1
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Han Y, Desai AA, Zupancic JM, Smith MD, Tessier PM, Ruotolo BT. Native ion mobility-mass spectrometry reveals the binding mechanisms of anti-amyloid therapeutic antibodies. Protein Sci 2024; 33:e5008. [PMID: 38723181 PMCID: PMC11081520 DOI: 10.1002/pro.5008] [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: 12/21/2023] [Revised: 04/02/2024] [Accepted: 04/13/2024] [Indexed: 05/13/2024]
Abstract
One of the most important attributes of anti-amyloid antibodies is their selective binding to oligomeric and amyloid aggregates. However, current methods of examining the binding specificities of anti-amyloid β (Aβ) antibodies have limited ability to differentiate between complexes that form between antibodies and monomeric or oligomeric Aβ species during the dynamic Aβ aggregation process. Here, we present a high-resolution native ion-mobility mass spectrometry (nIM-MS) method to investigate complexes formed between a variety of Aβ oligomers and three Aβ-specific IgGs, namely two antibodies with relatively high conformational specificity (aducanumab and A34) and one antibody with low conformational specificity (crenezumab). We found that crenezumab primarily binds Aβ monomers, while aducanumab preferentially binds Aβ monomers and dimers and A34 preferentially binds Aβ dimers, trimers, and tetrameters. Through collision induced unfolding (CIU) analysis, our data indicate that antibody stability is increased upon Aβ binding and, surprisingly, this stabilization involves the Fc region. Together, we conclude that nIM-MS and CIU enable the identification of Aβ antibody binding stoichiometries and provide important details regarding antibody binding mechanisms.
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Affiliation(s)
- Yilin Han
- Department of ChemistryUniversity of MichiganAnn ArborMichiganUSA
| | - Alec A. Desai
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Jennifer M. Zupancic
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Matthew D. Smith
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Peter M. Tessier
- Department of Chemical EngineeringUniversity of MichiganAnn ArborMichiganUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMichiganUSA
- Department of Pharmaceutical SciencesUniversity of MichiganAnn ArborMichiganUSA
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMichiganUSA
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2
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Vela‐Rodríguez C, Yang C, Alanen HI, Eki R, Abbas TA, Maksimainen MM, Glumoff T, Duman R, Wagner A, Paschal BM, Lehtiö L. Oligomerization mediated by the D2 domain of DTX3L is critical for DTX3L-PARP9 reading function of mono-ADP-ribosylated androgen receptor. Protein Sci 2024; 33:e4945. [PMID: 38511494 PMCID: PMC10955461 DOI: 10.1002/pro.4945] [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: 11/30/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Deltex proteins are a family of E3 ubiquitin ligases that encode C-terminal RING and DTC domains that mediate interactions with E2 ubiquitin-conjugating enzymes and recognize ubiquitination substrates. DTX3L is unique among the Deltex proteins based on its N-terminal domain architecture. The N-terminal D1 and D2 domains of DTX3L mediate homo-oligomerization, and the D3 domain interacts with PARP9, a protein that contains tandem macrodomains with ADP-ribose reader function. While DTX3L and PARP9 are known to heterodimerize, and assemble into a high molecular weight oligomeric complex, the nature of the oligomeric structure, including whether this contributes to the ADP-ribose reader function is unknown. Here, we report a crystal structure of the DTX3L N-terminal D2 domain and show that it forms a tetramer with, conveniently, D2 symmetry. We identified two interfaces in the structure: a major, conserved interface with a surface of 973 Å2 and a smaller one of 415 Å2. Using native mass spectrometry, we observed molecular species that correspond to monomers, dimers and tetramers of the D2 domain. Reconstitution of DTX3L knockout cells with a D1-D2 deletion mutant showed the domain is dispensable for DTX3L-PARP9 heterodimer formation, but necessary to assemble an oligomeric complex with efficient reader function for ADP-ribosylated androgen receptor. Our results suggest that homo-oligomerization of DTX3L is important for the DTX3L-PARP9 complex to read mono-ADP-ribosylation on a ligand-regulated transcription factor.
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Affiliation(s)
- Carlos Vela‐Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Chunsong Yang
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Heli I. Alanen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Rebeka Eki
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Tarek A. Abbas
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Bryce M. Paschal
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
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3
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Villacob RA, Feizi N, Beno SC, Solouki T. Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:13-30. [PMID: 38095581 DOI: 10.1021/jasms.3c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.
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Affiliation(s)
- Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Neda Feizi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sarah C Beno
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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4
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Nithya C, Kiran M, Nagarajaram HA. Hubs and Bottlenecks in Protein-Protein Interaction Networks. Methods Mol Biol 2024; 2719:227-248. [PMID: 37803121 DOI: 10.1007/978-1-0716-3461-5_13] [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] [Indexed: 10/08/2023]
Abstract
Protein-protein interaction networks (PPINs) represent the physical interactions among proteins in a cell. These interactions are critical in all cellular processes, including signal transduction, metabolic regulation, and gene expression. In PPINs, centrality measures are widely used to identify the most critical nodes. The two most commonly used centrality measures in networks are degree and betweenness centralities. Degree centrality is the number of connections a node has in the network, and betweenness centrality is the measure of the extent to which a node lies on the shortest paths between pairs of other nodes in the network. In PPINs, proteins with high degree and betweenness centrality are referred to as hubs and bottlenecks respectively. Hubs and bottlenecks are topologically and functionally essential proteins that play crucial roles in maintaining the network's structure and function. This article comprehensively reviews essential literature on hubs and bottlenecks, including their properties and functions.
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Affiliation(s)
- Chandramohan Nithya
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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5
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Paris T, Kiss A, Signor L, Lutfalla G, Blaise M, Boeri Erba E, Chaloin L, Yatime L. The IbeA protein from adherent invasive Escherichia coli is a flavoprotein sharing structural homology with FAD-dependent oxidoreductases. FEBS J 2024; 291:177-203. [PMID: 37786987 DOI: 10.1111/febs.16969] [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: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Invasion of brain endothelium protein A (IbeA) is a virulence factor specific to pathogenic Escherichia coli. Originally identified in the K1 strain causing neonatal meningitis, it was more recently found in avian pathogenic Escherichia coli (APEC) and adherent invasive Escherichia coli (AIEC). In these bacteria, IbeA facilitates host cell invasion and intracellular survival, in particular, under harsh conditions like oxidative stress. Furthermore, IbeA from AIEC contributes to intramacrophage survival and replication, thus enhancing the inflammatory response within the intestine. Therefore, this factor is a promising drug target for anti-AIEC strategies in the context of Crohn's disease. Despite such an important role, the biological function of IbeA remains largely unknown. In particular, its exact nature and cellular localization, i.e., membrane-bound invasin versus cytosolic factor, are still of debate. Here, we developed an efficient protocol for recombinant expression of IbeA under native conditions and demonstrated that IbeA from AIEC is a soluble, homodimeric flavoprotein. Using mass spectrometry and tryptophan fluorescence measurements, we further showed that IbeA preferentially binds flavin adenine dinucleotide (FAD), with an affinity in the one-hundred nanomolar range and optimal binding under reducing conditions. 3D-modeling with AlphaFold revealed that IbeA shares strong structural homology with FAD-dependent oxidoreductases. Finally, we used ligand docking, mutational analyses, and molecular dynamics simulations to identify the FAD binding pocket within IbeA and characterize possible conformational changes occurring upon ligand binding. Overall, we suggest that the role of IbeA in the survival of AIEC within host cells, notably macrophages, is linked to modulation of redox processes.
