1
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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2
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Chen X, Sailer C, Kammer KM, Fürsch J, Eisele MR, Sakata E, Pellarin R, Stengel F. Mono- and Intralink Filter (Mi-Filter) To Reduce False Identifications in Cross-Linking Mass Spectrometry Data. Anal Chem 2022; 94:17751-17756. [PMID: 36510358 PMCID: PMC9798375 DOI: 10.1021/acs.analchem.2c00494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has become an indispensable tool for the emerging field of systems structural biology over the recent years. However, the confidence in individual protein-protein interactions (PPIs) depends on the correct assessment of individual inter-protein cross-links. In this article, we describe a mono- and intralink filter (mi-filter) that is applicable to any kind of cross-linking data and workflow. It stipulates that only proteins for which at least one monolink or intra-protein cross-link has been identified within a given data set are considered for an inter-protein cross-link and therefore participate in a PPI. We show that this simple and intuitive filter has a dramatic effect on different types of cross-linking data ranging from individual protein complexes over medium-complexity affinity enrichments to proteome-wide cell lysates and significantly reduces the number of false-positive identifications for inter-protein links in all these types of XL-MS data.
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Affiliation(s)
- Xingyu Chen
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Carolin Sailer
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Kai Michael Kammer
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Julius Fürsch
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany
| | - Markus R. Eisele
- Department
of Molecular Structural Biology, Max Planck
Institute of Biochemistry, Martinsried 82152, Germany
| | - Eri Sakata
- Department
of Molecular Structural Biology, Max Planck
Institute of Biochemistry, Martinsried 82152, Germany,Institute
for Auditory Neuroscience, University Medical
Center Göttingen, Göttingen 37077, Germany
| | - Riccardo Pellarin
- Structural
Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, Paris 75015, France
| | - Florian Stengel
- Department
of Biology, University of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,Konstanz
Research School Chemical Biology, University
of Konstanz, Universitätsstrasse 10, Konstanz 78457, Germany,
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3
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Petrotchenko EV, Borchers CH. Protein Chemistry Combined with Mass Spectrometry for Protein Structure Determination. Chem Rev 2021; 122:7488-7499. [PMID: 34968047 DOI: 10.1021/acs.chemrev.1c00302] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The advent of soft-ionization mass spectrometry for biomolecules has opened up new possibilities for the structural analysis of proteins. Combining protein chemistry methods with modern mass spectrometry has led to the emergence of the distinct field of structural proteomics. Multiple protein chemistry approaches, such as surface modification, limited proteolysis, hydrogen-deuterium exchange, and cross-linking, provide diverse and often orthogonal structural information on the protein systems studied. Combining experimental data from these various structural proteomics techniques provides a more comprehensive examination of the protein structure and increases confidence in the ultimate findings. Here, we review various types of experimental data from structural proteomics approaches with an emphasis on the use of multiple complementary mass spectrometric approaches to provide experimental constraints for the solving of protein structures.
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Affiliation(s)
- Evgeniy V Petrotchenko
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
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4
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Cakir M, Obernier K, Forget A, Krogan NJ. Target Discovery for Host-Directed Antiviral Therapies: Application of Proteomics Approaches. mSystems 2021; 6:e0038821. [PMID: 34519533 PMCID: PMC8547474 DOI: 10.1128/msystems.00388-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Current epidemics, such as AIDS or flu, and the emergence of new threatening pathogens, such as the one causing the current coronavirus disease 2019 (COVID-19) pandemic, represent major global health challenges. While vaccination is an important part of the arsenal to counter the spread of viral diseases, it presents limitations and needs to be complemented by efficient therapeutic solutions. Intricate knowledge of host-pathogen interactions is a powerful tool to identify host-dependent vulnerabilities that can be exploited to dampen viral replication. Such host-directed antiviral therapies are promising and are less prone to the development of drug-resistant viral strains. Here, we first describe proteomics-based strategies that allow the rapid characterization of host-pathogen interactions. We then discuss how such data can be exploited to help prioritize compounds with potential host-directed antiviral activity that can be tested in preclinical models.
