1
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Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, Tänzler D, Shulman N, Riffle M, MacLean BX, Sinz A. A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline. Anal Chem 2024; 96:7373-7379. [PMID: 38696819 PMCID: PMC11099889 DOI: 10.1021/acs.analchem.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/04/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions. This study describes the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions by XL-MS. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundant cross-linked peptides, and a data acquisition bias, our current study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data-independent acquisition (DIA) in XL-MS with a vendor-neutral and open-source platform. A novel workflow is described for processing data-dependent acquisition (DDA) of PASEF-derived information. For this, software by Bruker Daltonics is used, enabling the conversion of these data into a format that is compatible with MeroX and Skyline software tools. Our approach significantly improves the identification of cross-linked products from complex mixtures, allowing the XL-MS community to overcome current analytical limitations.
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Affiliation(s)
- Juan Camilo Rojas Echeverri
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Frank Hause
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Institute
for Molecular Medicine, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Claudio Iacobucci
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
- Department
of Physical and Chemical Sciences, University
of L’Aquila, 67100 L’Aquila, Italy
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Dirk Tänzler
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
| | - Nicholas Shulman
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Brendan X. MacLean
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Martin-Luther-University Halle-Wittenberg, 06120 Halle, Germany
- Center
for Structural Mass Spectrometry, Martin-Luther-University
Halle-Wittenberg, 06120 Halle, Germany
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2
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Mandal K, Wicaksono G, Yu C, Adams JJ, Hoopmann MR, Temple WC, Izgutdina A, Escobar BP, Gorelik M, Ihling CH, Nix MA, Naik A, Xie WH, Hübner J, Rollins LA, Reid SM, Ramos E, Kasap C, Steri V, Serrano JAC, Salangsang F, Phojanakong P, McMillan M, Gavallos V, Leavitt AD, Logan AC, Rooney CM, Eyquem J, Sinz A, Huang BJ, Stieglitz E, Smith CC, Moritz RL, Sidhu SS, Huang L, Wiita AP. Structural surfaceomics reveals an AML-specific conformation of integrin β 2 as a CAR T cellular therapy target. Nat Cancer 2023; 4:1592-1609. [PMID: 37904046 PMCID: PMC10663162 DOI: 10.1038/s43018-023-00652-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/12/2023] [Indexed: 11/01/2023]
Abstract
Safely expanding indications for cellular therapies has been challenging given a lack of highly cancer-specific surface markers. Here we explore the hypothesis that tumor cells express cancer-specific surface protein conformations that are invisible to standard target discovery pipelines evaluating gene or protein expression, and these conformations can be identified and immunotherapeutically targeted. We term this strategy integrating cross-linking mass spectrometry with glycoprotein surface capture 'structural surfaceomics'. As a proof of principle, we apply this technology to acute myeloid leukemia (AML), a hematologic malignancy with dismal outcomes and no known optimal immunotherapy target. We identify the activated conformation of integrin β2 as a structurally defined, widely expressed AML-specific target. We develop and characterize recombinant antibodies to this protein conformation and show that chimeric antigen receptor T cells eliminate AML cells and patient-derived xenografts without notable toxicity toward normal hematopoietic cells. Our findings validate an AML conformation-specific target antigen and demonstrate a tool kit for applying these strategies more broadly.
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Affiliation(s)
- Kamal Mandal
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gianina Wicaksono
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Jarrett J Adams
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- School of Pharmacy, University of Waterloo, Kitchener, Ontario, Canada
| | | | - William C Temple
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California San Francisco, San Francisco, CA, USA
| | - Adila Izgutdina
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Bonell Patiño Escobar
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Maryna Gorelik
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Matthew A Nix
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Akul Naik
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - William H Xie
- UCSF/Gladstone Institute for Genomic Immunology, San Francisco, CA, USA
| | - Juwita Hübner
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa A Rollins
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA
| | - Sandy M Reid
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA
| | - Emilio Ramos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Corynn Kasap
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Veronica Steri
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Juan Antonio Camara Serrano
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Fernando Salangsang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Paul Phojanakong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Melanie McMillan
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Victor Gavallos
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Andrew D Leavitt
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Aaron C Logan
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Cliona M Rooney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston Methodist Hospital-Texas Children's Hospital, Houston, TX, USA
| | - Justin Eyquem
- UCSF/Gladstone Institute for Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Benjamin J Huang
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Catherine C Smith
- Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, CA, USA
| | | | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- School of Pharmacy, University of Waterloo, Kitchener, Ontario, Canada
| | - Lan Huang
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
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3
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Di Ianni A, Tüting C, Kipping M, Ihling CH, Köppen J, Iacobucci C, Arlt C, Kastritis PL, Sinz A. Structural assessment of the full-length wild-type tumor suppressor protein p53 by mass spectrometry-guided computational modeling. Sci Rep 2023; 13:8497. [PMID: 37231156 DOI: 10.1038/s41598-023-35437-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
The tetrameric tumor suppressor p53 represents a great challenge for 3D-structural analysis due to its high degree of intrinsic disorder (ca. 40%). We aim to shed light on the structural and functional roles of p53's C-terminal region in full-length, wild-type human p53 tetramer and their importance for DNA binding. For this, we employed complementary techniques of structural mass spectrometry (MS) in an integrated approach with computational modeling. Our results show no major conformational differences in p53 between DNA-bound and DNA-free states, but reveal a substantial compaction of p53's C-terminal region. This supports the proposed mechanism of unspecific DNA binding to the C-terminal region of p53 prior to transcription initiation by specific DNA binding to the core domain of p53. The synergies between complementary structural MS techniques and computational modeling as pursued in our integrative approach is envisioned to serve as general strategy for studying intrinsically disordered proteins (IDPs) and intrinsically disordered region (IDRs).
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Affiliation(s)
- Alessio Di Ianni
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Christian Tüting
- ZIK HALOmem and Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Marc Kipping
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Janett Köppen
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, Coppito, 67100, L'Aquila, Italy
| | - Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
| | - Panagiotis L Kastritis
- ZIK HALOmem and Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 01620, Halle (Saale), Germany.
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4
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Ubbiali D, Fratini M, Piersimoni L, Ihling CH, Kipping M, Heilmann I, Iacobucci C, Sinz A. Direct Observation of "Elongated" Conformational States in α-Synuclein upon Liquid-Liquid Phase Separation. Angew Chem Int Ed Engl 2022; 61:e202205726. [PMID: 36115020 PMCID: PMC9828221 DOI: 10.1002/anie.202205726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Indexed: 01/12/2023]
Abstract
α-Synuclein (α-syn) is an intrinsically disordered protein (IDP) that undergoes liquid-liquid phase separation (LLPS), fibrillation, and forms insoluble intracellular Lewy bodies in neurons, which are the hallmark of Parkinson's Disease (PD). Neurotoxicity precedes the formation of aggregates and might be related to α-syn LLPS. The molecular mechanisms underlying the early stages of LLPS are still elusive. To obtain structural insights into α-syn upon LLPS, we take advantage of cross-linking/mass spectrometry (XL-MS) and introduce an innovative approach, termed COMPASS (COMPetitive PAiring StatisticS). In this work, we show that the conformational ensemble of α-syn shifts from a "hairpin-like" structure towards more "elongated" conformational states upon LLPS. We obtain insights into the critical initial stages of LLPS and establish a novel mass spectrometry-based approach that will aid to solve open questions in LLPS structural biology.