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Affiliation(s)
- Théo Paris
- LPHI, Univ. Montpellier, CNRS, INSERM, France
| | - Agneta Kiss
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Luca Signor
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
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6
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Talbot FO, Suarez CM, Nagy AM, Chen JC, Djavani-Tabrizi I, Clotea I, Jockusch RA. Robust Fluorescence Collection Module for Wide-Bore Ion Cyclotron Resonance Mass Spectrometers. Anal Chem 2023; 95:17193-17202. [PMID: 37963234 DOI: 10.1021/acs.analchem.3c01801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Mass spectrometers are at the heart of the most powerful toolboxes available to scientists when studying molecular structure, conformation, and dynamics in controlled molecular environments. Improved molecular characterization brought about by the implementation of new orthogonal methods into mass spectrometry-enabled analyses opens deeper insight into the complex interplay of forces that underlie chemistry. Here, we detail how one can add fluorescence detection to commercial ultrahigh-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers without adverse effects to its preexisting analytical tools. This advance enables measurements based on fluorescence detection, such as Förster resonance energy transfer (FRET), to be used in conjunction with other MS/MS techniques to probe the conformation and dynamics of large biomolecules, such as proteins and their complexes, in the highly controlled environment of a Penning trap.
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Affiliation(s)
- Francis O Talbot
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Cynthia M Suarez
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Andrea M Nagy
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - JoAnn C Chen
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Iden Djavani-Tabrizi
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Ioana Clotea
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Rebecca A Jockusch
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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7
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Koy C, Glocker UM, Danquah BD, Glocker MO. Native and compactly folded in-solution conformers of pepsin are revealed and distinguished by mass spectrometric ITEM-TWO analyses of gas-phase pepstatin A - pepsin complex binding strength differences. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:303-312. [PMID: 37259551 DOI: 10.1177/14690667231178999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Pepsin, because of its optimal activity at low acidic pH, has gained importance in mass spectrometric proteome research as a readily available and easy-to-handle protease. Pepsin has also been study object of protein higher-order structure analyses, but questions about how to best investigate pepsin in-solution conformers still remain. We first determined dependencies of pepsin ion charge structures on solvent pH which indicated the in-solution existence of (a) natively folded pepsin (N) which by nanoESI-MS analysis gave rise to a narrow charge state distribution with an 11-fold protonated most intense ion signal, (b) unfolded pepsin (U) with a rather broad ion charge state distribution whose highest ion signal carried 25 protons, and (c) a compactly folded pepsin conformer (C) with a narrow charge structure and a 12-fold protonated ion signal in the center of its charge state envelope. Because pepsin is a protease, unfolded pepsin became its own substrate in solution at pH 6.6 since at this pH some portion of pepsin maintained a compact/native fold which displayed enzymatic activity. Subsequent mass spectrometric ITEM-TWO analyses of pepstatin A - pepsin complex dissociation reactions in the gas phase confirmed a very strong binding of pepstatin A by natively folded pepsin (N). ITEM-TWO further revealed the existence of two compactly folded in-solution pepsin conformers (Ca and Cb) which also were able to bind pepstatin A. Binding strengths of the respective compactly folded pepsin conformer-containing complexes could be determined and apparent gas phase complex dissociation constants and reaction enthalpies differentiated these from each other and from the pepstatin A - pepsin complex which had been formed from natively folded pepsin. Thus, ITEM-TWO turned out to be well suited to pinpoint in-solution pepsin conformers by interrogating quantitative traits of pepstatin A - pepsin complexes in the gas phase.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Ursula M Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Rostock, Germany
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8
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Aptamer-functionalized capacitive biosensors. Biosens Bioelectron 2023; 224:115014. [PMID: 36628826 DOI: 10.1016/j.bios.2022.115014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/17/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022]
Abstract
The growing use of aptamers as target recognition elements in label-free biosensing necessitates corresponding transducers that can be used in relevant environments. While popular in many fields, capacitive sensors have seen relatively little, but growing use in conjunction with aptamers for sensing diverse targets. Few reports have shown physiologically relevant sensitivity in laboratory conditions and a cohesive picture on how target capture modifies the measured capacitance has been lacking. In this review, we assess the current state of the field in three areas: small molecule, protein, and cell sensing. We critically analyze the proposed hypotheses on how aptamer-target capture modifies the capacitance, as many mechanistic postulations appear to conflict between published works. As the field matures, we encourage future works to investigate individual aptamer-target interactions and to interrogate the physical mechanisms leading to measured changes in capacitance. To this point, we provide recommendations on best practices for developing aptasensors with a particular focus on considerations for biosensing in clinical settings.
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9
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Fischer S, Bürgi J, Gabay-Maskit S, Maier R, Mastalski T, Yifrach E, Obarska-Kosinska A, Rudowitz M, Erdmann R, Platta HW, Wilmanns M, Schuldiner M, Zalckvar E, Oeljeklaus S, Drepper F, Warscheid B. Phosphorylation of the receptor protein Pex5p modulates import of proteins into peroxisomes. Biol Chem 2023; 404:135-155. [PMID: 36122347 PMCID: PMC9929924 DOI: 10.1515/hsz-2022-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 11/15/2022]
Abstract
Peroxisomes are organelles with vital functions in metabolism and their dysfunction is associated with human diseases. To fulfill their multiple roles, peroxisomes import nuclear-encoded matrix proteins, most carrying a peroxisomal targeting signal (PTS) 1. The receptor Pex5p recruits PTS1-proteins for import into peroxisomes; whether and how this process is posttranslationally regulated is unknown. Here, we identify 22 phosphorylation sites of Pex5p. Yeast cells expressing phospho-mimicking Pex5p-S507/523D (Pex5p2D) show decreased import of GFP with a PTS1. We show that the binding affinity between a PTS1-protein and Pex5p2D is reduced. An in vivo analysis of the effect of the phospho-mimicking mutant on PTS1-proteins revealed that import of most, but not all, cargos is affected. The physiological effect of the phosphomimetic mutations correlates with the binding affinity of the corresponding extended PTS1-sequences. Thus, we report a novel Pex5p phosphorylation-dependent mechanism for regulating PTS1-protein import into peroxisomes. In a broader view, this suggests that posttranslational modifications can function in fine-tuning the peroxisomal protein composition and, thus, cellular metabolism.
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Affiliation(s)
- Sven Fischer
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Jérôme Bürgi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Shiran Gabay-Maskit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Renate Maier
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Thomas Mastalski
- Biochemistry of Intracellular Transport, Medical Faculty, Ruhr University Bochum, D-44780Bochum, Germany
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Agnieszka Obarska-Kosinska
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Markus Rudowitz
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, D-44780Bochum, Germany
| | - Ralf Erdmann
- Systems Biochemistry, Medical Faculty, Ruhr-University Bochum, D-44780Bochum, Germany
| | - Harald W. Platta
- Biochemistry of Intracellular Transport, Medical Faculty, Ruhr University Bochum, D-44780Bochum, Germany
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, D-22607Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246Hamburg, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Silke Oeljeklaus
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
| | - Friedel Drepper
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
| | - Bettina Warscheid
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, D-79104Freiburg, Germany
- Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, D-79104Freiburg, Germany
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10
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Kurisaki I, Suzuki M. Simulation toolkits at the molecular scale for trans-scale thermal signaling. Comput Struct Biotechnol J 2023; 21:2547-2557. [PMID: 37102156 PMCID: PMC10123322 DOI: 10.1016/j.csbj.2023.03.040] [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: 02/19/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/28/2023] Open
Abstract
Thermogenesis is a physiological activity of releasing heat that originates from intracellular biochemical reactions. Recent experimental studies discovered that externally applied heat changes intracellular signaling locally, resulting in global changes in cell morphology and signaling. Therefore, we hypothesize an inevitable contribution of thermogenesis in modulating biological system functions throughout the spatial scales from molecules to individual organisms. One key issue examining the hypothesis, namely, the "trans-scale thermal signaling," resides at the molecular scale on the amount of heat released via individual reactions and by which mechanism the heat is employed for cellular function operations. This review introduces atomistic simulation tool kits for studying the mechanisms of thermal signaling processes at the molecular scale that even state-of-the-art experimental methodologies of today are hardly accessible. We consider biological processes and biomolecules as potential heat sources in cells, such as ATP/GTP hydrolysis and multiple biopolymer complex formation and disassembly. Microscopic heat release could be related to mesoscopic processes via thermal conductivity and thermal conductance. Additionally, theoretical simulations to estimate these thermal properties in biological membranes and proteins are introduced. Finally, we envisage the future direction of this research field.