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Affiliation(s)
- Merve Cakir
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Antoine Forget
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
| | - Nevan J. Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, California, USA
- Quantitative Biosciences Institute (QBI) COVID-19 Research Group (QCRG), San Francisco, California, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, California, USA
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5
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Haas P, Muralidharan M, Krogan NJ, Kaake RM, Hüttenhain R. Proteomic Approaches to Study SARS-CoV-2 Biology and COVID-19 Pathology. J Proteome Res 2021; 20:1133-1152. [PMID: 33464917 PMCID: PMC7839417 DOI: 10.1021/acs.jproteome.0c00764] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 12/17/2022]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), was declared a pandemic infection in March 2020. As of December 2020, two COVID-19 vaccines have been authorized for emergency use by the U.S. Food and Drug Administration, but there are no effective drugs to treat COVID-19, and pandemic mitigation efforts like physical distancing have had acute social and economic consequences. In this perspective, we discuss how the proteomic research community can leverage technologies and expertise to address the pandemic by investigating four key areas of study in SARS-CoV-2 biology. Specifically, we discuss how (1) mass spectrometry-based structural techniques can overcome limitations and complement traditional structural approaches to inform the dynamic structure of SARS-CoV-2 proteins, complexes, and virions; (2) virus-host protein-protein interaction mapping can identify the cellular machinery required for SARS-CoV-2 replication; (3) global protein abundance and post-translational modification profiling can characterize signaling pathways that are rewired during infection; and (4) proteomic technologies can aid in biomarker identification, diagnostics, and drug development in order to monitor COVID-19 pathology and investigate treatment strategies. Systems-level high-throughput capabilities of proteomic technologies can yield important insights into SARS-CoV-2 biology that are urgently needed during the pandemic, and more broadly, can inform coronavirus virology and host biology.
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Affiliation(s)
- Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Monita Muralidharan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nevan J. Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robyn M. Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
- J. David Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
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6
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Matzinger M, Mechtler K. Cleavable Cross-Linkers and Mass Spectrometry for the Ultimate Task of Profiling Protein-Protein Interaction Networks in Vivo. J Proteome Res 2021; 20:78-93. [PMID: 33151691 PMCID: PMC7786381 DOI: 10.1021/acs.jproteome.0c00583] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Indexed: 12/11/2022]
Abstract
Cross-linking mass spectrometry (XL-MS) has matured into a potent tool to identify protein-protein interactions or to uncover protein structures in living cells, tissues, or organelles. The unique ability to investigate the interplay of proteins within their native environment delivers valuable complementary information to other advanced structural biology techniques. This Review gives a comprehensive overview of the current possible applications as well as the remaining limitations of the technique, focusing on cross-linking in highly complex biological systems like cells, organelles, or tissues. Thanks to the commercial availability of most reagents and advances in user-friendly data analysis, validation, and visualization tools, studies using XL-MS can, in theory, now also be utilized by nonexpert laboratories.
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Affiliation(s)
- Manuel Matzinger
- Research
Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
| | - Karl Mechtler
- Research
Institute of Molecular Pathology (IMP), Campus-Vienna-Biocenter 1, Vienna 1030, Austria
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7
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Cross-linking of bovine rhodopsin with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate affects its functionality. Biochem J 2020; 477:2295-2312. [PMID: 32497171 DOI: 10.1042/bcj20200376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 02/08/2023]
Abstract
Rhodopsin is the photoreceptor protein involved in visual excitation in retinal rods. The functionality of bovine rhodopsin was determined following treatment with sulfosuccinimidyl 4-(N maleimidomethyl)cyclohexane-1-carboxylate (sulfo-SMCC), a bifunctional reagent capable of forming covalent cross-links between suitable placed lysines and cysteines. Denaturing polyacrylamide gel electrophoresis showed that rhodopsin incubated with sulfo-SMCC generated intermolecular dimers, trimers, and higher oligomers, although most of the sulfo-SMCC-treated protein remained as a monomer. Minor alterations on the absorption spectrum of light-activated sulfo-SMCC-treated rhodopsin were observed. However, only ∼2% stimulation of the guanine nucleotide binding activity of transducin was measured in the presence of sulfo-SMCC-cross-linked photolyzed rhodopsin. Moreover, rhodopsin kinase was not able of phosphorylating sulfo-SMCC-cross-linked rhodopsin after illumination. Rhodopsin was purified in the presence of either 0.1% or 1% n-dodecyl β-d-maltoside, to obtain dimeric and monomeric forms of the protein, respectively. Interestingly, no generation of the regular F1 and F2 thermolytic fragments was perceived with sulfo-SMCC-cross-linked rhodopsin either in the dimeric or monomeric state, implying the formation of intramolecular connections in the protein that might thwart the light-induced conformational changes required for interaction with transducin and rhodopsin kinase. Structural analysis of the rhodopsin three-dimensional structure suggested that the following lysine and cysteine pairs: Lys66/Lys67 and Cys316, Cys140 and Lys141, Cys140 and Lys248, Lys311 and Cys316, and/or Cys316 and Lys325 are potential candidates to generate intramolecular cross-links in the protein. Yet, the lack of fragmentation of sulfo-SMCC-treated Rho with thermolysin is consistent with the formation of cross-linking bridges between Lys66/Lys67 and Cys316, and/or Cys140 and Lys248.