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Affiliation(s)
- Daniele Ubbiali
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Marta Fratini
- Department of Plant BiochemistryCharles Tanford Protein CenterInstitute for Biochemistry and BiotechnologyMartin-Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Lolita Piersimoni
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Marc Kipping
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Ingo Heilmann
- Department of Plant BiochemistryCharles Tanford Protein CenterInstitute for Biochemistry and BiotechnologyMartin-Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Department of Physical and Chemical SciencesUniversity of L'AquilaVia Vetoio, Coppito67100L'AquilaItaly
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of PharmacyMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany,Center for Structural Mass SpectrometryMartin Luther University Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
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5
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Sinz A, Wei AAJ, Iacobucci C, Schultze W, Ihling CH, Arlt C. Different Oligomeric States of the Tumor Suppressor p53 Show Identical Binding Behavior Towards the S100β Homodimer. Chembiochem 2022; 23:e202100665. [PMID: 35333001 PMCID: PMC9400850 DOI: 10.1002/cbic.202100665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/01/2022] [Indexed: 12/01/2022]
Abstract
The tumor suppressor protein p53 is a transcription factor that is referred to as the “guardian of the genome” and plays an important role in cancer development. p53 is active as a homotetramer; the S100β homodimer binds to the intrinsically disordered C‐terminus of p53 affecting its transcriptional activity. The p53/S100β complex is regarded as highly promising therapeutic target in cancer. It has been suggested that S100β exerts its oncogenic effects by altering the p53 oligomeric state. Our aim was to study the structures and oligomerization behavior of different p53/S100β complexes by ESI‐MS, XL‐MS, and SPR. Wild‐type p53 and single amino acid variants, representing different oligomeric states of p53 were individually investigated regarding their binding behavior towards S100β. The stoichiometry of the different p53/S100β complexes were determined by ESI‐MS showing that tetrameric, dimeric, and monomeric p53 variants all bind to an S100β dimer. In addition, XL‐MS revealed the topologies of the p53/S100β complexes to be independent of p53’s oligomeric state. With SPR, the thermodynamic parameters were determined for S100β binding to tetrameric, dimeric, or monomeric p53 variants. Our data prove that the S100β homodimer binds to different oligomeric states of p53 with similar binding affinities. This emphasizes the need for alternative explanations to describe the molecular mechanisms underlying p53/S100β interaction.
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Affiliation(s)
- Andrea Sinz
- Martin-Luther-University Halle-Wittenberg, Institute of Pharmacy, Wolfgang-Langenbeck-Strasse 4, 6120, Halle, GERMANY
| | - Alan An Jung Wei
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Department of Pharm.Chem. & Bioanalytics, 06120, Halle, GERMANY
| | - Claudio Iacobucci
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Department of Pharm. Chem. & Bioanalytics, 06120, Halle, GERMANY
| | - Wiebke Schultze
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Department of Pharm. Chem. & Bioanalytics, 06120, Halle, GERMANY
| | - Christian H Ihling
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Department of Pharm. Chem. & Bioanalytics, 06120, Halle, GERMANY
| | - Christian Arlt
- Martin-Luther-Universität Halle-Wittenberg: Martin-Luther-Universitat Halle-Wittenberg, Department of Pharm. Chem. & Bioanalytics, 06120, Halle, GERMANY
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6
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Ihling CH, Piersimoni L, Kipping M, Sinz A. Cross-Linking/Mass Spectrometry Combined with Ion Mobility on a timsTOF Pro Instrument for Structural Proteomics. Anal Chem 2021; 93:11442-11450. [PMID: 34375526 DOI: 10.1021/acs.analchem.1c01317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The combination of cross-linking/mass spectrometry (XL-MS) and ion mobility is still underexplored for conducting protein conformational and protein-protein interaction studies. We present a method for analyzing cross-linking mixtures on a timsTOF Pro mass spectrometer that allows separating ions based on their gas-phase mobilities. Cross-linking was performed with three urea-based MS-cleavable cross-linkers that deliver distinct fragmentation patterns for cross-linked species upon collisional activation. The discrimination of cross-linked species from non-cross-linked peptides was readily performed based on their collisional cross sections. We demonstrate the general feasibility of our combined XL-MS/ion mobility approach for three protein systems of increasing complexity: (i) bovine serum albumin (BSA), (ii) Escherichia coli ribosome, and (iii) HEK293T cell nuclear lysates. We identified a total of 623 unique cross-linking sites for BSA, 670 for the E. coli ribosome, and 1623 unique cross-links for nuclear lysates, corresponding to 1088 intra- and 535 interprotein interactions and yielding 564 distinct protein-protein interactions. Our results underline the strength of combining XL-MS with ion mobility not only for deriving three-dimensional (3D) structures of single proteins but also for performing system-wide protein interaction studies.
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Affiliation(s)
- Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany
| | - Lolita Piersimoni
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany
| | - Marc Kipping
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, D-06120 Halle (Saale), Germany
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7
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Niemeyer M, Castillo EM, Ihling CH, Iacobucci C, Wilde V, Hellmuth A, Hoehenwarter W, Samodelov SL, Zurbriggen MD, Kastritis PL, Sinz A, Villalobos LIAC. Author Correction: Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies. Nat Commun 2021; 12:1768. [PMID: 33723268 PMCID: PMC7961026 DOI: 10.1038/s41467-021-22151-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Michael Niemeyer
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Elena Moreno Castillo
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Verona Wilde
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Antje Hellmuth
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Wolfgang Hoehenwarter
- Proteome Analytics, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Sophia L Samodelov
- Institute of Synthetic Biology & Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology & Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Panagiotis L Kastritis
- ZIK HALOMEM & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Luz Irina A Calderón Villalobos
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany.
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8
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Tüting C, Iacobucci C, Ihling CH, Kastritis PL, Sinz A. Structural analysis of 70S ribosomes by cross-linking/mass spectrometry reveals conformational plasticity. Sci Rep 2020; 10:12618. [PMID: 32724211 PMCID: PMC7387497 DOI: 10.1038/s41598-020-69313-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
The ribosome is not only a highly complex molecular machine that translates the genetic information into proteins, but also an exceptional specimen for testing and optimizing cross-linking/mass spectrometry (XL-MS) workflows. Due to its high abundance, ribosomal proteins are frequently identified in proteome-wide XL-MS studies of cells or cell extracts. Here, we performed in-depth cross-linking of the E. coli ribosome using the amine-reactive cross-linker disuccinimidyl diacetic urea (DSAU). We analyzed 143 E. coli ribosomal structures, mapping a total of 10,771 intramolecular distances for 126 cross-link-pairs and 3,405 intermolecular distances for 97 protein pairs. Remarkably, 44% of intermolecular cross-links covered regions that have not been resolved in any high-resolution E. coli ribosome structure and point to a plasticity of cross-linked regions. We systematically characterized all cross-links and discovered flexible regions, conformational changes, and stoichiometric variations in bound ribosomal proteins, and ultimately remodeled 2,057 residues (15,794 atoms) in total. Our working model explains more than 95% of all cross-links, resulting in an optimized E. coli ribosome structure based on the cross-linking data obtained. Our study might serve as benchmark for conducting biochemical experiments on newly modeled protein regions, guided by XL-MS. Data are available via ProteomeXchange with identifier PXD018935.
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Affiliation(s)
- Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
| | - 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
- Corporate Preclinical R&D, Analytics and Early Formulations Department, CHIESI FARMACEUTICI S.P.A., Via Palermo 26/A, 43122, Parma, Italy
| | - 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
- Center for Structural Mass Spectrometry, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany.
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 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.
