1
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Renzone G, Arena S, Scaloni A. Cross-linking reactions in food proteins and proteomic approaches for their detection. MASS SPECTROMETRY REVIEWS 2022; 41:861-898. [PMID: 34250627 DOI: 10.1002/mas.21717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 06/13/2023]
Abstract
Various protein cross-linking reactions leading to molecular polymerization and covalent aggregates have been described in processed foods. They are an undesired side effect of processes designed to reduce bacterial load, extend shelf life, and modify technological properties, as well as being an expected result of treatments designed to modify raw material texture and function. Although the formation of these products is known to affect the sensory and technological properties of foods, the corresponding cross-linking reactions and resulting protein polymers have not yet undergone detailed molecular characterization. This is essential for describing how their generation can be related to food processing conditions and quality parameters. Due to the complex structure of cross-linked species, bottom-up proteomic procedures developed to characterize various amino acid modifications associated with food processing conditions currently offer a limited molecular description of bridged peptide structures. Recent progress in cross-linking mass spectrometry for the topological characterization of protein complexes has facilitated the development of various proteomic methods and bioinformatic tools for unveiling bridged species, which can now also be used for the detailed molecular characterization of polymeric cross-linked products in processed foods. We here examine their benefits and limitations in terms of evaluating cross-linked food proteins and propose future scenarios for application in foodomics. They offer potential for understanding the protein cross-linking formation mechanisms in processed foods, and how the inherent beneficial properties of treated foodstuffs can be preserved or enhanced.
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Affiliation(s)
- Giovanni Renzone
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Simona Arena
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
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2
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Piersimoni L, Kastritis PL, Arlt C, Sinz A. Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons. Chem Rev 2021; 122:7500-7531. [PMID: 34797068 DOI: 10.1021/acs.chemrev.1c00786] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this review, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined. We summarize the most important cross-linking reagents, software tools, and XL-MS workflows and highlight prominent examples for characterizing proteins, their assemblies, and interaction networks in vitro and in vivo. Computational modeling plays a crucial role in deriving 3D-structural information from XL-MS data. Integrating XL-MS with other techniques of structural biology, such as cryo-electron microscopy, has been successful in addressing biological questions that to date could not be answered. XL-MS is therefore expected to play an increasingly important role in structural biology in the future.
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Affiliation(s)
- Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany.,Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Biozentrum, Weinbergweg 22, D-06120 Halle (Saale), Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Strasse 3, D-06120 Halle (Saale), Germany
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3
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Rey M, Dhenin J, Kong Y, Nouchikian L, Filella I, Duchateau M, Dupré M, Pellarin R, Duménil G, Chamot-Rooke J. Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions. Anal Chem 2021; 93:4166-4174. [DOI: 10.1021/acs.analchem.0c04430] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Martial Rey
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Jonathan Dhenin
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Youxin Kong
- Pathogenesis of Vascular Infections, Department of Cell Biology and Infection, Institut Pasteur, INSERM U1225, 28 rue du Docteur Roux, 75015 Paris France
| | - Lucienne Nouchikian
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Isaac Filella
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Mathieu Dupré
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28 rue du Docteur Roux, 75015 Paris, France
| | - Guillaume Duménil
- Pathogenesis of Vascular Infections, Department of Cell Biology and Infection, Institut Pasteur, INSERM U1225, 28 rue du Docteur Roux, 75015 Paris France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS USR 2000, 28 rue du Docteur Roux, 75015 Paris, France
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4
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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: 47] [Impact Index Per Article: 15.7] [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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5
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Maibom-Thomsen SL, Trier NH, Holm BE, Hansen KB, Rasmussen MI, Chailyan A, Marcatili P, Højrup P, Houen G. Immunoglobulin G structure and rheumatoid factor epitopes. PLoS One 2019; 14:e0217624. [PMID: 31199818 PMCID: PMC6568389 DOI: 10.1371/journal.pone.0217624] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 05/15/2019] [Indexed: 12/14/2022] Open
Abstract
Antibodies are important for immunity and exist in several classes (IgM, IgD, IgA, IgG, IgE). They are composed of symmetric dimeric molecules with two antigen binding regions (Fab) and a constant part (Fc), usually depicted as Y-shaped molecules. Rheumatoid factors found in patients with rheumatoid arthritis are autoantibodies binding to IgG and paradoxically appear to circulate in blood alongside with their antigen (IgG) without reacting with it. Here, it is shown that rheumatoid factors do not react with native IgG in solution, and that their epitopes only become accessible upon certain physico-chemical treatments (e.g. heat treatment at 57 °C), by physical adsorption on a hydrophobic surface or by antigen binding. Moreover, chemical cross-linking in combination with mass spectrometry showed that the native state of IgG is a compact (closed) form and that the Fab parts of IgG shield the Fc region and thereby control access of rheumatoid factors and presumably also some effector functions. It can be inferred that antibody binding to pathogen surfaces induces a conformational change, which exposes the Fc part with its effector sites and rheumatoid factor epitopes. This has strong implications for understanding antibody structure and physiology and necessitates a conceptual reformulation of IgG models.
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Affiliation(s)
| | - Nicole Hartwig Trier
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
| | - Bettina Eide Holm
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
| | - Kirsten Beth Hansen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anna Chailyan
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Paolo Marcatili
- Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Gunnar Houen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Autoimmunology, Statens Serum Institut, Copenhagen, Denmark
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6
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Nybo T, Davies MJ, Rogowska-Wrzesinska A. Analysis of protein chlorination by mass spectrometry. Redox Biol 2019; 26:101236. [PMID: 31181457 PMCID: PMC6557747 DOI: 10.1016/j.redox.2019.101236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 01/04/2023] Open
Abstract
Chlorination of tyrosine is a commonly known effect/consequence of myeloperoxidase activity at sites of inflammation, and detection of 3-chlorotyrosine has been used as biomarker for inflammatory diseases. However, few studies have addressed site specific chlorination in proteins, and no methods for large scale chloroproteomics studies have yet been published. In this study, we present an optimized mass spectrometry based protocol to identify and quantify chlorinated peptides from single proteins modified by HOCl (100 and 500 μM, within estimated pathophysiological levels), at a high level of sensitivity and accuracy. Particular emphasis was placed on 1) sensitive and precise detection of modification sites, 2) the avoidance of loss or artefactual creation of modifications, 3) accurate quantification of peptide abundance and reduction of missing values problem, 4) monitoring the dynamics of modification in samples exposed to different oxidant concentrations and 5) development of guidelines for verification of chlorination sites assignment. A combination of an optimised sample preparation protocol, and improved data analysis approaches have allowed identification of 33 and 15 chlorination sites in laminin and fibronectin, respectively, reported in previous manuscripts [1,2]. The method was subsequently tested on murine basement membrane extract, which contains high levels of laminin in a complex mixture. Here, 10 of the major chlorination sites in laminin were recapitulated, highlighting the utility of the method in detecting damage in complex samples. An optimized mass spectrometry method is presented to detect protein chlorination. Reduction and alkylation leads to loss of chlorinated residues. Identification of modification sites in fibronectin and laminin induced by HOCl. Quantification of relative site occupancy (RSO) of chlorinated residues. Largest chloroproteomics dataset to date.