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8
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Van Rompuy LS, Savić ND, Rodriguez A, Parac-Vogt TN. Selective Hydrolysis of Transferrin Promoted by Zr-Substituted Polyoxometalates. Molecules 2020; 25:E3472. [PMID: 32751602 PMCID: PMC7435656 DOI: 10.3390/molecules25153472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022] Open
Abstract
The hydrolysis of the iron-binding blood plasma glycoprotein transferrin (Tf) has been examined at pH = 7.4 in the presence of a series of Zr-substituted polyoxometalates (Zr-POMs) including Keggin (Et2NH2)10[Zr(PW11O39)2]∙7H2O (Zr-K 1:2), (Et2NH2)8[{α-PW11O39Zr-(μ-OH) (H2O)}2]∙7H2O (Zr-K 2:2), Wells-Dawson K15H[Zr(α2-P2W17O61)2]·25H2O (Zr-WD 1:2), Na14[Zr4(α-P2W16O59)2(μ3-O)2(μ-OH)2(H2O)4]·57H2O (Zr-WD 4:2) and Lindqvist (Me4N)2[ZrW5O18(H2O)3] (Zr-L 1:1), (nBu4N)6[(ZrW5O18(μ-OH))2]∙2H2O (Zr-L 2:2)) type POMs. Incubation of transferrin with Zr-POMs resulted in formation of 13 polypeptide fragments that were observed on sodium dodecyl sulfate poly(acrylamide) gel electrophoresis (SDS-PAGE), but the hydrolysis efficiency varied depending on the nature of Zr-POMs. Molecular interactions between Zr-POMs and transferrin were investigated by using a range of complementary techniques such as tryptophan fluorescence, circular dichroism (CD), 31P-NMR spectroscopy, in order to gain better understanding of different efficiency of investigated Zr-POMs. A tryptophan fluorescence quenching study revealed that the most reactive Zr-WD species show the strongest interaction toward transferrin. The CD results demonstrated that interaction of Zr-POMs and transferrin in buffer solution result in significant secondary structure changes. The speciation of Zr-POMs has been followed by 31P-NMR spectroscopy in the presence and absence of transferrin, providing insight into stability of the catalysts under reaction condition.
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Affiliation(s)
| | | | | | - Tatjana N. Parac-Vogt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium; (L.S.V.R.); (N.D.S.); (A.R.)
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9
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Chavez JD, Tang X, Campbell MD, Reyes G, Kramer PA, Stuppard R, Keller A, Zhang H, Rabinovitch PS, Marcinek DJ, Bruce JE. Mitochondrial protein interaction landscape of SS-31. Proc Natl Acad Sci U S A 2020; 117:15363-15373. [PMID: 32554501 PMCID: PMC7334473 DOI: 10.1073/pnas.2002250117] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial dysfunction underlies the etiology of a broad spectrum of diseases including heart disease, cancer, neurodegenerative diseases, and the general aging process. Therapeutics that restore healthy mitochondrial function hold promise for treatment of these conditions. The synthetic tetrapeptide, elamipretide (SS-31), improves mitochondrial function, but mechanistic details of its pharmacological effects are unknown. Reportedly, SS-31 primarily interacts with the phospholipid cardiolipin in the inner mitochondrial membrane. Here we utilize chemical cross-linking with mass spectrometry to identify protein interactors of SS-31 in mitochondria. The SS-31-interacting proteins, all known cardiolipin binders, fall into two groups, those involved in ATP production through the oxidative phosphorylation pathway and those involved in 2-oxoglutarate metabolic processes. Residues cross-linked with SS-31 reveal binding regions that in many cases, are proximal to cardiolipin-protein interacting regions. These results offer a glimpse of the protein interaction landscape of SS-31 and provide mechanistic insight relevant to SS-31 mitochondrial therapy.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA 98105
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, WA 98105
| | | | - Gustavo Reyes
- Department of Radiology, University of Washington, Seattle, WA 98105
| | - Philip A Kramer
- Department of Radiology, University of Washington, Seattle, WA 98105
| | - Rudy Stuppard
- Department of Radiology, University of Washington, Seattle, WA 98105
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA 98105
| | - Huiliang Zhang
- Department of Pathology, University of Washington, Seattle, WA 98195
| | | | - David J Marcinek
- Department of Radiology, University of Washington, Seattle, WA 98105
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98105;
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10
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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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11