- Center for Structural Mass Spectrometry, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle/Saale, Germany.
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9
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Niemeyer M, Moreno Castillo E, Ihling CH, Iacobucci C, Wilde V, Hellmuth A, Hoehenwarter W, Samodelov SL, Zurbriggen MD, Kastritis PL, Sinz A, Calderón Villalobos LIA. Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies. Nat Commun 2020; 11:2277. [PMID: 32385295 PMCID: PMC7210949 DOI: 10.1038/s41467-020-16147-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/17/2020] [Indexed: 12/31/2022] Open
Abstract
Cullin RING-type E3 ubiquitin ligases SCFTIR1/AFB1-5 and their AUX/IAA targets perceive the phytohormone auxin. The F-box protein TIR1 binds a surface-exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, by adopting biochemical, structural proteomics and in vivo approaches we unveil how flexibility in AUX/IAAs and regions in TIR1 affect their conformational ensemble allowing surface accessibility of degrons. We resolve TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) in the degron’s vicinity, cooperatively position AUX/IAAs on TIR1. We identify essential residues at the TIR1 N- and C-termini, which provide non-native interaction interfaces with IDRs and the folded PB1 domain of AUX/IAAs. We thereby establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for a multiplicity of functional states. Auxin-mediated recruitment of AUX/IAAs by the F-box protein TIR1 prompts rapid AUX/IAA ubiquitylation and degradation. By resolving auxin receptor topology, the authors show that intrinsically disordered regions near the degrons of two Aux/IAA proteins reinforce complex assembly and position Aux/IAAs for ubiquitylation.
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Affiliation(s)
- Michael Niemeyer
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Elena Moreno Castillo
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Verona Wilde
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Antje Hellmuth
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Wolfgang Hoehenwarter
- Proteome Analytics, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany
| | - Sophia L Samodelov
- Institute of Synthetic Biology & Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology & Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Panagiotis L Kastritis
- ZIK HALOMEM & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Straße 3a, 06120, Halle (Saale), Germany
| | - Luz Irina A Calderón Villalobos
- Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, 06120, Halle (Saale), Germany.
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10
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Ihling CH, Springorum P, Iacobucci C, Hage C, Götze M, Schäfer M, Sinz A. The Isotope-Labeled, MS-Cleavable Cross-Linker Disuccinimidyl Dibutyric Urea for Improved Cross-Linking/Mass Spectrometry Studies. J Am Soc Mass Spectrom 2020; 31:183-189. [PMID: 32031397 DOI: 10.1021/jasms.9b00008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Previous studies have shown the benefits of the amine-reactive, CID-MS/MS-cleavable cross-linker disuccinimidyl dibutyric urea (DSBU) for structural proteomics studies via cross-linking/MS (XL-MS). To further facilitate the automation of XL-MS experiments, we synthesized a deuterated (D12) version of the DSBU cross-linker combining the advantages of MS-cleavable linkers and isotope labeling. The rationale of conducting XL-MS with a mixture of unlabeled and stable isotope-labeled DSBU is to obtain characteristic mass differences at the MS level indicating cross-linked species. These cross-linked species can then be selected for fragmentation by collisional activation. At the MS/MS level, the characteristic 26-u doublets arising from cleavage of the central urea group in DSBU confirm the amino acid sequences of cross-linked peptides as well as the exact cross-linking sites. D12-labeled DSBU was tested on three systems with increasing complexity: (i) bovine serum albumin as purified protein, (ii) Escherichia coli ribosome as large, multimeric protein assembly, and (iii) Drosophila embryo extract as complete proteome. We demonstrate the benefits arising from the use of isotope-labeled DSBU for an automated assignment of cross-linked products. Combining isotope labeling and MS cleavability in one cross-linker resulted in higher cross-link identification numbers especially for highly complex protein mixtures.
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Affiliation(s)
- Christian H Ihling
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Patrizia Springorum
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Claudio Iacobucci
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Christoph Hage
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
| | - Michael Götze
- Institute of Biochemistry , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle (Saale) , Germany
| | - Mathias Schäfer
- Department of Chemistry , University Cologne , Greinstr. 4 , D-50939 Köln , Germany
| | - Andrea Sinz
- Institute of Pharmacy , Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center , Kurt-Mothes-Str. 3a , D-06120 Halle/Saale , Germany
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11
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Piotrowski C, Moretti R, Ihling CH, Haedicke A, Liepold T, Lipstein N, Meiler J, Jahn O, Sinz A. Delineating the Molecular Basis of the Calmodulin‒bMunc13-2 Interaction by Cross-Linking/Mass Spectrometry-Evidence for a Novel CaM Binding Motif in bMunc13-2. Cells 2020; 9:cells9010136. [PMID: 31936129 PMCID: PMC7017353 DOI: 10.3390/cells9010136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/23/2019] [Accepted: 01/02/2020] [Indexed: 01/20/2023] Open
Abstract
Exploring the interactions between the Ca2+ binding protein calmodulin (CaM) and its target proteins remains a challenging task. Members of the Munc13 protein family play an essential role in short-term synaptic plasticity, modulated via the interaction with CaM at the presynaptic compartment. In this study, we focus on the bMunc13-2 isoform expressed in the brain, as strong changes in synaptic transmission were observed upon its mutagenesis or deletion. The CaM–bMunc13-2 interaction was previously characterized at the molecular level using short bMunc13-2-derived peptides only, revealing a classical 1–5–10 CaM binding motif. Using larger protein constructs, we have now identified for the first time a novel and unique CaM binding site in bMunc13-2 that contains an N-terminal extension of a classical 1–5–10 CaM binding motif. We characterize this motif using a range of biochemical and biophysical methods and highlight its importance for the CaM–bMunc13-2 interaction.
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Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Rocco Moretti
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, TN 37221, USA
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - André Haedicke
- Biophysical Chemistry, Institute of Chemistry, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Thomas Liepold
- Proteomics Group, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
| | - Noa Lipstein
- Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
| | - Jens Meiler
- Center for Structural Biology, Department of Chemistry, Vanderbilt University, Nashville, TN 37221, USA
| | - Olaf Jahn
- Proteomics Group, Max Planck Institute of Experimental Medicine, D-37075 Göttingen, Germany
- Correspondence: (O.J.); (A.S.); Tel.: +49-551-3899-313 (O.J.); +49-345-5525170 (A.S.)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
- Correspondence: (O.J.); (A.S.); Tel.: +49-551-3899-313 (O.J.); +49-345-5525170 (A.S.)
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12
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Götze M, Iacobucci C, Ihling CH, Sinz A. A Simple Cross-Linking/Mass Spectrometry Workflow for Studying System-wide Protein Interactions. Anal Chem 2019; 91:10236-10244. [DOI: 10.1021/acs.analchem.9b02372] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Michael Götze
- Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, D-06120 Halle (Saale), Germany
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13
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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. J Am Soc Mass Spectrom 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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Rehkamp A, Tänzler D, Iacobucci C, Golbik RP, Ihling CH, Sinz A. Molecular Details of Retinal Guanylyl Cyclase 1/GCAP-2 Interaction. Front Mol Neurosci 2018; 11:330. [PMID: 30283299 PMCID: PMC6156451 DOI: 10.3389/fnmol.2018.00330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/27/2018] [Indexed: 12/13/2022] Open
Abstract
The rod outer segment guanylyl cyclase 1 (ROS-GC1) is an essential component of photo-transduction in the retina. In the light-induced signal cascade, membrane-bound ROS-GC1 restores cGMP levels in the dark in a calcium-dependent manner. With decreasing calcium concentration in the intracellular compartment, ROS-GC1 is activated via the intracellular site by guanylyl cyclase-activating proteins (GCAP-1/-2). Presently, the exact activation mechanism is elusive. To obtain structural insights into the ROS-GC1 regulation by GCAP-2, chemical cross-linking/mass spectrometry studies using GCAP-2 and three ROS-GC1 peptides were performed in the presence and absence of calcium. The majority of cross-links were identified with the C-terminal lobe of GCAP-2 and a peptide comprising parts of ROS-GC1's catalytic domain and C-terminal extension. Consistently with the cross-linking results, surface plasmon resonance and fluorescence measurements confirmed specific binding of this ROS-GC peptide to GCAP-2 with a dissociation constant in the low micromolar range. These results imply that a region of the catalytic domain of ROS-GC1 can participate in the interaction with GCAP-2. Additional binding surfaces upstream of the catalytic domain, in particular the juxtamembrane domain, can currently not be excluded.