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Affiliation(s)
- Tina Nybo
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark; Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen N, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
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7
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Iacobucci C, Piotrowski C, Rehkamp A, Ihling CH, Sinz A. The First MS-Cleavable, Photo-Thiol-Reactive Cross-Linker for Protein Structural Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:139-148. [PMID: 29679287 DOI: 10.1007/s13361-018-1952-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Cleavable cross-linkers are gaining increasing importance for chemical cross-linking/mass spectrometry (MS) as they permit a reliable and automated data analysis in structural studies of proteins and protein assemblies. Here, we introduce 1,3-diallylurea (DAU) as the first CID-MS/MS-cleavable, photo-thiol-reactive cross-linker. DAU is a commercially available, inexpensive reagent that efficiently undergoes an anti-Markovnikov hydrothiolation with cysteine residues in the presence of a radical initiator upon UV-A irradiation. Radical cysteine cross-linking proceeds via an orthogonal "click reaction" and yields stable alkyl sulfide products. DAU reacts at physiological pH and cross-linking reactions with peptides, and proteins can be performed at temperatures as low as 4 °C. The central urea bond is efficiently cleaved upon collisional activation during tandem MS experiments generating characteristic product ions. This improves the reliability of automated cross-link identification. Different radical initiators have been screened for the cross-linking reaction of DAU using the thiol-containing compounds cysteine and glutathione. Our concept has also been exemplified for the biologically relevant proteins bMunc13-2 and retinal guanylyl cyclase-activating protein-2. Graphical abstract ᅟ.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany.
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany.
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8
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Rey M, Dupré M, Lopez-Neira I, Duchateau M, Chamot-Rooke J. eXL-MS: An Enhanced Cross-Linking Mass Spectrometry Workflow To Study Protein Complexes. Anal Chem 2018; 90:10707-10714. [PMID: 30125099 DOI: 10.1021/acs.analchem.8b00737] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The analysis of proteins and protein complexes by cross-linking mass spectrometry (XL-MS) has expanded in the past decade. However, mostly used approaches suffer important limitations in term of efficiency and sensitivity. We describe here a new workflow based on the advanced use of the trifunctional cross-linker NNP9. NNP9 carries an azido group allowing the quantitative and selective introduction of a biotin molecule into cross-linked proteins. The incorporation is performed by click-chemistry using an adapted version of the enhanced filter-aided sample preparation (eFASP) protocol. This protocol, based on the use of a molecular filter, allows a very high recovery of peptides after enzymatic digestion and complete removal of contaminants. This in turn offers the possibility for one to analyze very large membrane proteins solubilized in detergent. After trypsin digestion, biotinylated peptides can be easily enriched on monoavidin beads and analyzed by LC-MS/MS. The whole workflow was developed on creatine kinase in the presence of detergent. It led to a drastic improvement in the number of identified cross-linked peptides (407 vs 81), compared to the conventional approach using a gel-based separation. One great advantage of our enhanced cross-linking mass spectrometry (eXL-MS) workflow is its high efficiency, allowing the analysis of a very low amount of material (15 μg). We also demonstrate that higher-energy collision dissociation (HCD) outperforms electron-transfer/higher-energy collision dissociation (EThcD) in terms of number of cross-linked peptides identified, but EThcD leads to better sequence coverage than HCD and thus easier localization of cross-linking sites.
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Affiliation(s)
- Martial Rey
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Mathieu Dupré
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Isabel Lopez-Neira
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, CNRS USR 2000 , Institut Pasteur , Paris , 75015 , France
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9
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Hägglund P, Mariotti M, Davies MJ. Identification and characterization of protein cross-links induced by oxidative reactions. Expert Rev Proteomics 2018; 15:665-681. [DOI: 10.1080/14789450.2018.1509710] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Per Hägglund
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Michele Mariotti
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael J. Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
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10
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Martin-Rodilla P, Panach JI, Gonzalez-Perez C, Pastor O. Assessing data analysis performance in research contexts: An experiment on accuracy, efficiency, productivity and researchers’ satisfaction. DATA KNOWL ENG 2018. [DOI: 10.1016/j.datak.2018.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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11
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Mariotti M, Leinisch F, Leeming DJ, Svensson B, Davies MJ, Hägglund P. Mass-Spectrometry-Based Identification of Cross-Links in Proteins Exposed to Photo-Oxidation and Peroxyl Radicals Using 18O Labeling and Optimized Tandem Mass Spectrometry Fragmentation. J Proteome Res 2018; 17:2017-2027. [DOI: 10.1021/acs.jproteome.7b00881] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michele Mariotti
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
| | - Fabian Leinisch
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
| | | | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
| | - Michael J. Davies
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
| | - Per Hägglund
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 224, Kongens Lyngby, DK 2800 Denmark
- Department of Biomedical Sciences, University of Copenhagen, Nørregade 10, Copenhagen, DK-1017 Denmark
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12
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Söderberg CAG, Månsson C, Bernfur K, Rutsdottir G, Härmark J, Rajan S, Al-Karadaghi S, Rasmussen M, Höjrup P, Hebert H, Emanuelsson C. Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface. Sci Rep 2018; 8:5199. [PMID: 29581438 PMCID: PMC5979959 DOI: 10.1038/s41598-018-23035-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/05/2018] [Indexed: 12/28/2022] Open
Abstract
The remarkably efficient suppression of amyloid fibril formation by the DNAJB6 chaperone is dependent on a set of conserved S/T-residues and an oligomeric structure, features unusual among DNAJ chaperones. We explored the structure of DNAJB6 using a combination of structural methods. Lysine-specific crosslinking mass spectrometry provided distance constraints to select a homology model of the DNAJB6 monomer, which was subsequently used in crosslink-assisted docking to generate a dimer model. A peptide-binding cleft lined with S/T-residues is formed at the monomer-monomer interface. Mixed isotope crosslinking showed that the oligomers are dynamic entities that exchange subunits. The purified protein is well folded, soluble and composed of oligomers with a varying number of subunits according to small-angle X-ray scattering (SAXS). Elongated particles (160 × 120 Å) were detected by electron microscopy and single particle reconstruction resulted in a density map of 20 Å resolution into which the DNAJB6 dimers fit. The structure of the oligomer and the S/T-rich region is of great importance for the understanding of the function of DNAJB6 and how it can bind aggregation-prone peptides and prevent amyloid diseases.
