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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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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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Shami AA, Misra SK, Jones LM, Sharp JS. Dimethylthiourea as a Quencher in Hydroxyl Radical Protein Footprinting Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2864-2867. [PMID: 37971787 DOI: 10.1021/jasms.3c00323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Hydroxyl radical protein footprinting (HRPF) is a mass-spectrometry-based method for studying protein structures, interactions, conformations, and folding. This method is based on the irreversible labeling of solvent-exposed amino acid side chains by hydroxyl radicals. While catalase is commonly used as a quencher after the labeling of a protein by the hydroxyl radicals to efficiently remove the remaining hydrogen peroxide, it has some disadvantages. Catalase quenching adds a relatively high amount of protein to the sample, limiting the sensitivity of the method due to dynamic range issues and causing significant issues when dealing with more complex samples. We evaluated dimethylthiourea (DMTU) as a replacement for catalase in the quenching HRPF reactions. We observed that DMTU is highly effective at quenching HRPF oxidation. DMTU does not cause the background protein issues that catalase does, resulting in an increased number of protein identifications from complex mixtures. We recommend the replacement of catalase quenching with DMTU for all HRPF experiments.
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Affiliation(s)
- Anter A Shami
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Lisa M Jones
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, Oxford, Mississippi 38677, United States
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Detection and Verification of a Key Intermediate in an Enantioselective Peptide Catalyzed Acylation Reaction. Molecules 2022; 27:molecules27196351. [PMID: 36234884 PMCID: PMC9571696 DOI: 10.3390/molecules27196351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Until now, the intermediate responsible for the acyl transfer of a highly enantioselective tetrapeptide organocatalyst for the kinetic resolution of trans-cycloalkane-1,2-diols has never been directly observed. It was proposed computationally that a π-methylhistidine moiety is acylated as an intermediate step in the catalytic cycle. In this study we set out to investigate whether we can detect and characterize this key intermediate using NMR-spectroscopy and mass spectrometry. Different mass spectrometric experiments using a nano-ElectroSpray Ionization (ESI) source and tandem MS-techniques allowed the identification of tetrapeptide acylium ions using different acylation reagents. The complexes of trans-cyclohexane-1,2-diols with the tetrapeptide were also detected. Additionally, we were able to detect acylated tetrapeptides in solution using NMR-spectroscopy and monitor the acetylation reaction of a trans-cyclohexane-1,2-diol. These findings are important steps towards the understanding of this highly enantioselective organocatalyst.
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Assortment of Frontiers in Protein Science. Int J Mol Sci 2022; 23:ijms23073685. [PMID: 35409045 PMCID: PMC8998612 DOI: 10.3390/ijms23073685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
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