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Affiliation(s)
- Ikuo Kurisaki
- Waseda Research Institute for Science and Engineering, Waseda University, Bldg. No.55, S Tower, 4th Floor, 3–4-1 Okubo Shinjuku-ku, Tokyo 169–8555, Japan
- Corresponding authors.
| | - Madoka Suzuki
- Institute for Protein Research, Osaka University, 3–2 Yamadaoka, Suita, Osaka 565–0871, Japan
- Corresponding authors.
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11
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Shao X, Huang Y, Wang G. Microfluidic devices for protein analysis using intact and top‐down mass spectrometry. VIEW 2022. [DOI: 10.1002/viw.20220032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Xinyang Shao
- Institute for Cell Analysis Shenzhen Bay Laboratory Shenzhen China
- Biomedical Pioneering Innovation Center Peking University Beijing China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing China
| | - Yanyi Huang
- Institute for Cell Analysis Shenzhen Bay Laboratory Shenzhen China
- Biomedical Pioneering Innovation Center Peking University Beijing China
- Peking‐Tsinghua Center for Life Sciences Peking University Beijing China
- College of Chemistry and Molecular Engineering and Beijing National Laboratory for Molecular Sciences Peking University Beijing China
| | - Guanbo Wang
- Institute for Cell Analysis Shenzhen Bay Laboratory Shenzhen China
- Biomedical Pioneering Innovation Center Peking University Beijing China
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12
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Villacob RA, Egbejiogu BC, Feizi N, Hogan C, Murray KK, Solouki T. Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2215-2225. [PMID: 36346890 DOI: 10.1021/jasms.2c00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis. It was found that the protein ion gas-phase charge-state distributions were comparable for direct infusion, liquid extraction, and laser ablation experiments. Moreover, calculated average collision cross section (CCS) values from direct injection, liquid extraction, and laser ablation experiments were consistent with previously reported literature values. Additionally, an equivalent number of mobility features and conformational turnovers were identified from unfolding pathways from all three methods for all charge states of each protein analyzed in this work. The presented work suggests that laser ablation yields intact proteins (BSA, BHb, and ConA), is compatible with native mass spectrometry, and could be suitable for spatially resolved interrogation of unfolding pathways of proteins.
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Affiliation(s)
| | | | - Neda Feizi
- Baylor University, Waco, Texas 76706, United States
| | - Cole Hogan
- Baylor University, Waco, Texas 76706, United States
| | - Kermit K Murray
- Louisiana State University, Baton Rouge, Louisiana 70803, United States
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13
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Hecht ES, Obiorah EC, Liu X, Morrison L, Shion H, Lauber M. Microflow size exclusion chromatography to preserve micromolar affinity complexes and achieve subunit separations for native state mass spectrometry. J Chromatogr A 2022; 1685:463638. [DOI: 10.1016/j.chroma.2022.463638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
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14
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Spittler D, Indorato RL, Boeri Erba E, Delaforge E, Signor L, Harris SJ, Garcia-Saez I, Palencia A, Gabel F, Blackledge M, Noirclerc-Savoye M, Petosa C. Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex. Life Sci Alliance 2022; 5:5/10/e202201431. [PMID: 35995566 PMCID: PMC9396022 DOI: 10.26508/lsa.202201431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Rev mediates the nuclear export of intron-containing viral RNA transcripts and is essential for viral replication. Rev is imported into the nucleus by the host protein importin β (Impβ), but how Rev associates with Impβ is poorly understood. Here, we report biochemical, mutational, and biophysical studies of the Impβ/Rev complex. We show that Impβ binds two Rev monomers through independent binding sites, in contrast to the 1:1 binding stoichiometry observed for most Impβ cargos. Peptide scanning data and charge-reversal mutations identify the N-terminal tip of Rev helix α2 within Rev's arginine-rich motif (ARM) as a primary Impβ-binding epitope. Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos.
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Affiliation(s)
- Didier Spittler
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Rose-Laure Indorato
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elise Delaforge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Luca Signor
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Simon J Harris
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Isabel Garcia-Saez
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences, Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Marjolaine Noirclerc-Savoye
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
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15
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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16
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van Dyck JF, Burns JR, Le Huray KIP, Konijnenberg A, Howorka S, Sobott F. Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility. Nat Commun 2022; 13:3610. [PMID: 35750666 PMCID: PMC9232653 DOI: 10.1038/s41467-022-31029-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Recent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.
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Affiliation(s)
- Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium
| | - Jonathan R Burns
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK
| | - Kyle I P Le Huray
- School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Albert Konijnenberg
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium.,Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Stefan Howorka
- Department of Chemistry & Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Chemistry Department, University of Antwerp, Antwerpen, Belgium. .,School of Molecular and Cellular Biology & Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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17
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Bian X, Zhuang X, Zheng Z, Liu S, Liu Z, Song F. Unfolding and aggregation of oxidized metal-deficient superoxide dismutase and isoflavone inhibition based on ion mobility mass spectrometry and ThT fluorescence assay. Arch Biochem Biophys 2022; 727:109306. [DOI: 10.1016/j.abb.2022.109306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/02/2022]
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18
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Li W, Chaihu L, Jiang J, Wu B, Zheng X, Dai R, Tian Y, Huang Y, Wang G, Men Y. Microfluidic Platform for Time-Resolved Characterization of Protein Higher-Order Structures and Dynamics Using Top-Down Mass Spectrometry. Anal Chem 2022; 94:7520-7527. [PMID: 35584038 DOI: 10.1021/acs.analchem.2c00077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of protein higher-order structures and dynamics is essential for understanding the biological functions of proteins and revealing the underlying mechanisms. Top-down mass spectrometry (MS) accesses structural information at both the intact protein level and the peptide fragment level. Native top-down MS allows analysis of a protein complex's architecture and subunits' identity and modifications. Top-down hydrogen/deuterium exchange (HDX) MS offers high spatial resolution for conformational or binding interface analysis and enables conformer-specific characterization. A microfluidic chip can provide superior performance for front-end reactions useful for these MS workflows, such as flexibility in manipulating multiple reactant flows, integrating various functional modules, and automation. However, most microchip-MS devices are designed for bottom-up approaches or top-down proteomics. Here, we demonstrate a strategy for designing a microchip for top-down MS analysis of protein higher-order structures and dynamics. It is suitable for time-resolved native MS and HDX MS, with designs aiming for efficient ionization of intact protein complexes, flexible manipulation of multiple reactant flows, and precise control of reaction times over a broad range of flow rates on the submicroliter per minute scale. The performance of the prototype device is demonstrated by measurements of systems including monoclonal antibodies, antibody-antigen complexes, and coexisting protein conformers. This strategy may benefit elaborate structural analysis of biomacromolecules and inspire method development using the microchip-MS approach.