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Affiliation(s)
- Anne Rehkamp
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dirk Tänzler
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ralph P Golbik
- Department of Microbial Biotechnology, Charles Tanford Protein Center, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle, Germany
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15
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Buttstedt A, Mureşan CI, Lilie H, Hause G, Ihling CH, Schulze SH, Pietzsch M, Moritz RFA. How Honeybees Defy Gravity with Royal Jelly to Raise Queens. Curr Biol 2018; 28:1095-1100.e3. [PMID: 29551410 DOI: 10.1016/j.cub.2018.02.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/12/2018] [Accepted: 02/13/2018] [Indexed: 02/07/2023]
Abstract
The female sex in honeybees (Apis spp.) comprises a reproductive queen and a sterile worker caste. Nurse bees feed all larvae progressively with a caste-specific food jelly until the prepupal stage. Only those larvae that are exclusively fed a large amount of royal jelly (RJ) develop into queens [1]. RJ is a composite secretion of two specialized head glands: the mandibular glands, which produce mainly fatty acids [2], and the hypopharyngeal glands, which contribute proteins, primarily belonging to the major royal jelly protein (MRJP) family [3]. Past research on RJ has focused on its nutritional function and overlooked its central role with regard to the orientation of the larva in the royal brood cell. Whereas workers are reared in the regular horizontal cells of the comb, the queen cells are specifically built outside of the normal comb area to accommodate for the larger queen [4, 5]. These cells hang freely along the bottom of the comb and are vertically oriented, opening downward [6]. Queen larvae are attached by their RJ diet to the cell ceiling. Thus, the physical properties of RJ are central to successful retention of larvae in the cell. Here, we show that the main protein of RJ (MRJP1) polymerizes in complex with another protein, apisimin, into long fibrous structures that build the basis for the high viscosity of RJ to hold queen larvae on the RJ surface.
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Affiliation(s)
- Anja Buttstedt
- Institut für Biologie, Zoologie-Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany.
| | - Carmen I Mureşan
- Institut für Biologie, Zoologie-Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany; Facultatea de Zootehnie şi Biotehnologii, Universitatea de Ştiinţe Agricole şi Medicină Veterinară, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania
| | - Hauke Lilie
- Institut für Biochemie und Biotechnologie-Technische Biochemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Straße 3, 06120 Halle (Saale), Germany
| | - Gerd Hause
- Biozentrum-Elektronenmikroskopie, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Christian H Ihling
- Institut für Pharmazie-Pharmazeutische Chemie und Bioanalytik, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Stefan-H Schulze
- Fraunhofer Institut für Mikrostruktur von Werkstoffen und Systemen IMWS, Walter-Hülse-Str. 1, 06120 Halle (Saale), Germany
| | - Markus Pietzsch
- Institut für Pharmazie-Pharmazeutische Technologie und Biopharmazie, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Robin F A Moritz
- Institut für Biologie, Zoologie-Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany; Facultatea de Zootehnie şi Biotehnologii, Universitatea de Ştiinţe Agricole şi Medicină Veterinară, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania; Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa
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16
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Scheffler L, Crane A, Heyne H, Tönjes A, Schleinitz D, Ihling CH, Stumvoll M, Freire R, Fiorentino M, Fasano A, Kovacs P, Heiker JT. Widely Used Commercial ELISA Does Not Detect Precursor of Haptoglobin2, but Recognizes Properdin as a Potential Second Member of the Zonulin Family. Front Endocrinol (Lausanne) 2018; 9:22. [PMID: 29459849 PMCID: PMC5807381 DOI: 10.3389/fendo.2018.00022] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 01/18/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND There is increasing evidence for the role of impaired intestinal permeability in obesity and associated metabolic diseases. Zonulin is an established serum marker for intestinal permeability and identical to pre-haptoglobin2. Here, we aimed to investigate the relationship between circulating zonulin and metabolic traits related to obesity. METHODS Serum zonulin was measured by using a widely used commercial ELISA kit in 376 subjects from the metabolically well-characterized cohort of Sorbs from Germany. In addition, haptoglobin genotype was determined in DNA samples from all study subjects. RESULTS As zonulin concentrations did not correlate to the haptoglobin genotypes, we investigated the specificity of the zonulin ELISA assay using antibody capture experiments, mass spectrometry, and Western blot analysis. Using serum samples that gave the highest or lowest ELISA signals, we detected several proteins that are likely to be captured by the antibody in the present kit. However, none of these proteins corresponds to pre-haptoglobin2. We used increasing concentrations of recombinant pre-haptoglobin2 and complement C3 as one of the representative captured proteins and the ELISA kit did not detect either. Western blot analysis using both the polyclonal antibodies used in this kit and monoclonal antibodies rose against zonulin showed a similar protein recognition pattern but with different intensity of detection. The protein(s) measured using the ELISA kit was (were) significantly increased in patients with diabetes and obesity and correlated strongly with markers of the lipid and glucose metabolism. Combining mass spectrometry and Western blot analysis using the polyclonal antibodies used in the ELISA kit, we identified properdin as another member of the zonulin family. CONCLUSION Our study suggests that the zonulin ELISA does not recognize pre-haptoglobin2, rather structural (and possibly functional) analog proteins belonging to the mannose-associated serine protease family, with properdin being the most likely possible candidate.