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Affiliation(s)
| | - Cecilia Månsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Johan Härmark
- School of Technology and Health, KTH Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Salam Al-Karadaghi
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Morten Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Peter Höjrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hans Hebert
- School of Technology and Health, KTH Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-221 00, Lund, Sweden.
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13
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Piotrowski C, Sinz A. Structural Investigation of Proteins and Protein Complexes by Chemical Cross-Linking/Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:101-121. [PMID: 30617826 DOI: 10.1007/978-981-13-2200-6_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
During the last two decades, cross-linking combined with mass spectrometry (MS) has evolved as a valuable tool to gain structural insights into proteins and protein assemblies. Structural information is obtained by introducing covalent connections between amino acids that are in spatial proximity in proteins and protein complexes. The distance constraints imposed by the cross-linking reagent provide information on the three-dimensional arrangement of the covalently connected amino acid residues and serve as basis for de-novo or homology modeling approaches. As cross-linking/MS allows investigating protein 3D-structures and protein-protein interactions not only in-vitro, but also in-vivo, it is especially appealing for studying protein systems in their native environment. In this chapter, we describe the principles of cross-linking/MS and illustrate its value for investigating protein 3D-structures and for unraveling protein interaction networks.
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Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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14
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Hage C, Falvo F, Schäfer M, Sinz A. Novel Concepts of MS-Cleavable Cross-linkers for Improved Peptide Structure Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2022-2038. [PMID: 28653243 DOI: 10.1007/s13361-017-1712-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/03/2017] [Accepted: 05/07/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is gaining increasing importance as an alternative method for studying protein conformation and for deciphering protein interaction networks. This study is part of our ongoing efforts to develop innovative cross-linking principles for a facile and efficient assignment of cross-linked products. We evaluate two homobifunctional, amine-reactive, and MS-cleavable cross-linkers regarding their potential for automated analysis of cross-linked products. We introduce the bromine phenylurea (BrPU) linker that possesses a unique structure yielding a distinctive fragmentation pattern on collisional activation. Moreover, BrPU delivers the characteristic bromine isotope pattern and mass defect for all cross-linker-decorated fragments. We compare the fragmentation behavior of the BrPU linker with that of our previously described MS-cleavable TEMPO-Bz linker (which consists of a 2,2,6,6-tetramethylpiperidine-1-oxy moiety connected to a benzyl group) that was developed to perform free-radical-initiated peptide sequencing. Comparative collisional activation experiments (collision-induced dissociation and higher-energy collision-induced dissociation) with both cross-linkers were conducted in negative electrospray ionization mode with an Orbitrap Fusion mass spectrometer using five model peptides. As hypothesized in a previous study, the presence of a cross-linked N-terminal aspartic acid residue seems to be the prerequisite for the loss of an intact peptide from the cross-linked products. As the BrPU linker combines a characteristic mass shift with an isotope signature, it presents a more favorable combination for automated assignment of cross-linked products compared with the TEMPO-Bz linker. ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Francesco Falvo
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
- Eurofins Umwelt West GmbH, Vorgebirgsstr. 20, 50389, Wesseling, Germany
| | - Mathias Schäfer
- Department of Chemistry, University of Cologne, Greinstr. 4, 50939, Cologne, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany.
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15
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Iacobucci C, Hage C, Schäfer M, Sinz A. A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2039-2053. [PMID: 28717933 DOI: 10.1007/s13361-017-1744-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 06/07/2023]
Abstract
The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS3 experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Claudio Iacobucci
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
| | - Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
| | - Mathias Schäfer
- Department of Chemistry, Institute of Organic Chemistry, University of Cologne, Greinstr. 4, D-50939, Kӧln, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany.
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16
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Barysz HM, Malmström J. Development of Large-scale Cross-linking Mass Spectrometry. Mol Cell Proteomics 2017; 17:1055-1066. [PMID: 28389583 DOI: 10.1074/mcp.r116.061663] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 03/26/2017] [Indexed: 11/06/2022] Open
Abstract
Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level. Specifically, there is an unmet need for comprehensive software that can reliably identify cross-linked peptides from large data sets. In this review we provide supporting information to reason that targeted proteomics of cross-links may provide the required sensitivity to reliably detect and quantify cross-linked peptides and that a reporter ion signature for cross-linked peptides may become a useful approach to increase confidence in the identification process of cross-linked peptides. In addition, the review summarizes the recent advances in CLMS workflows using the analysis of condensin complex in intact chromosomes as a model complex.
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Affiliation(s)
- Helena Maria Barysz
- From the ‡Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Johan Malmström
- From the ‡Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
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17
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Sundaramoorthy R, Hughes AL, Singh V, Wiechens N, Ryan DP, El-Mkami H, Petoukhov M, Svergun DI, Treutlein B, Quack S, Fischer M, Michaelis J, Böttcher B, Norman DG, Owen-Hughes T. Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes. eLife 2017; 6. [PMID: 28332978 PMCID: PMC5391205 DOI: 10.7554/elife.22510] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/15/2017] [Indexed: 12/11/2022] Open
Abstract
The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state. DOI:http://dx.doi.org/10.7554/eLife.22510.001
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Affiliation(s)
| | - Amanda L Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Vijender Singh
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nicola Wiechens
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel P Ryan
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hassane El-Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | - Maxim Petoukhov
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Dmitri I Svergun
- Hamburg Outstation, European Molecular Biology Laboratory, Hamburg, Germany
| | - Barbara Treutlein
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Salina Quack
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Monika Fischer
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Jens Michaelis
- Institute for Biophysics, Faculty of Natural Sciences, Ulm University, Ulm, Germany
| | - Bettina Böttcher
- Lehrstuhl für Biochemie, Rudolf-Virchow Zentrum, Universitat Würzburg, Würzburg, Germany
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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18
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Rutsdottir G, Härmark J, Weide Y, Hebert H, Rasmussen MI, Wernersson S, Respondek M, Akke M, Højrup P, Koeck PJB, Söderberg CAG, Emanuelsson C. Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity. J Biol Chem 2017; 292:8103-8121. [PMID: 28325834 PMCID: PMC5427286 DOI: 10.1074/jbc.m116.766816] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/16/2017] [Indexed: 01/14/2023] Open
Abstract
Small heat-shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have been hard to define due to limited structural information; currently, there is only one high-resolution structure of a plant sHsp published, that of the cytosolic Hsp16.9. We took interest in Hsp21, a chloroplast-localized sHsp crucial for plant stress resistance, which has even longer N-terminal arms than Hsp16.9, with a functionally important and conserved methionine-rich motif. To provide a framework for investigating structure-function relationships of Hsp21 and understanding these sequence variations, we developed a structural model of Hsp21 based on homology modeling, cryo-EM, cross-linking mass spectrometry, NMR, and small-angle X-ray scattering. Our data suggest a dodecameric arrangement of two trimer-of-dimer discs stabilized by the C-terminal tails, possibly through tail-to-tail interactions between the discs, mediated through extended IXVXI motifs. Our model further suggests that six N-terminal arms are located on the outside of the dodecamer, accessible for interaction with client proteins, and distinct from previous undefined or inwardly facing arms. To test the importance of the IXVXI motif, we created the point mutant V181A, which, as expected, disrupts the Hsp21 dodecamer and decreases chaperone activity. Finally, our data emphasize that sHsp chaperone efficiency depends on oligomerization and that client interactions can occur both with and without oligomer dissociation. These results provide a generalizable workflow to explore sHsps, expand our understanding of sHsp structural motifs, and provide a testable Hsp21 structure model to inform future investigations.