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Affiliation(s)
- Wen Li
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingxiao Chaihu
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.,Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Jialu Jiang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Bizhu Wu
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xuan Zheng
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Rongrong Dai
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Ye Tian
- Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yanyi Huang
- Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
| | - Guanbo Wang
- Institute of Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China.,Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
| | - Yongfan Men
- Research Center for Biomedical Optics and Molecular Imaging, Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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19
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Brue CR, Dukes MW, Masotti M, Holmgren R, Meade TJ. Functional Disruption of Gli1-DNA Recognition via a Cobalt(III) Complex. ChemMedChem 2022; 17:e202200025. [PMID: 35302712 PMCID: PMC10826845 DOI: 10.1002/cmdc.202200025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 12/29/2022]
Abstract
The aberrant activation of the Gli family of zinc finger transcription factors (ZFTFs) is associated with several types of human cancer, including medulloblastoma and basal cell carcinoma. We have reported the use of cobalt(III) Schiff-base complexes (Co(III)-sb) as potent inhibitors of ZFTFs in vivo. These complexes inhibit transcription by displacing the zinc finger domain's structural Zn(II) ion, destabilizing the alpha helix necessary for DNA recognition. Here, we describe the use of Co(III)-sb complexes for the selective inhibition of Gli1. Spectroscopic and computational studies of the Gli1 DNA binding domain found that Co(III)-sb displaced Zn(II) through direct coordination with the His residues of the Cys2 His2 Zn(II) binding site. As a result, there is a dose-dependent degradation of the alpha-helix content in the DNA binding domain of Gli1 and corresponding inhibition of consensus sequence recognition. We conclude that this strategy is well suited for the development of new and potent inhibitors of Gli1.
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Affiliation(s)
- Christopher R Brue
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Meghan W Dukes
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Meghan Masotti
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Robert Holmgren
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
| | - Thomas J Meade
- Departments of Chemistry, Molecular Biosciences, Neurobiology, and Radiology, Northwestern University, Evanston, IL, 60208-3113, USA
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20
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Assays to Estimate the Binding Affinity of Aptamers. Talanta 2022; 238:122971. [PMID: 34857318 DOI: 10.1016/j.talanta.2021.122971] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers have become coming-of-age molecular recognition elements in both diagnostic and therapeutic applications. Generated by SELEX, the 'quality control' of aptamers, which involves the validation of their binding affinity against their respective targets is pivotal to ascertain their potency prior to use in any downstream assays or applications. Several aptamers have been isolated thus far, however, the usage of inappropriate validation assays renders some of these aptamers dubitable in terms of their binding capabilities. Driven by this need, we provide an up-to-date critical review of the various strategies used to determine the aptamer-target binding affinity with the aim of providing researchers a better comprehension of the different analytical approaches in respect to the molecular properties of aptamers and their intended targets. The techniques reported have been classified as label-based techniques such as fluorescence intensity, fluorescence anisotropy, filter-binding assays, gel shift assays, ELISA; and label-free techniques such as UV-Vis spectroscopy, circular dichroism, isothermal titration calorimetry, native electrospray ionization-mass spectrometry, quartz crystal microbalance, surface plasmon resonance, NECEEM, backscattering interferometry, capillary electrophoresis, HPLC, and nanoparticle aggregation assays. Hybrid strategies combining the characteristics of both categories such as microscale thermophoresis have been also additionally emphasized. The fundamental principles, complexity, benefits, and challenges under each technique are elaborated in detail.
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21
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Weber P, Hoyas S, Halin É, Coulembier O, De Winter J, Cornil J, Gerbaux P. On the Conformation of Anionic Peptoids in the Gas Phase. Biomacromolecules 2022; 23:1138-1147. [PMID: 35041390 DOI: 10.1021/acs.biomac.1c01442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although N-(S)-phenylethyl peptoids are known to adopt helical structures in solutions, the corresponding positively charged ions lose their helical structure during the transfer from the solution to the gas phase due to the so-called charge solvation effect. We, here, considered negatively charged peptoids to investigate by ion mobility spectrometry-mass spectrometry whether the structural changes described in the positive ionization mode can be circumvented in the negative mode by a fine-tuning of the peptoid sequence, that is, by positioning the negative charge at the positive side of the helical peptoid macrodipole. N-(S)-(1-carboxy-2-phenylethyl) (Nscp) and N-(S)-phenylethyl (Nspe) were selected as the negative charge carrier and as the helix inductor, respectively. We, here, report the results of a joint theoretical and experimental study demonstrating that the structures adopted by the NspenNscp anions remain compactly folded in the gas phase for chains containing up to 10 residues, whereas no evidence of the presence of a helical structure was obtained, even if, for selected sequences and lengths, different gas phase conformations are detected.
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Affiliation(s)
- Perrine Weber
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.,Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Sébastien Hoyas
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium.,Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Émilie Halin
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Olivier Coulembier
- Laboratory of Polymeric and Composite Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis and Mass Spectrometry Laboratory, Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons, UMONS, 23 Place du Parc, 7000 Mons, Belgium
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22
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Swansiger AK, Marty MT, Prell JS. Fourier-Transform Approach for Reconstructing Macromolecular Mass Defect Profiles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:172-180. [PMID: 34913687 DOI: 10.1021/jasms.1c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
State-of-the-art native mass spectrometry (MS) methods have been developed for analysis of highly heterogeneous intact complexes and have provided much insight into the structure and properties of noncovalent assemblies that can be difficult to study using denatured proteins. These native MS methods can often be used to study even highly polydisperse membrane proteins embedded in detergent micelles, nanodiscs, and other membrane mimics. However, characterizing highly polydisperse native complexes which are also heterogeneous presents additional challenges for native MS. Macromolecular mass defect (MMD) analysis aims to characterize heterogeneous ion populations obfuscated by adduct polydispersity and reveal the distribution of "base" masses, and was recently implemented in the Bayesian analysis software UniDec. Here, we illustrate an alternative, orthogonal MMD analysis method implemented in the deconvolution program iFAMS, which takes advantage of Fourier transform (FT) to deconvolve low-resolution data with few user-input parameters and which can provide high quality results even for mass spectra with a signal-to-noise ratio of ∼5:1. Agreement between this method, which is based on frequency-domain data, and the mass-domain algorithm of UniDec provides strong evidence that both methods can accurately characterize highly polydisperse and heterogeneous ion populations. The FT algorithm is expected to be very useful in characterizing many types of analytes ranging from membrane proteins to polymer-conjugated proteins, branched polymers, and other large analytes, as well as for reconstructing isotope profiles for highly complex but still isotope-resolved mass spectra.
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Affiliation(s)
- Andrew K Swansiger
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
- Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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23
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Snyder DT, Jones BJ, Lin YF, Cooper-Shepherd DA, Hewitt D, Wildgoose J, Brown JM, Langridge JI, Wysocki VH. Surface-induced dissociation of protein complexes on a cyclic ion mobility spectrometer. Analyst 2021; 146:6861-6873. [PMID: 34632987 PMCID: PMC8574189 DOI: 10.1039/d1an01407b] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We describe the implementation of a simple three-electrode surface-induced dissociation (SID) cell on a cyclic ion mobility spectrometer (cIMS) and demonstrate the utility of multipass mobility separations for resolving multiple conformations of protein complexes generated during collision-induced and surface-induced unfolding (CIU & SIU) experiments. In addition to CIU and SIU, SID of protein complexes is readily accomplished within the native instrument software and with no additional external power supplies by entering a single SID collision energy, a simplification in user experience compared to prior implementations. A set of cyclic homomeric protein complexes and a heterohexamer with known CID and SID behavior were analyzed to investigate mass and mobility resolution improvements, the latter of which improved by 20-50% (median: 33%) compared to a linear travelling wave device. Multiple passes of intact complexes, or their SID fragments, increased the mobility resolution by an average of 15% per pass, with the racetrack effect being observed after ∼3 or 4 passes, depending on the drift time spread of the analytes. Even with modest improvements to apparent mobility resolving power, multipass experiments were particularly useful for separating conformations produced from CIU and SIU experiments. We illustrate several examples where either (1) multipass experiments revealed multiple overlapping conformations previously unobserved or obscured due to limited mobility resolution, or (2) CIU or SIU conformations that appeared 'native' in a single pass experiment were actually slightly compacted or expanded, with the change only being measurable through multipass experiments. The work conducted here, the first utilization of multipass cyclic ion mobility for CIU, SIU, and SID of protein assemblies and a demonstration of a wholly integrated SIU/SID workflow, paves the way for widespread adoption of SID technology for native mass spectrometry and also improves our understanding of gas-phase protein complex CIU and SIU conformationomes.
