/cbic.202200333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/16/2022] [Indexed: 01/25/2023]
Abstract
Spurred in part by the failure of recent therapeutics targeting amyloid β plaques in Alzheimer's Disease (AD), attention is increasingly turning to the oligomeric forms of this peptide that form early in the aggregation process. However, while numerous amyloid β fibril structures have been characterized, primarily by NMR spectroscopy and cryo-EM, obtaining structural information on the low molecular weight forms of amyloid β that presumably precede and/or seed fibril formation has proved challenging. These transient forms are heterogeneous, and depend heavily on experimental conditions such as buffer, temperature, concentration, and degree of quiescence during measurement. Here, we present the concept for a new approach to delineating structural features of early-stage low molecular weight amyloid β oligomers, using a solvent accessibility assay in conjunction with simultaneous fluorescence measurements.
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Affiliation(s)
- Sayan Gupta
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley CA 94720 (USA)
| | - Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Physical Science Building 356, 1156 High Street, Santa Cruz, CA 95064 (USA)
| | - Corie Y. Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley CA 94720 (USA)
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37
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Bertran O, Martí D, Torras J, Turon P, Alemán C. Computer simulations on oxidative stress-induced reactions in SARS-CoV-2 spike glycoprotein: a multi-scale approach. Mol Divers 2022; 26:3143-3155. [PMID: 35179698 PMCID: PMC8854484 DOI: 10.1007/s11030-021-10373-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
Abstract
Oxidative stress, which occurs when an organism is exposed to an adverse stimulus that results in a misbalance of antioxidant and pro-oxidants species, is the common denominator of diseases considered as a risk factor for SARS-CoV-2 lethality. Indeed, reactive oxygen species caused by oxidative stress have been related to many virus pathogenicity. In this work, simulations have been performed on the receptor binding domain of SARS-CoV-2 spike glycoprotein to study what residues are more susceptible to be attacked by ·OH, which is one of the most reactive radicals associated to oxidative stress. The results indicate that isoleucine (ILE) probably plays a crucial role in modification processes driven by radicals. Accordingly, QM/MM-MD simulations have been conducted to study both the ·OH-mediated hydrogen abstraction of ILE residues and the induced modification of the resulting ILE radical through hydroxylation or nitrosylation reactions. All in all, in silico studies show the importance of the chemical environment triggered by oxidative stress on the modifications of the virus, which is expected to help for foreseeing the identification or development of antioxidants as therapeutic drugs.
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Affiliation(s)
- Oscar Bertran
- Departament de Física EETAC, Universitat Politècnica de Catalunya, c/Esteve Terrades, 7, 08860, Castelldefels, Spain.
| | - Didac Martí
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center in Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya (UPC), C/Eduard Maristany 10-14, 08019, Barcelona, Spain
| | - Juan Torras
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center in Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya (UPC), C/Eduard Maristany 10-14, 08019, Barcelona, Spain.
| | - Pau Turon
- B. Braun Surgical, S.A.U. Carretera de Terrasa 121, 08191, Rubí, Barcelona, Spain.
| | - Carlos Alemán
- Departament d'Enginyeria Química (DEQ) and Barcelona Research Center in Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya (UPC), C/Eduard Maristany 10-14, 08019, Barcelona, Spain.
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028, Barcelona, Spain.
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38
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Fluorogenic toolbox for facile detecting of hydroxyl radicals: From designing principles to diagnostics applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Akbarian M, Chen SH. Instability Challenges and Stabilization Strategies of Pharmaceutical Proteins. Pharmaceutics 2022; 14:2533. [PMID: 36432723 PMCID: PMC9699111 DOI: 10.3390/pharmaceutics14112533] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Maintaining the structure of protein and peptide drugs has become one of the most important goals of scientists in recent decades. Cold and thermal denaturation conditions, lyophilization and freeze drying, different pH conditions, concentrations, ionic strength, environmental agitation, the interaction between the surface of liquid and air as well as liquid and solid, and even the architectural structure of storage containers are among the factors that affect the stability of these therapeutic biomacromolecules. The use of genetic engineering, side-directed mutagenesis, fusion strategies, solvent engineering, the addition of various preservatives, surfactants, and additives are some of the solutions to overcome these problems. This article will discuss the types of stress that lead to instabilities of different proteins used in pharmaceutics including regulatory proteins, antibodies, and antibody-drug conjugates, and then all the methods for fighting these stresses will be reviewed. New and existing analytical methods that are used to detect the instabilities, mainly changes in their primary and higher order structures, are briefly summarized.