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Affiliation(s)
| | - Johan Härmark
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Yoran Weide
- From the Departments of Biochemistry and Structural Biology and
| | - Hans Hebert
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Morten I Rasmussen
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | | | | | | | - Peter Højrup
- the Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Philip J B Koeck
- the School of Technology and Health, KTH/Royal Institute of Technology and Department of Biosciences and Nutrition, Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
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19
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Zhu X, Yu F, Yang Z, Liu S, Dai C, Lu X, Liu C, Yu W, Li N. In plantachemical cross-linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis. Proteomics 2016; 16:1915-27. [DOI: 10.1002/pmic.201500310] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 04/18/2016] [Accepted: 05/17/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Xinliang Zhu
- Division of Life Science; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an Shaanxi Province P. R. China
| | - Fengchao Yu
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
| | - Zhu Yang
- Division of Life Science; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
| | - Shichang Liu
- Division of Life Science; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
| | - Chen Dai
- Proteomics Center; Nanjing Agriculture University; Nanjing P. R. China
| | - Xiaoyun Lu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education; School of Life Science and Technology; Xi'an Jiaotong University; Xi'an Shaanxi Province P. R. China
| | - Chenyu Liu
- Division of Life Science; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
| | - Weichuan Yu
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
- Department of Electronic and Computer Engineering; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
| | - Ning Li
- Division of Life Science; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Hong Kong SAR P. R. China
- HKUST Shenzhen Research Institute; Shenzhen P. R. China
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20
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Al-Eryani Y, Ib Rasmussen M, Kjellström S, Højrup P, Emanuelsson C, von Wachenfeldt C. Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry. Proteins 2016; 84:1234-45. [DOI: 10.1002/prot.25072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/21/2016] [Accepted: 05/08/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Yusra Al-Eryani
- Department of Biochemistry and Structural Biology; Lund University; PO Box 124 Lund SE-221 00 Sweden
- Department of Biology; Lund University; Sölvegatan 35 Lund SE-223 62 Sweden
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Campusvej 55 Odense M DK-5230 Denmark
| | - Sven Kjellström
- Department of Biochemistry and Structural Biology; Lund University; PO Box 124 Lund SE-221 00 Sweden
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology; University of Southern Denmark; Campusvej 55 Odense M DK-5230 Denmark
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology; Lund University; PO Box 124 Lund SE-221 00 Sweden
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21
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Boelt SG, Norn C, Rasmussen MI, André I, Čiplys E, Slibinskas R, Houen G, Højrup P. Mapping the Ca(2+) induced structural change in calreticulin. J Proteomics 2016; 142:138-48. [PMID: 27195812 DOI: 10.1016/j.jprot.2016.05.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/09/2016] [Accepted: 05/14/2016] [Indexed: 01/04/2023]
Abstract
UNLABELLED Calreticulin is a highly conserved multifunctional protein implicated in many different biological systems and has therefore been the subject of intensive research. It is primarily present in the endoplasmatic reticulum where its main functions are to regulate Ca(2+) homeostasis, act as a chaperone and stabilize the MHC class I peptide-loading complex. Although several high-resolution structures of calreticulin exist, these only cover three-quarters of the entire protein leaving the extended structures unsolved. Additionally, the structure of calreticulin is influenced by the presence of Ca(2+). The conformational changes induced by Ca(2+) have not been determined yet as they are hard to study with traditional approaches. Here, we investigated the Ca(2+)-induced conformational changes with a combination of chemical cross-linking, mass spectrometry, bioinformatics analysis and modelling in Rosetta. Using a bifunctional linker, we found a large Ca(2+)-induced change to the cross-linking pattern in calreticulin. Our results are consistent with a high flexibility in the P-loop, a stabilization of the acidic C-terminal and a relatively close interaction of the P-loop and the acidic C-terminal. BIOLOGICAL SIGNIFICANCE The function of calreticulin, an endoplasmatic reticulin chaperone, is affected by fluctuations in Ca(2+)concentration, but the structural mechanism is unknown. The present work suggests that Ca(2+)-dependent regulation is caused by different conformations of a long proline-rich loop that changes the accessibility to the peptide/lectin-binding site. Our results indicate that the binding of Ca(2+) to calreticulin may thus not only just be a question of Ca(2+) storage but is likely to have an impact on the chaperone activity.
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Affiliation(s)
- Sanne Grundvad Boelt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, DK 2300 Copenhagen, Denmark
| | - Christoffer Norn
- Department of Biochemistry and Structural Biology, Lund University, Paradisgatan 2, SE 221 00 Lund, Sweden
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark
| | - Ingemar André
- Department of Biochemistry and Structural Biology, Lund University, Paradisgatan 2, SE 221 00 Lund, Sweden
| | - Evaldas Čiplys
- Department of Eukayote Gene Engineering, Institute of Biotechnology, Vilnius University, V. Graičiūno St, LT 02241 Vilnius, Lithuania
| | - Rimantas Slibinskas
- Department of Eukayote Gene Engineering, Institute of Biotechnology, Vilnius University, V. Graičiūno St, LT 02241 Vilnius, Lithuania
| | - Gunnar Houen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, DK 2300 Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark.