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Affiliation(s)
- Dalton T Snyder
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210
| | - Benjamin J Jones
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
| | - Yu-Fu Lin
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
| | | | - Darren Hewitt
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Jason Wildgoose
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - James I Langridge
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Vicki H Wysocki
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, OH, USA 43210.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA 43210.
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24
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Pääkkönen J, Penttinen L, Andberg M, Koivula A, Hakulinen N, Rouvinen J, Jänis J. Xylonolactonase from Caulobacter crescentus Is a Mononuclear Nonheme Iron Hydrolase. Biochemistry 2021; 60:3046-3049. [PMID: 34633186 PMCID: PMC8529709 DOI: 10.1021/acs.biochem.1c00249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Caulobacter crescentus xylonolactonase (Cc XylC, EC 3.1.1.68) catalyzes an intramolecular ester bond hydrolysis over a nonenzymatic acid/base catalysis. Cc XylC is a member of the SMP30 protein family, whose members have previously been reported to be active in the presence of bivalent metal ions, such as Ca2+, Zn2+, and Mg2+. By native mass spectrometry, we studied the binding of several bivalent metal ions to Cc XylC and observed that it binds only one of them, namely, the Fe2+ cation, specifically and with a high affinity (Kd = 0.5 μM), pointing out that Cc XylC is a mononuclear iron protein. We propose that bivalent metal cations also promote the reaction nonenzymatically by stabilizing a short-lived bicyclic intermediate on the lactone isomerization reaction. An analysis of the reaction kinetics showed that Cc XylC complexed with Fe2+ can speed up the hydrolysis of d-xylono-1,4-lactone by 100-fold and that of d-glucono-1,5-lactone by 10-fold as compared to the nonenzymatic reaction. To our knowledge, this is the first discovery of a nonheme mononuclear iron-binding enzyme that catalyzes an ester bond hydrolysis reaction.
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Affiliation(s)
- Johan Pääkkönen
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Leena Penttinen
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Martina Andberg
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Anu Koivula
- VTT Technical Research Centre of Finland Ltd, P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Juha Rouvinen
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
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25
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Koy C, Opuni KFM, Danquah BD, Neamtu A, Glocker MO. Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions. Int J Mol Sci 2021; 22:ijms221910183. [PMID: 34638522 PMCID: PMC8508491 DOI: 10.3390/ijms221910183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022] Open
Abstract
We investigated the influence of a solvent’s composition on the stability of desorbed and multiply charged RNAse S ions by analyzing the non-covalent complex’s gas-phase dissociation processes. RNAse S was dissolved in electrospray ionization-compatible buffers with either increasing organic co-solvent content or different pHs. The direct transition of all the ions and the evaporation of the solvent from all the in-solution components of RNAse S under the respective in-solution conditions by electrospray ionization was followed by a collision-induced dissociation of the surviving non-covalent RNAse S complex ions. Both types of changes of solvent conditions yielded in mass spectrometrically observable differences of the in-solution complexation equilibria. Through quantitative analysis of the dissociation products, i.e., from normalized ion abundances of RNAse S, S-protein, and S-peptide, the apparent kinetic and apparent thermodynamic gas-phase complex properties were deduced. From the experimental data, it is concluded that the stability of RNAse S in the gas phase is independent of its in-solution equilibrium but is sensitive to the complexes’ gas-phase charge states. Bio-computational in-silico studies showed that after desolvation and ionization by electrospray, the remaining binding forces kept the S-peptide and S-protein together in the gas phase predominantly by polar interactions, which indirectly stabilized the in-bulk solution predominating non-polar intermolecular interactions. As polar interactions are sensitive to in-solution protonation, bio-computational results provide an explanation of quantitative experimental data with single amino acid residue resolution.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
| | - Kwabena F. M. Opuni
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, P.O. Box LG43, Legon, Ghana
| | - Bright D. Danquah
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
| | - Andrei Neamtu
- Department of Physiology, Grigore T. Popa University of Medicine and Pharmacy of Iasi, Str. Universitatii nr. 16, 700051 Iasi, Romania;
| | - Michael O. Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Schillingallee 69, 18057 Rostock, Germany; (C.K.); (K.F.M.O.); (B.D.D.)
- Correspondence: ; Tel.: +49-381-494-4930; Fax: +49-381-494-4932
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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27
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Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
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Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
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28
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Daems E, Moro G, Campos R, De Wael K. Mapping the gaps in chemical analysis for the characterisation of aptamer-target interactions. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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29
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Santos IC, Brodbelt JS. Structural Characterization of Carbonic Anhydrase-Arylsulfonamide Complexes Using Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1370-1379. [PMID: 33683877 PMCID: PMC8377746 DOI: 10.1021/jasms.1c00004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Numerous mass spectrometry-based strategies ranging from hydrogen-deuterium exchange to ion mobility to native mass spectrometry have been developed to advance biophysical and structural characterization of protein conformations and determination of protein-ligand interactions. In this study, we focus on the use of ultraviolet photodissociation (UVPD) to examine the structure of human carbonic anhydrase II (hCAII) and its interactions with arylsulfonamide inhibitors. Carbonic anhydrase, which catalyzes the conversion of carbon dioxide to bicarbonate, has been the target of countless thermodynamic and kinetic studies owing to its well-characterized active site, binding cavity, and mechanism of inhibition by hundreds of ligands. Here, we showcase the application of UVPD for evaluating structural changes of hCAII upon ligand binding on the basis of variations in fragmentation of hCAII versus hCAII-arylsulfonamide complexes, particularly focusing on the hydrophobic pocket. To extend the coverage in the midregion of the protein sequence, a supercharging agent was added to the solutions to increase the charge states of the complexes. The three arylsulfonamides examined in this study largely shift the fragmentation patterns in similar ways, despite their differences in binding affinities.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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30
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Cheng Z, Mobley C, Misra SK, Gadepalli RS, Hammond RI, Brown LS, Rimoldi JM, Sharp JS. Self-Organized Amphiphiles Are Poor Hydroxyl Radical Scavengers in Fast Photochemical Oxidation of Proteins Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1155-1161. [PMID: 33881849 PMCID: PMC8790760 DOI: 10.1021/jasms.0c00457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Analysis of membrane protein topography using fast photochemical oxidation of proteins (FPOP) has been reported in recent years but is still underrepresented in literature. Based on the hydroxyl radical reactivity of lipids and other amphiphiles, it is believed that the membrane environment acts as a hydroxyl radical scavenger decreasing effective hydroxyl radical doses and resulting in less observed oxidation of proteins. We found no significant change in bulk solvent radical scavenging activity upon the addition of disrupted cellular membranes up to 25600 cells/μL using an inline radical dosimeter. We confirmed the nonscavenging nature of the membrane in bulk solution with the FPOP results of a soluble model protein in the presence of cell membranes, which showed no significant difference in oxidation with or without membranes. The use of detergents revealed that, while soluble detergent below the critical micelle concentration is a potent hydroxyl radical scavenger, additional detergent has little to no hydroxyl radical scavenging effect once the critical micelle concentration is reached. Examination of both an extracellular peptide of the integral membrane protein bacteriorhodopsin as well as a novel hydroxyl radical dosimeter tethered to a Triton X-series amphiphile indicate that proximity to the membrane surface greatly decreases reaction with hydroxyl radicals, even though the oxidation target is equally solvent accessible. These results suggest that the observed reduced oxidation of solvent-accessible surfaces of integral membrane proteins is due to the high local concentration of radical scavengers in the membrane or membrane mimetics competing for the local concentration of hydroxyl radicals.