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Affiliation(s)
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan 701, Taiwan
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40
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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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41
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Borotto NB, Richards TK. Rapid Online Oxidation of Proteins and Peptides via Electrospray-Accelerated Ozonation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2078-2086. [PMID: 36194498 DOI: 10.1021/jasms.2c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry-based analyses of protein conformation continue to grow in utilization due their speed, low sample requirements, and applicability to most protein systems. These techniques typically rely on chemical derivatization of proteins and as with all label-based analyses must ensure the integrity of the protein conformation throughout the duration of the labeling reaction. Hydroxyl radical footprinting of proteins and the recently developed fast fluoroalkylation of proteins attempt to bypass this consideration via rapid reactions that occur on time scales faster than protein folding, but they often require microfluidic setups or electromagnetic radiation sources. In this work, we demonstrate that ozonation of proteins and peptides, which normally occurs in the second to minute time scales, can be accelerated to the submillisecond to millisecond time scale with an electrospray ionization source. This rapid ozonation results in selective labeling of tryptophan and methionine residues. When applied to cytochrome C and carbonic anhydrase, this labeling technique is sensitive to solution conditions and correlates with solution-phase analyses of conformation. While significant work is still needed to characterize this fast chemical labeling strategy, it requires no complicated sample handling, electromagnetic radiation sources, or microfluidic systems outside of the electrospray source and may represent a facile alternative to other rapid labeling technologies that are utilized today.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Nevada, 1664 N. Virginia Street, Reno, Nevada 89557, United States
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42
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Hamid M, Khalid MF, Chaudhary SU, Khan S. The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS. Int J Mol Sci 2022; 23:ijms232112771. [PMID: 36361564 PMCID: PMC9659070 DOI: 10.3390/ijms232112771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar CheY residue positions. The polar residues around and including the 57D phosphorylated site had an elevated hydroxy radical reactivity. Bioinformatic measures revealed that a water-mediated hydrogen bond network connected this ring of residues with the central 57D. These residues solvated 57D to energetically stabilize the apo-CheY fold. The abundance of these reactive residues was reduced upon activation. This result was supported by the bioinformatics and consistent with the previously reported activation-induced increase in core hydrophobicity. It further illustrated XFMS detection of structural waters. Direct contacts between the ring residues and the phosphorylation site would stabilize the aspartyl phosphate. In addition, we report that the ring residue, 18R, is a constant central node in the 57D solvation network and that 18R non-polar substitutions determine CheY diversity as assessed by its evolutionary trace in bacteria with well-studied chemotaxis. These results showcase the importance of structured water dynamics for phosphorylation-mediated signal transduction.
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Affiliation(s)
- Maham Hamid
- Biomedical Informatics and Engineering Research Laboratory (BIRL), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics and Engineering Research Laboratory (BIRL), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics and Engineering Research Laboratory (BIRL), Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
- Correspondence: (S.U.C.); (S.K.)
| | - Shahid Khan
- Syed Babar Ali School of Science & Engineering, Lahore University of Management Sciences (LUMS), Lahore 54792, Pakistan
- Molecular Biology Consortium, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence: (S.U.C.); (S.K.)