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22
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Scavenius C, Nikolajsen CL, Stenvang M, Thøgersen IB, Wyrożemski Ł, Wisniewski HG, Otzen DE, Sanggaard KW, Enghild JJ. The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations. J Biol Chem 2016; 291:4658-70. [PMID: 26728454 DOI: 10.1074/jbc.m115.678748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Indexed: 11/06/2022] Open
Abstract
Inter-α-inhibitor is a proteoglycan of unique structure. The protein consists of three subunits, heavy chain 1, heavy chain 2, and bikunin covalently joined by a chondroitin sulfate chain originating at Ser-10 of bikunin. Inter-α-inhibitor interacts with an inflammation-associated protein, tumor necrosis factor-inducible gene 6 protein, in the extracellular matrix. This interaction leads to transfer of the heavy chains from the chondroitin sulfate of inter-α-inhibitor to hyaluronan and consequently to matrix stabilization. Divalent cations and heavy chain 2 are essential co-factors in this transfer reaction. In the present study, we have investigated how divalent cations in concert with the chondroitin sulfate chain influence the structure and stability of inter-α-inhibitor. The results showed that Mg(2+) or Mn(2+), but not Ca(2+), induced a conformational change in inter-α-inhibitor as evidenced by a decrease in the Stokes radius and a bikunin chondroitin sulfate-dependent increase of the thermodynamic stability. This structure was shown to be essential for the ability of inter-α-inhibitor to participate in extracellular matrix stabilization. In addition, the data revealed that bikunin was positioned adjacent to both heavy chains and that the two heavy chains also were in close proximity. The chondroitin sulfate chain interacted with all protein components and inter-α-inhibitor dissociated when it was degraded. Conventional purification protocols result in the removal of the Mg(2+) found in plasma and because divalent cations influence the conformation and affect function it is important to consider this when characterizing the biological activity of inter-α-inhibitor.
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Affiliation(s)
- Carsten Scavenius
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Camilla Lund Nikolajsen
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
| | - Marcel Stenvang
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
| | - Ida B Thøgersen
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Łukasz Wyrożemski
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Hans-Georg Wisniewski
- the Department of Microbiology, New York University School of Medicine, New York, New York 10016
| | - Daniel E Otzen
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
| | - Kristian W Sanggaard
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Jan J Enghild
- From the Department of Molecular Biology and Genetics, Science Park, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark, the Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark, and
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23
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Protein Structural Analysis via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:397-431. [PMID: 27975228 DOI: 10.1007/978-3-319-41448-5_19] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography.
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24
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Koldsø H, Andersen OJ, Nikolajsen CL, Scavenius C, Sørensen CS, Underhaug J, Runager K, Nielsen NC, Enghild JJ, Schiøtt B. Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor β-Induced Protein in Corneal Dystrophies Compared to the Nonfibrillating R555W and R555Q Mutants. Biochemistry 2015; 54:5546-56. [PMID: 26305369 DOI: 10.1021/acs.biochem.5b00473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human transforming growth factor β-induced protein (TGFBIp) is involved in several types of corneal dystrophies where protein aggregation and amyloid fibril formation severely impair vision. Most disease-causing mutations are located in the last of four homologous fasciclin-1 (FAS1) domains of the protein, and it has been shown that when isolated, the fourth FAS1 domain (FAS1-4) mimics the behavior of full-length TGFBIp. In this study, we use molecular dynamics simulations and principal component analysis to study the wild-type FAS1-4 domain along with three disease-causing mutations (R555W, R555Q, and A546T) to decipher any internal difference in dynamical properties of the domains that may explain their varied stabilities and aggregation properties. In addition, we use a protein-protein docking method in combination with chemical cross-linking experiments and mass spectrometry of the cross-linked species to obtain information about interaction faces between identical FAS1-4 domains. The results show that the pathogenic mutations A546T and R555W affect the packing in the hydrophobic core of FAS1-4 in different directions. We further show that the FAS1-4 monomers associate using their β-rich regions, consistent with peptides observed to be part of the amyloid fibril core in lattice corneal dystrophy patients.
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Affiliation(s)
- Heidi Koldsø
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Ole Juul Andersen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Camilla Lund Nikolajsen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Carsten Scavenius
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Charlotte S Sørensen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Jarl Underhaug
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Kasper Runager
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Niels Chr Nielsen
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
| | - Jan J Enghild
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University , Aarhus, Denmark
| | - Birgit Schiøtt
- Center for Insoluble Protein Structures (inSPIN) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Aarhus, Denmark.,Department of Chemistry, Aarhus University , Aarhus, Denmark
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25
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Sinz A, Arlt C, Chorev D, Sharon M. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology. Protein Sci 2015; 24:1193-209. [PMID: 25970732 PMCID: PMC4534171 DOI: 10.1002/pro.2696] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/14/2015] [Accepted: 04/29/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein-protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies.
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Affiliation(s)
- Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-WittenbergD-06120, Halle, Germany
| | - Dror Chorev
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
| | - Michal Sharon
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, 76100, Israel
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Nguyen-Huynh NT, Sharov G, Potel C, Fichter P, Trowitzsch S, Berger I, Lamour V, Schultz P, Potier N, Leize-Wagner E. Chemical cross-linking and mass spectrometry to determine the subunit interaction network in a recombinant human SAGA HAT subcomplex. Protein Sci 2015; 24:1232-46. [PMID: 25753033 DOI: 10.1002/pro.2676] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/03/2015] [Accepted: 03/03/2015] [Indexed: 01/04/2023]
Abstract
Understanding the way how proteins interact with each other to form transient or stable protein complexes is a key aspect in structural biology. In this study, we combined chemical cross-linking with mass spectrometry to determine the binding stoichiometry and map the protein-protein interaction network of a human SAGA HAT subcomplex. MALDI-MS equipped with high mass detection was used to follow the cross-linking reaction using bis[sulfosuccinimidyl] suberate (BS3) and confirm the heterotetrameric stoichiometry of the specific stabilized subcomplex. Cross-linking with isotopically labeled BS3 d0-d4 followed by trypsin digestion allowed the identification of intra- and intercross-linked peptides using two dedicated search engines: pLink and xQuest. The identified interlinked peptides suggest a strong network of interaction between GCN5, ADA2B and ADA3 subunits; SGF29 is interacting with GCN5 and ADA3 but not with ADA2B. These restraint data were combined to molecular modeling and a low-resolution interacting model for the human SAGA HAT subcomplex could be proposed, illustrating the potential of an integrative strategy using cross-linking and mass spectrometry for addressing the structural architecture of multiprotein complexes.