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Affiliation(s)
- Zhi Cheng
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Charles Mobley
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Sandeep K. Misra
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Rama S. Gadepalli
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Rachel I. Hammond
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Leonid S. Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - John M. Rimoldi
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Joshua S. Sharp
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677
- GenNext Technologies, Inc. Half Moon Bay, CA 94019
- Correspondence to
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31
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Daems E, Moro G, Berghmans H, Moretto LM, Dewilde S, Angelini A, Sobott F, De Wael K. Native mass spectrometry for the design and selection of protein bioreceptors for perfluorinated compounds. Analyst 2021; 146:2065-2073. [PMID: 33538714 DOI: 10.1039/d0an02005b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biosensing platforms are answering the increasing demand for analytical tools for environmental monitoring of small molecules, such as per- and polyfluoroalkyl substances (PFAS). By transferring toxicological findings in bioreceptor design we can develop innovative pathways for biosensor design. Indeed, toxicological studies provide fundamental information about PFAS-biomolecule complexes that can help evaluate the applicability of the latter as bioreceptors. The toolbox of native mass spectrometry (MS) can support this evaluation, as shown by the two case studies reported in this work. The analysis of model proteins' (i.e. albumin, haemoglobin, cytochrome c and neuroglobin) interactions with well-known PFAS, such as perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), demonstrated the potential of this native MS screening approach. In the first case study, untreated albumin and delipidated albumin were compared in the presence and absence of PFOA confirming that the delipidation step increases albumin affinity for PFOA without affecting protein stability. In the second case study, the applicability of our methodology to identify potential bioreceptors for PFOS/PFOA was extended to other proteins. Structurally related haemoglobin and neuroglobin revealed a 1 : 1 complex, whereas no binding was observed for cytochrome c. These studies have value as a proof-of-concept for a general application of native MS to identify bioreceptors for toxic compounds.
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Affiliation(s)
- Elise Daems
- AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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32
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Tiwari P, Czar MF, Zenobi R. Fluorescence-Based Detection of the Desolvation Process of Protein Ions Generated in an Aqueous Electrospray Plume. Anal Chem 2021; 93:3635-3642. [PMID: 33557519 DOI: 10.1021/acs.analchem.0c05396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new experimental setup to study laser-induced fluorescence from analytes at different locations in an electrospray plume has been developed. The high fluorescence collection efficiency (∼2%) of the setup, along with a sensitive charge coupled device (CCD) detector, enabled the study of low ion concentrations (down to ∼fM) in the plume. The use of small electrospray tip inner diameters (<1 μm) facilitated the fast desolvation of gaseous protein ions in an aqueous electrospray plume. Fluorescence spectra were acquired from specific locations along the plume axis in different aqueous electrospray plumes with three different analytes: a rhodamine dye and two proteins (ubiquitin and apomyoglobin) labeled with rhodamine dyes. To confirm the presence of gaseous ions, pure gas-phase fluorescence spectra were acquired in the vacuum of a modified ion trap mass spectrometer. These spectra were used to fit to confirm the presence of gaseous species in the corresponding spectra obtained from the electrospray plume. This study shows that with small inner diameter spray capillaries, gaseous protein ions generated at atmospheric pressure in an electrospray plume can be detected with fluorescence-based techniques. Fluorescence measurements can be used to study their structure in the electrospray plume, and the dynamics as they transition from solution to the gas phase and in the early stages after desolvation from charged droplets. Other techniques can also be applied to further study gaseous biomolecular structures under ambient conditions immediately after desolvation.
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Affiliation(s)
- Prince Tiwari
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093Zürich, Switzerland
| | - Martin F Czar
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, 8093Zürich, Switzerland
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33
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Development of a target identification approach using native mass spectrometry. Sci Rep 2021; 11:2387. [PMID: 33504855 PMCID: PMC7840913 DOI: 10.1038/s41598-021-81859-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/07/2021] [Indexed: 02/06/2023] Open
Abstract
A key step in the development of new pharmaceutical drugs is the identification of the molecular target and distinguishing this from all other gene products that respond indirectly to the drug. Target identification remains a crucial process and a current bottleneck for advancing hits through the discovery pipeline. Here we report a method, that takes advantage of the specific detection of protein-ligand complexes by native mass spectrometry (MS) to probe the protein partner of a ligand in an untargeted method. The key advantage is that it uses unmodified small molecules for binding and, thereby, it does not require labelled ligands and is not limited by the chemistry required to tag the molecule. We demonstrate the use of native MS to identify known ligand-protein interactions in a protein mixture under various experimental conditions. A protein-ligand complex was successfully detected between parthenolide and thioredoxin (PfTrx) in a five-protein mixture, as well as when parthenolide was mixed in a bacterial cell lysate spiked with PfTrx. We provide preliminary data that native MS could be used to identify binding targets for any small molecule.
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34
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Favier A, Gans P, Boeri Erba E, Signor L, Muthukumar SS, Pfannschmidt T, Blanvillain R, Cobessi D. The Plastid-Encoded RNA Polymerase-Associated Protein PAP9 Is a Superoxide Dismutase With Unusual Structural Features. FRONTIERS IN PLANT SCIENCE 2021; 12:668897. [PMID: 34276730 PMCID: PMC8278866 DOI: 10.3389/fpls.2021.668897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/28/2021] [Indexed: 05/09/2023]
Abstract
In Angiosperms, the plastid-encoded RNA polymerase (PEP) is a multimeric enzyme, essential for the proper expression of the plastid genome during chloroplast biogenesis. It is especially required for the light initiated expression of photosynthesis genes and the subsequent build-up of the photosynthetic apparatus. The PEP complex is composed of a prokaryotic-type core of four plastid-encoded subunits and 12 nuclear-encoded PEP-associated proteins (PAPs). Among them, there are two iron superoxide dismutases, FSD2/PAP9 and FSD3/PAP4. Superoxide dismutases usually are soluble enzymes not bound into larger protein complexes. To investigate this unusual feature, we characterized PAP9 using molecular genetics, fluorescence microscopy, mass spectrometry, X-ray diffraction, and solution-state NMR. Despite the presence of a predicted nuclear localization signal within the sequence of the predicted chloroplast transit peptide, PAP9 was mainly observed within plastids. Mass spectrometry experiments with the recombinant Arabidopsis PAP9 suggested that monomers and dimers of PAP9 could be associated to the PEP complex. In crystals, PAP9 occurred as a dimeric enzyme that displayed a similar fold to that of the FeSODs or manganese SOD (MnSODs). A zinc ion, instead of the expected iron, was found to be penta-coordinated with a trigonal-bipyramidal geometry in the catalytic center of the recombinant protein. The metal coordination involves a water molecule and highly conserved residues in FeSODs. Solution-state NMR and DOSY experiments revealed an unfolded C-terminal 34 amino-acid stretch in the stand-alone protein and few internal residues interacting with the rest of the protein. We hypothesize that this C-terminal extension had appeared during evolution as a distinct feature of the FSD2/PAP9 targeting it to the PEP complex. Close vicinity to the transcriptional apparatus may allow for the protection against the strongly oxidizing aerial environment during plant conquering of terrestrial habitats.