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Chakrabarty JK, Sadananda SC, Bhat A, Naik AJ, Ostwal DV, Chowdhury SM. High Confidence Identification of Cross-Linked Peptides by an Enrichment-Based Dual Cleavable Cross-Linking Technology and Data Analysis tool Cleave-XL. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:173-182. [PMID: 32031390 DOI: 10.1021/jasms.9b00111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cleavable cross-linking technology requires further MS/MS of the cleavable fragments for unambiguous identification of cross-linked peptides. These spectra are sometimes very ambiguous due to the sensitivity and complex fragmentation pattern of the peptides with the cross-linked residues. We recently reported a dual cleavable cross-linking technology (DUCCT), which can enhance the confidence in the identification of cross-linked peptides. The heart of this strategy is a novel dual mass spectrometry cleavable cross linker that can be cleaved preferentially by two differential tandem mass spectrometry methods, collision induced dissociation and electron transfer dissociation (CID and ETD). Different signature ions from two different mass spectra for the same cross-linked peptide helped identify the cross-linked peptides with high confidence. In this study, we developed an enrichment-based photocleavable DUCCT (PC-DUCCT-biotin), where cross-linked products were enriched from biological samples using affinity purification, and subsequently, two sequential tandem (CID and ETD) mass spectrometry processes were utilized. Furthermore, we developed a prototype software called Cleave-XL to analyze cross-linked products generated by DUCCT. Photocleavable DUCCT was demonstrated in standard peptides and proteins. Efficiency of the software tools to search and compare CID and ETD data of photocleavable DUCCT biotin in standard peptides and proteins as well as regular DUCCT in protein complexes from immune cells were tested. The software is efficient in pinpointing cross-linked sites using CID and ETD cross-linking data. We believe this new DUCCT and associated software tool Cleave-XL will advance high confidence identification of protein cross-linking sites and automated identification of low-resolution protein structures.
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Affiliation(s)
- Jayanta K Chakrabarty
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Sandhya C Sadananda
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Apeksha Bhat
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Aishwarya J Naik
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Dhanashri V Ostwal
- Department of Computer Science , University of Texas at Arlington , Arlington , Texas 76019 , United States
| | - Saiful M Chowdhury
- Department of Chemistry and Biochemistry , University of Texas at Arlington , Arlington , Texas 76019 , United States
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12
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Fürsch J, Kammer KM, Kreft SG, Beck M, Stengel F. Proteome-Wide Structural Probing of Low-Abundant Protein Interactions by Cross-Linking Mass Spectrometry. Anal Chem 2020; 92:4016-4022. [DOI: 10.1021/acs.analchem.9b05559] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Julius Fürsch
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Kai-Michael Kammer
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Stefan G. Kreft
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Max Planck Institute of Biophysics, Max-von-Laue-Straße 3. 60438 Frankfurt am Main, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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13
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Dal Cortivo G, Marino V, Iacobucci C, Vallone R, Arlt C, Rehkamp A, Sinz A, Dell'Orco D. Oligomeric state, hydrodynamic properties and target recognition of human Calcium and Integrin Binding protein 2 (CIB2). Sci Rep 2019; 9:15058. [PMID: 31636333 PMCID: PMC6803640 DOI: 10.1038/s41598-019-51573-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/12/2019] [Indexed: 11/23/2022] Open
Abstract
Calcium- and Integrin-Binding protein 2 (CIB2) is a small and ubiquitously expressed protein with largely unknown biological function but ascertained role in hearing physiology and disease. Recent studies found that CIB2 binds Ca2+ with moderate affinity and dimerizes under conditions mimicking the physiological ones. Here we provided new lines of evidence on CIB2 oligomeric state and the mechanism of interaction with the α7B integrin target. Based on a combination of native mass spectrometry, chemical cross-linking/mass spectrometry, analytical gel filtration, dynamic light scattering and molecular dynamics simulations we conclude that CIB2 is monomeric under all tested conditions and presents uncommon hydrodynamic properties, most likely due to the high content of hydrophobic solvent accessible surface. Surface plasmon resonance shows that the interaction with α7B occurs with relatively low affinity and is limited to the cytosolic region proximal to the membrane, being kinetically favored in the presence of physiological Mg2+ and in the absence of Ca2+. Although CIB2 binds to an α7B peptide in a 1:1 stoichiometry, the formation of the complex might induce binding of another CIB2 molecule.
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Affiliation(s)
- Giuditta Dal Cortivo
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - Valerio Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Rosario Vallone
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Daniele Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy.
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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