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Affiliation(s)
- Nha-Thi Nguyen-Huynh
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Grigory Sharov
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Clément Potel
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Pélagie Fichter
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Simon Trowitzsch
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Imre Berger
- European Molecular Biology Laboratory (EMBL), Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Valérie Lamour
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Patrick Schultz
- Integrated Structural Biology Department, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), UMR 7104, INSERM U964, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Noëlle Potier
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes (LSMIS) UMR 7140 CNRS/Université de Strasbourg - "Chimie de la Matière Complexe", 1 Rue Blaise Pascal, 67008, Strasbourg, France
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27
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Kosinski J, von Appen A, Ori A, Karius K, Müller CW, Beck M. Xlink Analyzer: software for analysis and visualization of cross-linking data in the context of three-dimensional structures. J Struct Biol 2015; 189:177-83. [PMID: 25661704 PMCID: PMC4359615 DOI: 10.1016/j.jsb.2015.01.014] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/26/2015] [Accepted: 01/28/2015] [Indexed: 12/25/2022]
Abstract
Structural characterization of large multi-subunit protein complexes often requires integrating various experimental techniques. Cross-linking mass spectrometry (XL-MS) identifies proximal protein residues and thus is increasingly used to map protein interactions and determine the relative orientation of subunits within the structure of protein complexes. To fully adapt XL-MS as a structure characterization technique, we developed Xlink Analyzer, a software tool for visualization and analysis of XL-MS data in the context of the three-dimensional structures. Xlink Analyzer enables automatic visualization of cross-links, identifies cross-links violating spatial restraints, calculates violation statistics, maps chemically modified surfaces, and allows interactive manipulations that facilitate analysis of XL-MS data and aid designing new experiments. We demonstrate these features by mapping interaction sites within RNA polymerase I and the Rvb1/2 complex. Xlink Analyzer is implemented as a plugin to UCSF Chimera, a standard structural biology software tool, and thus enables seamless integration of XL-MS data with, e.g. fitting of X-ray structures to EM maps. Xlink Analyzer is available for download at http://www.beck.embl.de/XlinkAnalyzer.html.
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Affiliation(s)
- Jan Kosinski
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alexander von Appen
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alessandro Ori
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Kai Karius
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Christoph W Müller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Martin Beck
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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28
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Lima DB, de Lima TB, Balbuena TS, Neves-Ferreira AGC, Barbosa VC, Gozzo FC, Carvalho PC. SIM-XL: A powerful and user-friendly tool for peptide cross-linking analysis. J Proteomics 2015; 129:51-55. [PMID: 25638023 DOI: 10.1016/j.jprot.2015.01.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 12/21/2022]
Abstract
Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677). This article is part of a Special Issue entitled: Computational Proteomics.
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Affiliation(s)
- Diogo B Lima
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
| | - Tatiani B de Lima
- Dalton Mass Spectrometry Laboratory, University of Campinas, São Paulo, Brazil
| | - Tiago S Balbuena
- College of Agricultural and Veterinary Sciences, State University of São Paulo, Jaboticabal, São Paulo, Brazil
| | | | - Valmir C Barbosa
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fábio C Gozzo
- Dalton Mass Spectrometry Laboratory, University of Campinas, São Paulo, Brazil.
| | - Paulo C Carvalho
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil.
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29
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Nury C, Redeker V, Dautrey S, Romieu A, van der Rest G, Renard PY, Melki R, Chamot-Rooke J. A Novel Bio-Orthogonal Cross-Linker for Improved Protein/Protein Interaction Analysis. Anal Chem 2015; 87:1853-60. [DOI: 10.1021/ac503892c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Catherine Nury
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Virginie Redeker
- Neuroscience Paris-Saclay Institute, CNRS, Gif-sur-Yvette, France
| | - Sébastien Dautrey
- Normandie Université, COBRA UMR 6014 & FR 3038; UNIV Rouen; INSA Rouen; CNRS, IRCOF, 1, rue Tesnières, 76821 Mont-Saint-Aignan Cedex, France
| | - Anthony Romieu
- ICMUB, UMR CNRS 6302, Université de Bourgogne, 9, Avenue Alain Savary, 21078 Dijon, France
- Institut Universitaire de France, 103, Boulevard
Saint-Michel, 75005 Paris, France
| | | | - Pierre-Yves Renard
- Normandie Université, COBRA UMR 6014 & FR 3038; UNIV Rouen; INSA Rouen; CNRS, IRCOF, 1, rue Tesnières, 76821 Mont-Saint-Aignan Cedex, France
| | - Ronald Melki
- Neuroscience Paris-Saclay Institute, CNRS, Gif-sur-Yvette, France
| | - Julia Chamot-Rooke
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
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30
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Petrotchenko EV, Makepeace KA, Borchers CH. DXMSMS Match Program for Automated Analysis of LC‐MS/MS Data Obtained Using Isotopically Coded CID‐Cleavable Cross‐Linking Reagents. ACTA ACUST UNITED AC 2014; 48:8.18.1-8.18.19. [DOI: 10.1002/0471250953.bi0818s48] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Evgeniy V. Petrotchenko
- University of Victoria – Genome British Columbia Proteomics Centre, University of Victoria Victoria Canada
| | - Karl A.T. Makepeace
- University of Victoria – Genome British Columbia Proteomics Centre, University of Victoria Victoria Canada
| | - Christoph H. Borchers
- University of Victoria – Genome British Columbia Proteomics Centre, University of Victoria Victoria Canada
- Department of Biochemistry & Microbiology, University of Victoria, University of Victoria Victoria Canada
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31
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Sinz A. The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks. Expert Rev Proteomics 2014; 11:733-43. [DOI: 10.1586/14789450.2014.960852] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Clavier S, Du X, Sagan S, Bolbach G, Sachon E. An integrated cross-linking-MS approach to investigate cell penetrating peptides interacting partners. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Peng L, Rasmussen MI, Chailyan A, Houen G, Højrup P. Probing the structure of human protein disulfide isomerase by chemical cross-linking combined with mass spectrometry. J Proteomics 2014; 108:1-16. [PMID: 24792702 DOI: 10.1016/j.jprot.2014.04.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/07/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022]
Abstract
UNLABELLED Protein disulfide-isomerase (PDI) is a four-domain flexible protein that catalyzes the formation of disulfide bonds in the endoplasmic reticulum. Here we have analyzed native PDI purified from human placenta by chemical cross-linking followed by mass spectrometry (CXMS). In addition to PDI the sample contained soluble calnexin and ERp72. Extensive cross-linking was observed within the PDI molecule, both intra- and inter-domain, as well as between the different components in the mixture. The high sensitivity of the analysis in the current experiments, combined with a likely promiscuous interaction pattern of the involved proteins, revealed relatively densely populated cross-link heat maps. The established X-ray structure of the monomeric PDI could be confirmed; however, the dimer as presented in the existing models does not seem to be prevalent in solution as modeling on the observed cross-links revealed new models of dimeric PDI. The observed inter-protein cross-links confirmed the existence of a peptide binding area on calnexin that binds strongly both PDI and ERp72. On the other hand, interaction sites on PDI and ERp72 could not be uniquely identified, indicating a more non-specific interaction pattern. BIOLOGICAL SIGNIFICANCE The present work demonstrates the use of chemical cross-linking and mass spectrometry (CXMS) for the determination of a solution structure of natural human PDI and its interaction with the chaperones ERp72 and calnexin. The data shows that the dimeric structure of PDI may be more diverse than indicated by present models. We further observe that the temperature influences the cross-linking pattern of PDI, but this does not influence the overall folding pattern of the molecule.