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Affiliation(s)
- Lucas Scheffler
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Alyce Crane
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Henrike Heyne
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Anke Tönjes
- Divisions of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Dorit Schleinitz
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Michael Stumvoll
- Divisions of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Rachel Freire
- Mucosal Immunology And Biology Research Center, Massachusetts General Hospital––Harvard Medical School, Boston, MA, United States
| | - Maria Fiorentino
- Mucosal Immunology And Biology Research Center, Massachusetts General Hospital––Harvard Medical School, Boston, MA, United States
| | - Alessio Fasano
- Mucosal Immunology And Biology Research Center, Massachusetts General Hospital––Harvard Medical School, Boston, MA, United States
| | - Peter Kovacs
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig, Germany
- *Correspondence: John T. Heiker, ; Peter Kovacs,
| | - John T. Heiker
- Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
- *Correspondence: John T. Heiker, ; Peter Kovacs,
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17
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Häupl B, Ihling CH, Sinz A. Combining affinity enrichment, cross-linking with photo amino acids, and mass spectrometry for probing protein kinase D2 interactions. Proteomics 2017; 17:e1600459. [DOI: 10.1002/pmic.201600459] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 02/21/2017] [Accepted: 03/24/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Björn Häupl
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Halle (Saale) Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Halle (Saale) Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics; Institute of Pharmacy; Martin Luther University Halle-Wittenberg; Halle (Saale) Germany
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18
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Hage C, Ihling CH, Götze M, Schäfer M, Sinz A. Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS. J Am Soc Mass Spectrom 2017; 28:56-68. [PMID: 27418170 DOI: 10.1007/s13361-016-1426-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
We have synthesized a homobifunctional amine-reactive cross-linking reagent, containing a TEMPO (2,2,6,6-tetramethylpiperidine-1-oxy) and a benzyl group (Bz), termed TEMPO-Bz-linker, to derive three-dimensional structural information of proteins. The aim for designing this novel cross-linker was to facilitate the mass spectrometric analysis of cross-linked products by free radical initiated peptide sequencing (FRIPS). In an initial study, we had investigated the fragmentation behavior of TEMPO-Bz-derivatized peptides upon collision activation in (+)-electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS) experiments. In addition to the homolytic NO-C bond cleavage FRIPS pathway delivering the desired odd-electron product ions, an alternative heterolytic NO-C bond cleavage, resulting in even-electron product ions mechanism was found to be relevant. The latter fragmentation route clearly depends on the protonation of the TEMPO-Bz-moiety itself, which motivated us to conduct (-)-ESI-MS, CID-MS/MS, and MS3 experiments of TEMPO-Bz-cross-linked peptides to further clarify the fragmentation behavior of TEMPO-Bz-peptide molecular ions. We show that the TEMPO-Bz-linker is highly beneficial for conducting FRIPS in negative ionization mode as the desired homolytic cleavage of the NO-C bond is the major fragmentation pathway. Based on characteristic fragments, the isomeric amino acids leucine and isoleucine could be discriminated. Interestingly, we observed pronounced amino acid side chain losses in cross-linked peptides if the cross-linked peptides contain a high number of acidic amino acids. Graphical Abstract ᅟ.
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Affiliation(s)
- Christoph Hage
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Christian H Ihling
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany
| | - Michael Götze
- Institute of Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, D-06120, Halle, Saale, Germany
| | - Mathias Schäfer
- Department of Chemistry, University Cologne, Greinstr. 4, D-50939, Köln, Germany.
| | - Andrea Sinz
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle, Saale, Germany.
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19
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Arlt C, Flegler V, Ihling CH, Schäfer M, Thondorf I, Sinz A. An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full‐Length Wild‐Type Tetrameric p53 Tumor Suppressor. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609826] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics Institute of Pharmacy Martin-Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Vanessa Flegler
- Department of Pharmaceutical Chemistry and Bioanalytics Institute of Pharmacy Martin-Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics Institute of Pharmacy Martin-Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
| | - Mathias Schäfer
- Department Mass Spectrometry Institute of Organic Chemistry University of Cologne Greinstraße 4 50939 Cologne Germany
| | - Iris Thondorf
- Department of Technical Biochemistry Institute of Biochemistry and Biotechnology Martin-Luther University Halle-Wittenberg Kurt-Mothes-Str. 3 06120 Halle/Saale Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics Institute of Pharmacy Martin-Luther University Halle-Wittenberg Wolfgang-Langenbeck-Str. 4 06120 Halle/Saale Germany
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20
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Arlt C, Flegler V, Ihling CH, Schäfer M, Thondorf I, Sinz A. An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor. Angew Chem Int Ed Engl 2016; 56:275-279. [PMID: 27897373 DOI: 10.1002/anie.201609826] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/10/2016] [Indexed: 12/31/2022]
Abstract
We present an integrated approach for investigating the topology of proteins through native mass spectrometry (MS) and cross-linking/MS, which we applied to the full-length wild-type p53 tetramer. For the first time, the two techniques were combined in one workflow to obtain not only structural insight in the p53 tetramer, but also information on the cross-linking efficiency and the impact of cross-linker modification on the conformation of an intrinsically disordered protein (IDP). P53 cross-linking was monitored by native MS and as such, our strategy serves as a quality control for different cross-linking reagents. Our approach can be applied to the structural investigation of various protein systems, including IDPs and large protein assemblies, which are challenging to study by the conventional methods used for protein structure characterization.
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Affiliation(s)
- Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
| | - Vanessa Flegler
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
| | - Mathias Schäfer
- Department Mass Spectrometry, Institute of Organic Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Iris Thondorf
- Department of Technical Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/Saale, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle/Saale, Germany
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21
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Schumann M, Ihling CH, Prell E, Schierhorn A, Sinz A, Fischer G, Schiene-Fischer C, Malešević M. Identification of low abundance cyclophilins in human plasma. Proteomics 2016; 16:2815-2826. [PMID: 27586231 DOI: 10.1002/pmic.201600221] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/19/2016] [Accepted: 08/22/2016] [Indexed: 11/08/2022]
Abstract
Cylophilins (Cyps) belong to the ubiquitously distributed enzyme class of peptidyl prolyl cis/trans isomerases (EC5.2.1.8), which are foldases capable of accelerating slow steps in the refolding of denatured proteins. At least 20 different Cyp isoenzymes are broadly distributed among all organs and cellular compartments in humans. Extracellularly localized Cyps came into the scientific focus recently because of their involvement in the control of inflammatory diseases, as well as viral and bacterial infections. However, detailed insights into Cyp functions are often hampered by the lack of sensitive detection methods. We present an improved method for affinity purification and detection of Cyp in biotic samples in this manuscript. The procedure takes advantage of two novel cyclosporine A derivatives. Derivative 1 was used to capture Cyps from the sample while derivative 2 was applied for selective release from the affinity matrix. Using this approach, eight different Cyp (CypA, CypB, CypC, Cyp40 (PPID), CypE, CypD (PPIF), CypH, and CypL1) were unambiguously detected in healthy human blood plasma. Moreover, extracellular CypA was found to be partially modified by Nε acetylation on residues Lys44, Lys133, Lys155, as well as Nα acetylation at the N-terminal Val residue. Nα acetylation of Ser2 residue was also found for Cyp40.
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Affiliation(s)
- Michael Schumann
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Erik Prell
- Branch Office Halle, Max-Planck Institute for Biophysical Chemistry, Göttingen, Halle, Germany
| | - Angelika Schierhorn
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Gunter Fischer
- Branch Office Halle, Max-Planck Institute for Biophysical Chemistry, Göttingen, Halle, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Miroslav Malešević
- Department of Enzymology, Institute of Biochemistry und Biotechnology, Martin-Luther-University Halle-Wittenberg, Halle, Germany.