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Kielb PJ, Teutloff C, Bittl R, Gray HB, Winkler JR. Does Tyrosine Protect S. coelicolor Laccase from Oxidative Degradation or Act as an Extended Catalytic Site? J Phys Chem B 2022; 126:7943-7949. [PMID: 36191240 PMCID: PMC10231039 DOI: 10.1021/acs.jpcb.2c04835] [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] [Indexed: 11/28/2022]
Abstract
We have investigated the roles of tyrosine (Tyr) and tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by Streptomyces coelicolor laccase (SLAC). During normal enzymatic turnover in laccases, reducing equivalents are delivered to a type 1 Cu center (CuT1) and then are transferred over 13 Å to a trinuclear Cu site (TNC: (CuT3)2CuT2) where O2 reduction occurs. The TNC in SLAC is surrounded by a large cluster of Tyr and Trp residues that can provide reducing equivalents when the normal flow of electrons is disrupted. Prior studies by Canters and co-workers [J. Am. Chem. Soc. 2009, 131 (33), 11680-11682] have shown that when O2 reacts with a reduced SLAC variant lacking the CuT1 center, a Tyr108• radical near the TNC forms rapidly. We have found that the Tyr108• radical is reduced 10 times faster than CuT12+ by excess ascorbate, possibly because of radical transfer along Tyr/Trp chains.
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Affiliation(s)
- Patrycja J. Kielb
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | | | - Robert Bittl
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena CA 91125, United States
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Żyżyńska-Granica B, Mollica A, Stefanucci A, Granica S, Kleczkowska P. Comparative Study of Chemical Stability of a PK20 Opioid-Neurotensin Hybrid Peptide and Its Analogue [Ile 9]PK20-The Effect of Isomerism of a Single Amino Acid. Int J Mol Sci 2022; 23:ijms231810839. [PMID: 36142749 PMCID: PMC9500858 DOI: 10.3390/ijms231810839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 12/02/2022] Open
Abstract
Chemical stability is one of the main problems during the discovery and development of potent drugs. When ignored, it may lead to unreliable biological and pharmacokinetics data, especially regarding the degradation of products’ possible toxicity. Recently, two biologically active drug candidates were presented that combine both opioid and neurotensin pharmacophores in one entity, thus generating a hybrid compound. Importantly, these chimeras are structurally similar except for an amino acid change at position 9 of the peptide chain. In fact, isoleucine (C6H13NO2) was replaced with its isomer tert-leucine. These may further lead to various differences in hybrids’ behavior under specific conditions (temperature, UV, oxidative, acid/base environment). Therefore, the purpose of the study is to assess and compare the chemical stability of two hybrid peptides that differ in nature by way of one amino acid (tert-leucine vs. isoleucine). The obtained results indicate that, opposite to biological activity, the substitution of tert-leucine into isoleucine did not substantially influence the compound’s chemical stability. In fact, neither hydrolysis under alkaline and acidic conditions nor oxidative degradation resulted in spectacular differences between the two compounds—although the number of potential degradation products increased, particularly under acidic pH. However, such a modification significantly reduced the compound’s half-life from 204.4 h (for PK20 exposed to 1M HCl) to 117.7 h for [Ile9]PK20.
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Affiliation(s)
- Barbara Żyżyńska-Granica
- Chair and Department of Biochemistry, Faculty of Medicine, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Adriano Mollica
- Department of Pharmacy, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Azzurra Stefanucci
- Department of Pharmacy, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
| | - Sebastian Granica
- Microbiota Lab, Department of Pharmacognosy and Molecular Basis of Phytotherapy, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Patrycja Kleczkowska
- Military Institute of Hygiene and Epidemiology, 01-163 Warsaw, Poland
- Maria Sklodowska-Curie Medical Academy in Warsaw, 03-411 Warsaw, Poland
- Correspondence: ; Tel.: +48-690-888-774
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Cornwell O, Ault JR. Fast photochemical oxidation of proteins coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140829. [PMID: 35933084 DOI: 10.1016/j.bbapap.2022.140829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/17/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Fast photochemical oxidation of proteins (FPOP) is a hydroxyl radical footprinting approach whereby radicals, produced by UV laser photolysis of hydrogen peroxide, induce oxidation of amino acid side-chains. Mass Spectrometry (MS) is employed to locate and quantify the resulting irreversible, covalent oxidations to use as a surrogate for side-chain solvent accessibility. Modulation of oxidation levels under different conditions allows for the characterisation of protein conformation, dynamics and binding epitopes. FPOP has been applied to structurally diverse and biopharmaceutically relevant systems from small, monomeric aggregation-prone proteins to proteome-wide analysis of whole organisms. This review evaluates the current state of FPOP, the progress needed to address data analysis bottlenecks, particularly for residue-level analysis, and highlights significant developments of the FPOP platform that have enabled its versatility and complementarity to other structural biology techniques.