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Affiliation(s)
- Adrien Favier
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Pierre Gans
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | - Luca Signor
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | | | | | - Robert Blanvillain
- Université Grenoble-Alpes, CNRS, CEA, INRA, IRIG-LPCV, Grenoble, France
- *Correspondence: Robert Blanvillain,
| | - David Cobessi
- Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
- David Cobessi,
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35
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Divalent cations influence the dimerization mode of murine S100A9 protein by modulating its disulfide bond pattern. J Struct Biol 2020; 213:107689. [PMID: 33359632 DOI: 10.1016/j.jsb.2020.107689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022]
Abstract
S100A9, with its congener S100A8, belongs to the S100 family of calcium-binding proteins found exclusively in vertebrates. These two proteins are major constituents of neutrophils. In response to a pathological condition, they can be released extracellularly and become alarmins that induce both pro- and anti-inflammatory signals, through specific cell surface receptors. They also act as antimicrobial agents, mainly as a S100A8/A9 heterocomplex, through metal sequestration. The mechanisms whereby divalent cations modulate the extracellular functions of S100A8 and S100A9 are still unclear. Importantly, it has been proposed that these ions may affect both the ternary and quaternary structure of these proteins, thereby influencing their physiological properties. In the present study, we report the crystal structures of WT and C80A murine S100A9 (mS100A9), determined at 1.45 and 2.35 Å resolution, respectively, in the presence of calcium and zinc. These structures reveal a canonical homodimeric form for the protein. They also unravel an intramolecular disulfide bridge that stabilizes the C-terminal tail in a rigid conformation, thus shaping a second Zn-binding site per S100A9 protomer. In solution, mS100A9 apparently binds only two zinc ions per homodimer, with an affinity in the micromolar range, and aggregates in the presence of excess zinc. Using mass spectrometry, we demonstrate that mS100A9 can form both non-covalent and covalent homodimers with distinct disulfide bond patterns. Interestingly, calcium and zinc seem to affect differentially the relative proportion of these forms. We discuss how the metal-dependent interconversion between mS100A9 homodimers may explain the versatility of physiological functions attributed to the protein.
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36
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Drepper F, Biernat J, Kaniyappan S, Meyer HE, Mandelkow EM, Warscheid B, Mandelkow E. A combinatorial native MS and LC-MS/MS approach reveals high intrinsic phosphorylation of human Tau but minimal levels of other key modifications. J Biol Chem 2020; 295:18213-18225. [PMID: 33106314 PMCID: PMC7939451 DOI: 10.1074/jbc.ra120.015882] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/21/2020] [Indexed: 12/22/2022] Open
Abstract
Abnormal changes of neuronal Tau protein, such as phosphorylation and aggregation, are considered hallmarks of cognitive deficits in Alzheimer's disease. Abnormal phosphorylation is thought to precede aggregation and therefore to promote aggregation, but the nature and extent of phosphorylation remain ill-defined. Tau contains ∼85 potential phosphorylation sites, which can be phosphorylated by various kinases because the unfolded structure of Tau makes them accessible. However, methodological limitations (e.g. in MS of phosphopeptides, or antibodies against phosphoepitopes) led to conflicting results regarding the extent of Tau phosphorylation in cells. Here we present results from a new approach based on native MS of intact Tau expressed in eukaryotic cells (Sf9). The extent of phosphorylation is heterogeneous, up to ∼20 phosphates per molecule distributed over 51 sites. The medium phosphorylated fraction Pm showed overall occupancies of ∼8 Pi (± 5) with a bell-shaped distribution; the highly phosphorylated fraction Ph had 14 Pi (± 6). The distribution of sites was highly asymmetric (with 71% of all P-sites in the C-terminal half of Tau). All sites were on Ser or Thr residues, but none were on Tyr. Other known posttranslational modifications were near or below our detection limit (e.g. acetylation, ubiquitination). These findings suggest that normal cellular Tau shows a remarkably high extent of phosphorylation, whereas other modifications are nearly absent. This implies that abnormal phosphorylations at certain sites may not affect the extent of phosphorylation significantly and do not represent hyperphosphorylation. By implication, the pathological aggregation of Tau is not likely a consequence of high phosphorylation.
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Affiliation(s)
- Friedel Drepper
- Group of Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Jacek Biernat
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany
| | - Senthilvelrajan Kaniyappan
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany; Department of Neurodegenerative Diseases and Geriatric Psychiatry, University of Bonn, Bonn, Germany
| | - Helmut E Meyer
- Medical Proteome Center, Ruhr-University Bochum, Bochum, Germany; Department of Biomedical Research, Leibniz-Institute for Analytical Sciences (ISAS), Dortmund, Germany
| | - Eva Maria Mandelkow
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany; CAESAR Research Center, Bonn, Germany
| | - Bettina Warscheid
- Group of Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
| | - Eckhard Mandelkow
- DZNE (German Center for Neurodegenerative Diseases), Bonn, Germany; CAESAR Research Center, Bonn, Germany.
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37
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Daems E, Dewaele D, Barylyuk K, De Wael K, Sobott F. Aptamer-ligand recognition studied by native ion mobility-mass spectrometry. Talanta 2020; 224:121917. [PMID: 33379118 DOI: 10.1016/j.talanta.2020.121917] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/19/2020] [Accepted: 11/21/2020] [Indexed: 12/31/2022]
Abstract
The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamer-ligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobility-mass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.
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Affiliation(s)
- Elise Daems
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Debbie Dewaele
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Konstantin Barylyuk
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Karolien De Wael
- AXES Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Frank Sobott
- BAMS Research Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK; School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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38
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Bottari F, Daems E, de Vries AM, Van Wielendaele P, Trashin S, Blust R, Sobott F, Madder A, Martins JC, De Wael K. Do Aptamers Always Bind? The Need for a Multifaceted Analytical Approach When Demonstrating Binding Affinity between Aptamer and Low Molecular Weight Compounds. J Am Chem Soc 2020; 142:19622-19630. [DOI: 10.1021/jacs.0c08691] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Fabio Bottari
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
| | - Elise Daems
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
- BAMS Research Group, Department of Chemistry, University of Antwerp, Antwerp, 2020, Belgium
| | - Anne-Mare de Vries
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Pieter Van Wielendaele
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Stanislav Trashin
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
| | - Ronny Blust
- Sphere Research Group, Department of Biology, University of Antwerp, Antwerp, 2020, Belgium
| | - Frank Sobott
- BAMS Research Group, Department of Chemistry, University of Antwerp, Antwerp, 2020, Belgium
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - José C. Martins
- NMR and Structure Analysis Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Karolien De Wael
- AXES Research Group, Department of Bioscience Engineering, University of Antwerp, Antwerp, 2020, Belgium
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39
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Pallares RM, Panyala NR, Sturzbecher-Hoehne M, Illy MC, Abergel RJ. Characterizing the general chelating affinity of serum protein fetuin for lanthanides. J Biol Inorg Chem 2020; 25:941-948. [DOI: 10.1007/s00775-020-01815-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/31/2020] [Indexed: 12/27/2022]
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40
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Yan Y, Xing T, Wang S, Daly TJ, Li N. Online coupling of analytical hydrophobic interaction chromatography with native mass spectrometry for the characterization of monoclonal antibodies and related products. J Pharm Biomed Anal 2020; 186:113313. [DOI: 10.1016/j.jpba.2020.113313] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/25/2022]
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41
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Kaur U, Johnson DT, Jones LM. Validation of the Applicability of In-Cell Fast Photochemical Oxidation of Proteins across Multiple Eukaryotic Cell Lines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1372-1379. [PMID: 32142260 DOI: 10.1021/jasms.0c00014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fast photochemical oxidation of proteins (FPOP), a hydroxyl radical-based protein footprinting method, coupled to mass spectrometry has been extensively used to study protein structure and protein-protein interactions in vitro. This method utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids and has recently been demonstrated to modify proteins within live cells (IC-FPOP) and Caenorhabditis elegans. Here, we have expanded the application of IC-FPOP into a variety of commonly used cell lines to verify the applicability of the method across various cellular systems. IC-FPOP was able to successfully modify proteins in five different cell lines (Vero, HEK 293T, CHO, MCF-10A, and MCF-7). To increase the number of oxidatively modified proteins identified, we have also employed the use of offline high pH reversed-phase liquid chromatography (RPLC) followed by concatenation and online low-pH RPLC. The coupling of IC-FPOP to 2D-LC MS/MS resulted in a 1.7-fold increase in total identifications of oxidatively modified proteins, which expanded the dynamic range of the method. This work demonstrates the efficacy of using IC-FPOP to study protein-protein interactions in cells.