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Affiliation(s)
- Li Peng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anna Chailyan
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Gunnar Houen
- Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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34
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Tinnefeld V, Sickmann A, Ahrends R. Catch me if you can: challenges and applications of cross-linking approaches. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2014; 20:99-116. [PMID: 24881459 DOI: 10.1255/ejms.1259] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Biomolecular complexes are the groundwork of life and the basis for cell signaling, energy transfer, motion, stability and cellular metabolism. Understanding the underlying complex interactions on the molecular level is an essential step to obtain a comprehensive insight into cellular and systems biology. For the investigation of molecular interactions, various methods, including Förster resonance energy transfer, nuclear magnetic resonance spectroscopy, X-ray crystallography and yeast two-hybrid screening, can be utilized. Nevertheless, the most reliable approach for structural proteomics and the identification of novel protein-binding partners is chemical cross-linking. The rationale is that upon forming a covalent bond between a protein and its interaction partner (protein, lipid, RNA/DNA, carbohydrate) the native complex state is "frozen" and accessible for detailed mass spectrometric analysis. In this review we provide a synopsis on crosslinker design, chemistry, pitfalls, limitations and novel applications in the field, and feature an overview of current software applications.
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35
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Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat Protoc 2013; 9:120-37. [DOI: 10.1038/nprot.2013.168] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Holding AN, Lamers MH, Stephens E, Skehel JM. Hekate: software suite for the mass spectrometric analysis and three-dimensional visualization of cross-linked protein samples. J Proteome Res 2013; 12:5923-33. [PMID: 24010795 PMCID: PMC3859183 DOI: 10.1021/pr4003867] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Chemical cross-linking
of proteins combined with mass spectrometry
provides an attractive and novel method for the analysis of native
protein structures and protein complexes. Analysis of the data however
is complex. Only a small number of cross-linked peptides are produced
during sample preparation and must be identified against a background
of more abundant native peptides. To facilitate the search and identification
of cross-linked peptides, we have developed a novel software suite,
named Hekate. Hekate is a suite of tools that address the challenges
involved in analyzing protein cross-linking experiments when combined
with mass spectrometry. The software is an integrated pipeline for
the automation of the data analysis workflow and provides a novel
scoring system based on principles of linear peptide analysis. In
addition, it provides a tool for the visualization of identified cross-links
using three-dimensional models, which is particularly useful when
combining chemical cross-linking with other structural techniques.
Hekate was validated by the comparative analysis of cytochrome c (bovine heart) against previously reported data.1 Further validation was carried out on known structural
elements of DNA polymerase III, the catalytic α-subunit of the Escherichia coli DNA replisome along with new insight
into the previously uncharacterized C-terminal domain of the protein.
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Affiliation(s)
- Andrew N Holding
- MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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37
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Olsen DT, Peng L, Træholt SD, Duus K, Højrup P, Houen G. Purification and characterization of a soluble calnexin from human placenta. Protein Expr Purif 2013; 92:105-11. [PMID: 24056258 DOI: 10.1016/j.pep.2013.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 08/26/2013] [Accepted: 09/10/2013] [Indexed: 11/16/2022]
Abstract
Calreticulin (Crt) and calnexin (Cnx) are homologous endoplasmic reticulum (ER) chaperones involved in protein folding and quality control. Crt is a soluble ER luminal Mr 46 kDa protein and Cnx is a Mr 67kDa ER membrane protein. During purification of Crt from human placenta a soluble form of Cnx (sCnx) was consistently identified in a separate ion exchange chromatography peak. The sCnx was further purified and characterised. This showed that the protein had been cleaved after residue 472 (between Gln and Met), thus liberating it from the transmembrane and cytoplasmic parts of Cnx. The extraction and initial purification steps were carried out in the presence of protease inhibitors, thus ruling out that the cleavage was an artefact of the isolation procedure. This indicates that sCnx may have a physiological chaperone function similar to that of Crt.
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Affiliation(s)
- Dorthe T Olsen
- Department of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark
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38
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Lauber MA, Rappsilber J, Reilly JP. Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry. Mol Cell Proteomics 2012; 11:1965-76. [PMID: 23033476 PMCID: PMC3518124 DOI: 10.1074/mcp.m112.019562] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 09/19/2012] [Indexed: 11/23/2022] Open
Abstract
Ribosomal protein S1 has been shown to be a significant effector of prokaryotic translation. The protein is in fact capable of efficiently initiating translation, regardless of the presence of a Shine-Dalgarno sequence in mRNA. Structural insights into this process have remained elusive, as S1 is recalcitrant to traditional techniques of structural analysis, such as x-ray crystallography. Through the application of protein cross-linking and high resolution mass spectrometry, we have detailed the ribosomal binding site of S1 and have observed evidence of its dynamics. Our results support a previous hypothesis that S1 acts as the mRNA catching arm of the prokaryotic ribosome. We also demonstrate that in solution the major domains of the 30S subunit are remarkably flexible, capable of moving 30-50Å with respect to one another.