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22
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Buttstedt A, Ihling CH, Pietzsch M, Moritz RFA. Royalactin is not a royal making of a queen. Nature 2016; 537:E10-2. [PMID: 27652566 DOI: 10.1038/nature19349] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/17/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Anja Buttstedt
- Institut für Biologie, Zoologie - Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany.,Institut für Pharmazie - Aufarbeitung biotechnischer Produkte, Martin-Luther-Universität Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
| | - Christian H Ihling
- Institut für Pharmazie - Pharmazeutische Chemie &Bioanalytik, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Markus Pietzsch
- Institut für Biologie, Zoologie - Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany
| | - Robin F A Moritz
- Institut für Biologie, Zoologie - Molekulare Ökologie, Martin-Luther-Universität Halle-Wittenberg, Hoher Weg 4, 06120 Halle (Saale), Germany.,Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa
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23
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Bosse K, Haneder S, Arlt C, Ihling CH, Seufferlein T, Sinz A. Mass spectrometry-based secretome analysis of non-small cell lung cancer cell lines. Proteomics 2016; 16:2801-2814. [DOI: 10.1002/pmic.201600297] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Konstanze Bosse
- Department of Pharmaceutical Chemistry & Bioanalytics; Institute of Pharmacy; Martin-Luther University Halle-Wittenberg; Halle (Saale) Germany
| | | | - Christian Arlt
- Department of Pharmaceutical Chemistry & Bioanalytics; Institute of Pharmacy; Martin-Luther University Halle-Wittenberg; Halle (Saale) Germany
| | - Christian H. Ihling
- 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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24
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Abstract
We investigated the interaction network of human PKD2 in the cytosol and in Golgi-enriched subcellular protein fractions by an affinity enrichment strategy combined with chemical cross-linking/mass spectrometry (MS). Analysis of the subproteomes revealed the presence of distinct proteins in the cytosolic and Golgi fractions. The covalent fixation of transient or weak interactors by chemical cross-linking allowed capturing interaction partners that might otherwise disappear during conventional pull-down experiments. In total, 31 interaction partners were identified for PKD2, including glycogen synthase kinase-3 beta (GSK3B), 14-3-3 protein gamma (YWHAG), and the alpha isoform of 55 kDa regulatory subunit B of protein phosphatase 2A (PPP2R2A). Remarkably, the entire seven-subunit Arp2/3 complex (ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ACTR3, ACTR2) as well as ARPC1A and ARPC5L, which are putative substitutes of ARPC1B and ARPC5, were identified. We provide evidence of a direct protein-protein interaction between PKD2 and Arp2/3. Our findings will pave the way for further structural and functional studies of PKD2 complexes, especially the PKD2/Arp2/3 interaction, to elucidate the role of PKD2 for transport processes at the trans-Golgi network. Data are available via ProteomeXchange with identifiers PXD003909 (enrichment from cytosolic fractions), PXD003913 (enrichment from Golgi fractions), and PXD003917 (subcellular fractionation).
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Affiliation(s)
- Björn Häupl
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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25
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Arlt C, Götze M, Ihling CH, Hage C, Schäfer M, Sinz A. Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker. Anal Chem 2016; 88:7930-7. [DOI: 10.1021/acs.analchem.5b04853] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Christian Arlt
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Michael Götze
- Institute
of Biochemistry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str.
3, D-06120 Halle
(Saale), Germany
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Christoph Hage
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
| | - Mathias Schäfer
- Institute
for Organic Chemistry, Department of Chemistry, University of Cologne, Greinstr. 4, D-50939 Cologne, Germany
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-St. 4, D-06120 Halle (Saale), Germany
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26
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Schwarz R, Tänzler D, Ihling CH, Sinz A. Monitoring Solution Structures of Peroxisome Proliferator-Activated Receptor β/δ upon Ligand Binding. PLoS One 2016; 11:e0151412. [PMID: 26992147 PMCID: PMC4798536 DOI: 10.1371/journal.pone.0151412] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/26/2016] [Indexed: 01/21/2023] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) have been intensively studied as drug targets to treat type 2 diabetes, lipid disorders, and metabolic syndrome. This study is part of our ongoing efforts to map conformational changes in PPARs in solution by a combination of chemical cross-linking and mass spectrometry (MS). To our best knowledge, we performed the first studies addressing solution structures of full-length PPAR-β/δ. We monitored the conformations of the ligand-binding domain (LBD) as well as full-length PPAR-β/δ upon binding of two agonists. (Photo-) cross-linking relied on (i) a variety of externally introduced amine- and carboxyl-reactive linkers and (ii) the incorporation of the photo-reactive amino acid p-benzoylphenylalanine (Bpa) into PPAR-β/δ by genetic engineering. The distances derived from cross-linking experiments allowed us to monitor conformational changes in PPAR-β/δ upon ligand binding. The cross-linking/MS approach proved highly advantageous to study nuclear receptors, such as PPARs, and revealed the interplay between DBD (DNA-binding domain) and LDB in PPAR-β/δ. Our results indicate the stabilization of a specific conformation through ligand binding in PPAR-β/δ LBD as well as full-length PPAR-β/δ. Moreover, our results suggest a close distance between the N- and C-terminal regions of full-length PPAR-β/δ in the presence of GW1516. Chemical cross-linking/MS allowed us gaining detailed insights into conformational changes that are induced in PPARs when activating ligands are present. Thus, cross-linking/MS should be added to the arsenal of structural methods available for studying nuclear receptors.
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Affiliation(s)
- Rico Schwarz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120, Halle/Saale, Germany
| | - Dirk Tänzler
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120, Halle/Saale, Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120, Halle/Saale, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120, Halle/Saale, Germany
- * E-mail:
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27
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Abstract
Under various pathological conditions, such as inflammation, ischemia and in solid tumors, physiological parameters (local oxygen tension or extracellular pH) show distinct tissue abnormalities (hypoxia and acidosis). For tumors, the prevailing microenvironment exerts a strong influence on the phenotype with respect to proliferation, invasion, and metastasis formation and therefore influences prognosis. In this study, we investigate the impact of extracellular metabolic acidosis (pH 7.4 versus 6.6) on the proteome patterns of a prostate cancer-derived tumor cell type (AT-1) using isobaric labeling and LC-MS/MS analysis. In total, 2710 proteins were identified and quantified across four biological replicates, of which seven were significantly affected with changes >50% and used for validation. Glucose transporter 1 and farnesyl pyrophosphatase were found to be down-regulated after 48 h of acidic treatment, and metallothionein 2A was reduced after 24 h and returned to control values after 48 h. After 24 and 48 h at pH 6.6, glutathione S transferase A3 and NAD(P)H dehydrogenase 1, cellular retinoic acid-binding protein 2, and Na-bicarbonate transporter 3 levels were found to be increased. The changes in protein levels were confirmed by transcriptome and functional analyses. In addition to the experimental in-depth investigation of proteins with changes >50%, functional profiling (statistical enrichment analysis) including proteins with changes >20% revealed that acidosis upregulates GSH metabolic processes, citric acid cycle, and respiratory electron transport. Metabolism of lipids and cholesterol biosynthesis were downregulated. Our data comprise the first comprehensive report on acidosis-induced changes in proteome patterns of a tumor cell line.
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Affiliation(s)
- Angelika Ihling
- Julius Bernstein Institute of Physiology, Martin-Luther University Halle-Wittenberg , Magdeburgerstrasse 6, D-06112 Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg , Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Michael Gekle
- Julius Bernstein Institute of Physiology, Martin-Luther University Halle-Wittenberg , Magdeburgerstrasse 6, D-06112 Halle (Saale), Germany
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28
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Arlt C, Ihling CH, Sinz A. Structure of full-length p53 tumor suppressor probed by chemical cross-linking and mass spectrometry. Proteomics 2015; 15:2746-55. [PMID: 25728495 DOI: 10.1002/pmic.201400549] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 01/15/2015] [Accepted: 02/24/2015] [Indexed: 11/12/2022]
Abstract
The tumor suppressor p53 presents a great challenge for 3D structural analysis due to its inherent flexibility. In this work, we gained insight into the structure of full-length wild-type human p53 in solution by chemical cross-linking/MS. This approach allowed us obtaining structural information of free wild-type p53 in solution without making use of the ultrastable quadruple p53 variant. The cross-links within one p53 monomer are in good agreement with the small-angle X-ray scattering based model of full-length p53. Our cross-linking data between different p53 molecules in the tetramer however indicate a large degree of flexibility in the C-terminal regulatory domain of full-length p53 in the absence of DNA. The cross-links suggest that the C-terminal regulatory domains are much closer to each other, resulting in a more compact arrangement of the p53 tetramer than perceived by the small-angle X-ray scattering model.