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Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Danté T Johnson
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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42
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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43
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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44
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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45
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Puglisi R, Boeri Erba E, Pastore A. A Guide to Native Mass Spectrometry to determine complex interactomes of molecular machines. FEBS J 2020; 287:2428-2439. [PMID: 32142206 PMCID: PMC8647915 DOI: 10.1111/febs.15281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/01/2020] [Accepted: 03/04/2020] [Indexed: 01/17/2023]
Abstract
Native mass spectrometry is an emerging technique in biology that gives the possibility to study noncovalently bound complexes with high sensitivity and accuracy. It thus allows the characterization of macromolecular assemblies, assessing their mass and stoichiometries and mapping the interacting surfaces. In this review, we discuss the application of native mass spectrometry to dynamic molecular machines based on multiple weak interactions. In the study of these machines, it is crucial to understand which and under which conditions various complexes form at any time point. We focus on the specific example of the iron-sulfur cluster biogenesis machine because this is an archetype of a dynamic machine that requires very specific and demanding experimental conditions, such as anaerobicity and the need of retaining the fold of marginally folded proteins. We describe the advantages, challenges and current limitations of the technique by providing examples from our own experience and suggesting possible future solutions.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, UK
| | - Elisabetta Boeri Erba
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Annalisa Pastore
- UK Dementia Research Institute at the Wohl Institute of King's College London, UK
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46
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Ziemianowicz DS, MacCallum JL, Schriemer DC. Correlation between Labeling Yield and Surface Accessibility in Covalent Labeling Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:207-216. [PMID: 32031402 DOI: 10.1021/jasms.9b00083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The functional properties of a protein are strongly influenced by its topography, or the solvent-facing contour map of its surface. Together with crosslinking, covalent labeling mass spectrometry (CL-MS) has the potential to contribute topographical data through the measurement of surface accessibility. However, recent efforts to correlate measures of surface accessibility with labeling yield have been met with mixed success. Most applications of CL-MS involve differential analysis of protein interactions (i.e., footprinting experiments) where such inconsistencies have limited effect. Extending CL-MS into structural analysis requires an improved evaluation of the relationship between labeling and surface exposure. In this study, we applied recently developed diazirine reagents to obtain deep coverage of the large motor domain of Eg5 (a mitotic kinesin), and together with computational methods we correlated labeling yields with accessibility data in a number of ways. We observe that correlations can indeed be seen at a local structural level, but these correlations do not extend across the structure. The lack of correlation arises from the influence of protein dynamics and chemical composition on reagent partitioning and, thus, also on labeling yield. We conclude that our use of CL-MS data should be considered in light of "chemical accessibility" rather than "solvent accessibility" and suggest that CL-MS data would be a useful tool in the fundamental study of protein-solute interactions.
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Affiliation(s)
- Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - Justin L MacCallum
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
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47
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Wolff P, Ennifar E. Native Electrospray Ionization Mass Spectrometry of RNA-Ligand Complexes. Methods Mol Biol 2020; 2113:111-118. [PMID: 32006311 DOI: 10.1007/978-1-0716-0278-2_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Native electrospray ionization mass spectrometry (native ESI-MS) is a powerful tool to investigate non-covalent biomolecular interactions. It has been widely used to study protein complexes, but only few examples are described for the analysis of complexes involving RNA-RNA interactions. Here, we provide a detailed protocol for native ESI-MS analysis of RNA complexes. As an example, we present the analysis of the HIV-1 genomic RNA dimerization initiation site (DIS) extended duplex dimer bound to the aminoglycoside antibiotic lividomycin.
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Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France. .,Plateforme protéomique Strasbourg Esplanade, FRC1589 du CNRS, Université de Strasbourg, Strasbourg, France.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
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48
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Olinares PDB, Chait BT. Native Mass Spectrometry Analysis of Affinity-Captured Endogenous Yeast RNA Exosome Complexes. Methods Mol Biol 2020; 2062:357-382. [PMID: 31768985 DOI: 10.1007/978-1-4939-9822-7_17] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Native mass spectrometry (MS) enables direct mass measurement of intact protein assemblies generating relevant subunit composition and stoichiometry information. Combined with cross-linking and structural data, native MS-derived information is crucial for elucidating the architecture of macromolecular assemblies by integrative structural methods. The exosome complex from budding yeast was among the first endogenous protein complexes to be affinity isolated and subsequently characterized by this technique, providing improved understanding of its composition and structure. We present a protocol that couples efficient affinity capture of yeast exosome complexes and sensitive native MS analysis, including rapid affinity isolation of the endogenous exosome complex from cryolysed yeast cells, elution in nondenaturing conditions by protease cleavage, depletion of the protease, buffer exchange, and native MS measurements using an Orbitrap-based instrument (Exactive Plus EMR).
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Affiliation(s)
- Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA.
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
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49
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Breitgoff FD, Keller K, Qi M, Klose D, Yulikov M, Godt A, Jeschke G. UWB DEER and RIDME distance measurements in Cu(II)-Cu(II) spin pairs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 308:106560. [PMID: 31377151 DOI: 10.1016/j.jmr.2019.07.047] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Distance determination by Electron Paramagnetic Resonance (EPR) based on measurements of the dipolar coupling are technically challenging for electron spin systems with broad spectra due to comparatively narrow microwave pulse excitation bandwidths. With Na4[{CuII(PyMTA)}-(stiff spacer)-{CuII(PyMTA)}] as a model compound, we compared DEER and RIDME measurements and investigated the use of frequency-swept pulses. We found very large improvements in sensitivity when substituting the monochromatic pump pulse by a frequency-swept one in DEER experiments with monochromatic observer pulses. This effect was especially strong in X band, where nearly the whole spectrum can be included in the experiment. The RIDME experiment is characterised by a trade-off in signal intensity and modulation depth. Optimal parameters are further influenced by varying steepness of the background decay. A simple 2-point optimization experiment was found to serve as good estimate to identify the mixing time of highest sensitivity. Using frequency-swept pulses in the observer sequences resulted in lower SNR in both the RIDME and the DEER experiment. Orientation selectivity was found to vary in both experiments with the detection position as well as with the settings of the pump pulse in DEER. In RIDME, orientation selection by relaxation anisotropy of the inverted spin appeared to be negligible as form factors remain relatively constant with varying mixing time. This reduces the overall observed orientation selection to the one given by the detection position. Field-averaged data from RIDME and DEER with a shaped pump pulse resulted in the same dipolar spectrum. We found that both methods have their advantages and disadvantages for given instrumental limitations and sample properties. Thus the choice of method depends on the situation at hand and we discuss which parameters should be considered for optimization.
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Affiliation(s)
- Frauke D Breitgoff
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Katharina Keller
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland.
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Daniel Klose
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Maxim Yulikov
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM(2)), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Gunnar Jeschke
- ETH Zürich, Lab. Phys. Chem., Vladimir-Prelog-Weg 2, 8063 Zürich 3 Switzerland
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50
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Zheng J, Strutzenberg T, Pascal BD, Griffin PR. Protein dynamics and conformational changes explored by hydrogen/deuterium exchange mass spectrometry. Curr Opin Struct Biol 2019; 58:305-313. [DOI: 10.1016/j.sbi.2019.06.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 06/15/2019] [Accepted: 06/25/2019] [Indexed: 12/31/2022]
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