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Affiliation(s)
- Matthew A. Lauber
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Juri Rappsilber
- §Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, UK and Institut für Biotechnologie, Technische Universität Berlin, 13353 Berlin, Germany
| | - James P. Reilly
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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39
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Schulze WX, Sanggaard KW, Kreuzer I, Knudsen AD, Bemm F, Thøgersen IB, Bräutigam A, Thomsen LR, Schliesky S, Dyrlund TF, Escalante-Perez M, Becker D, Schultz J, Karring H, Weber A, Højrup P, Hedrich R, Enghild JJ. The protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms. Mol Cell Proteomics 2012; 11:1306-19. [PMID: 22891002 PMCID: PMC3494193 DOI: 10.1074/mcp.m112.021006] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/26/2012] [Indexed: 11/06/2022] Open
Abstract
The Venus flytrap (Dionaea muscipula) is one of the most well-known carnivorous plants because of its unique ability to capture small animals, usually insects or spiders, through a unique snap-trapping mechanism. The animals are subsequently killed and digested so that the plants can assimilate nutrients, as they grow in mineral-deficient soils. We deep sequenced the cDNA from Dionaea traps to obtain transcript libraries, which were used in the mass spectrometry-based identification of the proteins secreted during digestion. The identified proteins consisted of peroxidases, nucleases, phosphatases, phospholipases, a glucanase, chitinases, and proteolytic enzymes, including four cysteine proteases, two aspartic proteases, and a serine carboxypeptidase. The majority of the most abundant proteins were categorized as pathogenesis-related proteins, suggesting that the plant's digestive system evolved from defense-related processes. This in-depth characterization of a highly specialized secreted fluid from a carnivorous plant provides new information about the plant's prey digestion mechanism and the evolutionary processes driving its defense pathways and nutrient acquisition.
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Affiliation(s)
- Waltraud X. Schulze
- From the ‡Max Planck Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Kristian W. Sanggaard
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Ines Kreuzer
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Anders D. Knudsen
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Felix Bemm
- ‖Department of Bioinformatics, Biozentrum, Am Hubland, Universität Würzburg, D-97074 Wuerzburg, Germany
| | - Ida B. Thøgersen
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Andrea Bräutigam
- ‡‡Department of Plant Biochemistry, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Line R. Thomsen
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Simon Schliesky
- ‡‡Department of Plant Biochemistry, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Thomas F. Dyrlund
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
| | - Maria Escalante-Perez
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Dirk Becker
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Jörg Schultz
- ‖Department of Bioinformatics, Biozentrum, Am Hubland, Universität Würzburg, D-97074 Wuerzburg, Germany
| | - Henrik Karring
- §§University of Southern Denmark, Institute of Chemical Engineering, Biotechnology and Environmental Technology, Niels Bohrs Allé 1, 5230 Odense M, Denmark
| | - Andreas Weber
- ‡‡Department of Plant Biochemistry, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Peter Højrup
- ¶¶Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Rainer Hedrich
- ¶Department of Molecular Plant Physiology & Biophysics, Universität Würzburg, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
- ‖‖Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Jan J. Enghild
- §Department of Molecular Biology and Genetics, Aarhus University, Gustav Wiedsvej 10C, 8000 Aarhus C, Denmark
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Greibe E, Fedosov S, Sorensen BS, Højrup P, Poulsen SS, Nexo E. A single rainbow trout cobalamin-binding protein stands in for three human binders. J Biol Chem 2012; 287:33917-25. [PMID: 22872637 DOI: 10.1074/jbc.m112.398016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cobalamin uptake and transport in mammals are mediated by three cobalamin-binding proteins: haptocorrin, intrinsic factor, and transcobalamin. The nature of cobalamin-binding proteins in lower vertebrates remains to be elucidated. The aim of this study was to characterize the cobalamin-binding proteins of the rainbow trout (Oncorhynchus mykiss) and to compare their properties with those of the three human cobalamin-binding proteins. High cobalamin-binding capacity was found in trout stomach (210 pmol/g), roe (400 pmol/g), roe fluid (390 nmol/liter), and plasma (2500 nmol/liter). In all cases, it appeared to be the same protein based on analysis of partial sequences and immunological responses. The trout cobalamin-binding protein was purified from roe fluid, sequenced, and further characterized. Like haptocorrin, the trout cobalamin-binding protein was stable at low pH and had a high binding affinity for the cobalamin analog cobinamide. Like haptocorrin and transcobalamin, the trout cobalamin-binding protein was present in plasma and recognized ligands with altered nucleotide moiety. Like intrinsic factors, the trout cobalamin-binding protein was present in the stomach and resisted degradation by trypsin and chymotrypsin. It also resembled intrinsic factor in the composition of conserved residues in the primary cobalamin-binding site in the C terminus. The trout cobalamin-binding protein was glycosylated and displayed spectral properties comparable with those of haptocorrin and intrinsic factor. In conclusion, only one soluble cobalamin-binding protein was identified in the rainbow trout, a protein that structurally behaves like an intermediate between the three human cobalamin-binding proteins.
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Affiliation(s)
- Eva Greibe
- Department of Clinical Biochemistry, Aarhus University Hospital, 8000 Aarhus, Denmark.
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Söderberg CAG, Lambert W, Kjellström S, Wiegandt A, Wulff RP, Månsson C, Rutsdottir G, Emanuelsson C. Detection of crosslinks within and between proteins by LC-MALDI-TOFTOF and the software FINDX to reduce the MSMS-data to acquire for validation. PLoS One 2012; 7:e38927. [PMID: 22723907 PMCID: PMC3377668 DOI: 10.1371/journal.pone.0038927] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 05/14/2012] [Indexed: 11/19/2022] Open
Abstract
Lysine-specific chemical crosslinking in combination with mass spectrometry is emerging as a tool for the structural characterization of protein complexes and protein-protein interactions. After tryptic digestion of crosslinked proteins there are thousands of peptides amenable to MSMS, of which only very few are crosslinked peptides of interest. Here we describe how the advantage offered by off-line LC-MALDI-TOF/TOF mass spectrometry is exploited in a two-step workflow to focus the MSMS-acquisition on crosslinks mainly. In a first step, MS-data are acquired and all the peak list files from the LC-separated fractions are merged by the FINDX software and screened for presence of crosslinks which are recognized as isotope-labeled doublet peaks. Information on the isotope doublet peak mass and intensity can be used as search constraints to reduce the number of false positives that match randomly to the observed peak masses. Based on the MS-data a precursor ion inclusion list is generated and used in a second step, where a restricted number of MSMS-spectra are acquired for crosslink validation. The decoupling of MS and MSMS and the peptide sorting with FINDX based on MS-data has the advantage that MSMS can be restricted to and focused on crosslinks of Type 2, which are of highest biological interest but often lowest in abundance. The LC-MALDI TOF/TOF workflow here described is applicable to protein multisubunit complexes and using (14)N/(15)N mixed isotope strategy for the detection of inter-protein crosslinks within protein oligomers.
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Affiliation(s)
- Christopher A. G. Söderberg
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Wietske Lambert
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Sven Kjellström
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Alena Wiegandt
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Ragna Peterson Wulff
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Cecilia Månsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Gudrun Rutsdottir
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, Lund, Sweden
- * E-mail:
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