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Affiliation(s)
- Christian Arlt
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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29
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Piotrowski C, Ihling CH, Sinz A. Extending the cross-linking/mass spectrometry strategy: Facile incorporation of photo-activatable amino acids into the model protein calmodulin in Escherichia coli cells. Methods 2015; 89:121-7. [PMID: 25726908 DOI: 10.1016/j.ymeth.2015.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/06/2015] [Accepted: 02/22/2015] [Indexed: 11/19/2022] Open
Abstract
Photo-induced cross-linking is a highly promising technique to investigate protein conformations and protein-protein interactions in their natural cellular environment. One strategy relies on the non-directed incorporation of diazirine-containing photo-activatable amino acids into proteins and a subsequent cross-link formation induced by UV-A irradiation. The advantage of this photo-cross-linking strategy is that it is not restricted to lysine residues and that hydrophobic regions in proteins can also be targeted, which is advantageous for investigating membrane proteins. Here, we present a simplified protocol that relies on the use of mineral salts medium without any special requirements for the incorporation of photo-methionines into proteins in Escherichia coli cells. The possibility to perform these experiments in E. coli is especially valuable as it is the major system for recombinant protein production. The method is exemplified for the Ca(2+) regulating protein calmodulin containing nine methionines, which were found to be replaced by their photo-activatable analogues. Our protocol allows the facile and stochastic incorporation of photo-methionines as the basis for conducting photo-cross-linking experiments in E. coli in an efficient manner.
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Affiliation(s)
- Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Christian H Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany.
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30
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Götze M, Pettelkau J, Fritzsche R, Ihling CH, Schäfer M, Sinz A. Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. J Am Soc Mass Spectrom 2015; 26:83-97. [PMID: 25261217 DOI: 10.1007/s13361-014-1001-1] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 05/03/2023]
Abstract
CID-MS/MS cleavable cross-linkers hold an enormous potential for an automated analysis of cross-linked products, which is essential for conducting structural proteomics studies. The created characteristic fragment ion patterns can easily be used for an automated assignment and discrimination of cross-linked products. To date, there are only a few software solutions available that make use of these properties, but none allows for an automated analysis of cleavable cross-linked products. The MeroX software fills this gap and presents a powerful tool for protein 3D-structure analysis in combination with MS/MS cleavable cross-linkers. We show that MeroX allows an automatic screening of characteristic fragment ions, considering static and variable peptide modifications, and effectively scores different types of cross-links. No manual input is required for a correct assignment of cross-links and false discovery rates are calculated. The self-explanatory graphical user interface of MeroX provides easy access for an automated cross-link search platform that is compatible with commonly used data file formats, enabling analysis of data originating from different instruments. The combination of an MS/MS cleavable cross-linker with a dedicated software tool for data analysis provides an automated workflow for 3D-structure analysis of proteins. MeroX is available at www.StavroX.com .
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Affiliation(s)
- Michael Götze
- Institute for Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany,
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Lössl P, Kölbel K, Tänzler D, Nannemann D, Ihling CH, Keller MV, Schneider M, Zaucke F, Meiler J, Sinz A. Analysis of nidogen-1/laminin γ1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes. PLoS One 2014; 9:e112886. [PMID: 25387007 PMCID: PMC4227867 DOI: 10.1371/journal.pone.0112886] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/16/2014] [Indexed: 11/18/2022] Open
Abstract
We describe the detailed structural investigation of nidogen-1/laminin γ1 complexes using full-length nidogen-1 and a number of laminin γ1 variants. The interactions of nidogen-1 with laminin variants γ1 LEb2–4, γ1 LEb2–4 N836D, γ1 short arm, and γ1 short arm N836D were investigated by applying a combination of (photo-)chemical cross-linking, high-resolution mass spectrometry, and computational modeling. In addition, surface plasmon resonance and ELISA studies were used to determine kinetic constants of the nidogen-1/laminin γ1 interaction. Two complementary cross-linking strategies were pursued to analyze solution structures of laminin γ1 variants and nidogen-1. The majority of distance information was obtained with the homobifunctional amine-reactive cross-linker bis(sulfosuccinimidyl)glutarate. In a second approach, UV-induced cross-linking was performed after incorporation of the diazirine-containing unnatural amino acids photo-leucine and photo-methionine into laminin γ1 LEb2–4, laminin γ1 short arm, and nidogen-1. Our results indicate that Asn-836 within laminin γ1 LEb3 domain is not essential for complex formation. Cross-links between laminin γ1 short arm and nidogen-1 were found in all protein regions, evidencing several additional contact regions apart from the known interaction site. Computational modeling based on the cross-linking constraints indicates the existence of a conformational ensemble of both the individual proteins and the nidogen-1/laminin γ1 complex. This finding implies different modes of interaction resulting in several distinct protein-protein interfaces.
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Affiliation(s)
- Philip Lössl
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Knut Kölbel
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Dirk Tänzler
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - David Nannemann
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Manuel V. Keller
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Marian Schneider
- Research Group Artificial Binding Proteins, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Frank Zaucke
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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Zorn M, Ihling CH, Golbik R, Sawers RG, Sinz A. Mapping Cell Envelope and Periplasm Protein Interactions of Escherichia coli Respiratory Formate Dehydrogenases by Chemical Cross-Linking and Mass Spectrometry. J Proteome Res 2014; 13:5524-35. [DOI: 10.1021/pr5004906] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Michael Zorn
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
| | | | | | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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Pettelkau J, Ihling CH, Frohberg P, van Werven L, Jahn O, Sinz A. Reliable identification of cross-linked products in protein interaction studies by 13C-labeled p-benzoylphenylalanine. J Am Soc Mass Spectrom 2014; 25:1628-1641. [PMID: 25031183 DOI: 10.1007/s13361-014-0944-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/22/2014] [Accepted: 05/26/2014] [Indexed: 06/03/2023]
Abstract
We describe the use of the (13)C-labeled artificial amino acid p-benzoyl-L-phenylalanine (Bpa) to improve the reliability of cross-linked product identification. Our strategy is exemplified for two protein-peptide complexes. These studies indicate that in many cases the identification of a cross-link without additional stable isotope labeling would result in an ambiguous assignment of cross-linked products. The use of a (13)C-labeled photoreactive amino acid is considered to be preferred over the use of deuterated cross-linkers as retention time shifts in reversed phase chromatography can be ruled out. The observation of characteristic fragment ions additionally increases the reliability of cross-linked product assignment. Bpa possesses a broad reactivity towards different amino acids and the derived distance information allows mapping of spatially close amino acids and thus provides more solid structural information of proteins and protein complexes compared to the longer deuterated amine-reactive cross-linkers, which are commonly used for protein 3D-structure analysis and protein-protein interaction studies.