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Affiliation(s)
- Owen Cornwell
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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46
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Rosi M, Russell B, Kristensen LG, Farquhar ER, Jain R, Abel D, Sullivan M, Costello SM, Dominguez-Martin MA, Chen Y, Marqusee S, Petzold CJ, Kerfeld CA, DePonte DP, Farahmand F, Gupta S, Ralston CY. An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins. Commun Biol 2022; 5:866. [PMID: 36008591 PMCID: PMC9411504 DOI: 10.1038/s42003-022-03775-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 07/27/2022] [Indexed: 12/02/2022] Open
Abstract
X-ray radiolytic labeling uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation. High flux density beams are essential to overcome radical scavengers. However, conventional sample delivery environments, such as capillary flow, limit the use of a fully unattenuated focused broadband beam. An alternative is to use a liquid jet, and we have previously demonstrated that use of this form of sample delivery can increase labeling by tenfold at an unfocused X-ray source. Here we report the first use of a liquid jet for automated inline quantitative fluorescence dosage characterization and sample exposure at a high flux density microfocused synchrotron beamline. Our approach enables exposure times in single-digit microseconds while retaining a high level of side-chain labeling. This development significantly boosts the method’s overall effectiveness and efficiency, generates high-quality data, and opens up the arena for high throughput and ultrafast time-resolved in situ hydroxyl radical labeling. A high-speed liquid jet delivery system improves the X-ray footprinting and mass spectrometry method to label proteins for structural studies.
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Affiliation(s)
- Matthew Rosi
- Sonoma State University, Rohnert Park, Sonoma, CA, 94928, US
| | - Brandon Russell
- Sonoma State University, Rohnert Park, Sonoma, CA, 94928, US
| | - Line G Kristensen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Erik R Farquhar
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Rohit Jain
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Donald Abel
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Michael Sullivan
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Maria Agustina Dominguez-Martin
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, US.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, US.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | | | - Farid Farahmand
- Sonoma State University, Rohnert Park, Sonoma, CA, 94928, US
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US.
| | - Corie Y Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US.
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47
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Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
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Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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48
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Jain R, Dhillon NS, Farquhar ER, Wang B, Li X, Kiselar J, Chance MR. Multiplex Chemical Labeling of Amino Acids for Protein Footprinting Structure Assessment. Anal Chem 2022; 94:9819-9825. [PMID: 35763792 PMCID: PMC9983563 DOI: 10.1021/acs.analchem.2c01640] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein footprinting with mass spectrometry is an established structural biology technique for mapping solvent accessibility and assessing molecular-level interactions of proteins. In hydroxyl radical protein footprinting (HRPF), hydroxyl (OH) radicals generated by water radiolysis or other methods covalently label protein side chains. Because of the wide dynamic range of OH reactivity, not all side chains are easily detected in a single experiment. Novel reagent development and the use of radical chain reactions for labeling, including trifluoromethyl radicals, is a potential approach to normalize the labeling across a diverse set of residues. HRPF in the presence of a trifluoromethylation reagent under the right conditions could provide a "one-pot" reaction for multiplex labeling of protein side chains. Toward this goal, we have systematically evaluated amino acid labeling with the recently investigated Langlois' reagent (LR) activated by X-ray-mediated water radiolysis, followed by three different mass spectrometry methods. We compared the reactivity of CF3 and OH radical labeling for all 20 protein side chains in a competition-free environment. We found that all 20 amino acids exhibited CF3 or OH labeling in LR. Our investigations provide the evidence and knowledge set to perfect hydroxyl radical-activated trifluoromethyl chemistry as "one-pot" reaction for multiplex labeling of protein side chains to achieve higher resolution in HRPF.
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Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Nanak S. Dhillon
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Erik R. Farquhar
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Benlian Wang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Xiaolin Li
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Janna Kiselar
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Corresponding Author: Mark R. Chance - Center for Synchrotron Biosciences; Center for Proteomics and Bioinformatics; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
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49
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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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50
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Liang C, Qi PX, Garcia RA, Lee C. Molecular basis for the performance and mechanisms of methylated decolorized bovine hemoglobin flocculants. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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