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Affiliation(s)
- Jens Pettelkau
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
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Doberenz C, Zorn M, Falke D, Nannemann D, Hunger D, Beyer L, Ihling CH, Meiler J, Sinz A, Sawers RG. Pyruvate formate-lyase interacts directly with the formate channel FocA to regulate formate translocation. J Mol Biol 2014; 426:2827-39. [PMID: 24887098 DOI: 10.1016/j.jmb.2014.05.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 11/26/2022]
Abstract
The FNT (formate-nitrite transporters) form a superfamily of pentameric membrane channels that translocate monovalent anions across biological membranes. FocA (formate channel A) translocates formate bidirectionally but the mechanism underlying how translocation of formate is controlled and what governs substrate specificity remains unclear. Here we demonstrate that the normally soluble dimeric enzyme pyruvate formate-lyase (PflB), which is responsible for intracellular formate generation in enterobacteria and other microbes, interacts specifically with FocA. Association of PflB with the cytoplasmic membrane was shown to be FocA dependent and purified, Strep-tagged FocA specifically retrieved PflB from Escherichia coli crude extracts. Using a bacterial two-hybrid system, it could be shown that the N-terminus of FocA and the central domain of PflB were involved in the interaction. This finding was confirmed by chemical cross-linking experiments. Using constraints imposed by the amino acid residues identified in the cross-linking study, we provide for the first time a model for the FocA-PflB complex. The model suggests that the N-terminus of FocA is important for interaction with PflB. An in vivo assay developed to monitor changes in formate levels in the cytoplasm revealed the importance of the interaction with PflB for optimal translocation of formate by FocA. This system represents a paradigm for the control of activity of FNT channel proteins.
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Affiliation(s)
- Claudia Doberenz
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Michael Zorn
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Dörte Falke
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - David Nannemann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA
| | - Doreen Hunger
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Lydia Beyer
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany
| | - Christian H Ihling
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Nashville, TN 37235, USA
| | - Andrea Sinz
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - R Gary Sawers
- Institute of Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany.
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Ihling CH, Schröder T, Pettelkau J, Tischer A, Lange C, Sinz A. Accessibilities of N-terminal myristoyl chain and cysteines in guanylyl cyclase-activating protein-2 (GCAP-2) studied by covalent labeling and mass spectrometry. Rapid Commun Mass Spectrom 2014; 28:835-838. [PMID: 24573816 DOI: 10.1002/rcm.6846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 01/17/2014] [Accepted: 01/19/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Christian H Ihling
- Department of Pharmaceutical Chemistry &Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
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Pettelkau J, Thondorf I, Theisgen S, Lilie H, Schröder T, Arlt C, Ihling CH, Sinz A. Structural analysis of guanylyl cyclase-activating protein-2 (GCAP-2) homodimer by stable isotope-labeling, chemical cross-linking, and mass spectrometry. J Am Soc Mass Spectrom 2013; 24:1969-1979. [PMID: 24026978 DOI: 10.1007/s13361-013-0734-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 06/02/2023]
Abstract
The topology of the GCAP-2 homodimer was investigated by chemical cross-linking and high resolution mass spectrometry. Complementary conducted size-exclusion chromatography and analytical ultracentrifugation studies indicated that GCAP-2 forms a homodimer both in the absence and in the presence of Ca(2+). In-depth MS and MS/MS analysis of the cross-linked products was aided by (15)N-labeled GCAP-2. The use of isotope-labeled protein delivered reliable structural information on the GCAP-2 homodimer, enabling an unambiguous discrimination between cross-links within one monomer (intramolecular) or between two subunits (intermolecular). The limited number of cross-links obtained in the Ca(2+)-bound state allowed us to deduce a defined homodimeric GCAP-2 structure by a docking and molecular dynamics approach. In the Ca(2+)-free state, GCAP-2 is more flexible as indicated by the higher number of cross-links. We consider stable isotope-labeling to be indispensable for deriving reliable structural information from chemical cross-linking data of multi-subunit protein assemblies.
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Affiliation(s)
- Jens Pettelkau
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120, Halle (Saale), Germany
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Herbst S, Maucher D, Schneider M, Ihling CH, Jahn O, Sinz A. Munc13-like skMLCK variants cannot mimic the unique calmodulin binding mode of Munc13 as evidenced by chemical cross-linking and mass spectrometry. PLoS One 2013; 8:e75119. [PMID: 24130683 PMCID: PMC3794949 DOI: 10.1371/journal.pone.0075119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
Among the neuronal binding partners of calmodulin (CaM) are Munc13 proteins as essential presynaptic regulators that play a key role in synaptic vesicle priming and are crucial for presynaptic short-term plasticity. Recent NMR structural investigations of a CaM/Munc13-1 peptide complex have revealed an extended structure, which contrasts the compact structures of most classical CaM/target complexes. This unusual binding mode is thought to be related to the presence of an additional hydrophobic anchor residue at position 26 of the CaM binding motif of Munc13-1, resulting in a novel 1-5-8-26 motif. Here, we addressed the question whether the 1-5-8-26 CaM binding motif is a Munc13-related feature or whether it can be induced in other CaM targets by altering the motif's core residues. For this purpose, we chose skeletal muscle myosin light chain kinase (skMLCK) with a classical 1-5-8-14 CaM binding motif and constructed three skMLCK peptide variants mimicking Munc13-1, in which the hydrophobic anchor amino acid at position 14 was moved to position 26. Chemical cross-linking between CaM and skMLCK peptide variants combined with high-resolution mass spectrometry yielded insights into the peptides' binding modes. This structural comparison together with complementary binding data from surface plasmon resonance experiments revealed that skMLCK variants with an artificial 1-5-8-26 motif cannot mimic CaM binding of Munc13-1. Apparently, additional features apart from the spacing of the hydrophobic anchor residues are required to define the functional 1-5-8-26 motif of Munc13-1. We conclude that Munc13 proteins display a unique CaM binding behavior to fulfill their role as efficient presynaptic calcium sensors over broad range of Ca(2+) concentrations.
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Affiliation(s)
- Sabine Herbst
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Daniel Maucher
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Marian Schneider
- Research Group Artificial Binding Proteins, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Göttingen, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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Schwarz R, Tänzler D, Ihling CH, Müller MQ, Kölbel K, Sinz A. Monitoring conformational changes in peroxisome proliferator-activated receptor α by a genetically encoded photoamino acid, cross-linking, and mass spectrometry. J Med Chem 2013; 56:4252-63. [PMID: 23639233 DOI: 10.1021/jm400446b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical cross-linking combined with an enzymatic digestion and mass spectrometric analysis of the reaction products has evolved into an alternative strategy to structurally resolve protein complexes. We investigated conformational changes in peroxisome proliferator-activated receptor α (PPARα) upon ligand binding. Using E. coli cells with a special tRNA/aminoacyl-tRNA synthetase pair, two PPARα variants were prepared in which Leu-258 or Phe-273 were site-specifically replaced by the genetically encoded photoreactive amino acid p-benzoylphenylalanine (Bpa). PPARα variants were subjected to UV-induced cross-linking, both in the absence and in the presence of ligands. After the photo-cross-linking reaction, reaction mixtures were enzymatically digested and peptides were analyzed by mass spectrometry. The inter-residue distances disclosed by the photochemical cross-links served to monitor conformational changes in PPARα upon agonist and antagonist binding. The data obtained with our strategy emphasize the potential of genetically encoded internal photo-cross-linkers in combination with mass spectrometry as an alternative method to monitor in-solution 3D-protein structures.
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Affiliation(s)
- Rico Schwarz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, D-06120 Halle/Saale, Germany
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Zorn M, Ihling CH, Golbik R, Sawers RG, Sinz A. Selective selC-independent selenocysteine incorporation into formate dehydrogenases. PLoS One 2013; 8:e61913. [PMID: 23634217 PMCID: PMC3636253 DOI: 10.1371/journal.pone.0061913] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 03/14/2013] [Indexed: 11/18/2022] Open
Abstract
The formate dehydrogenases (Fdh) Fdh-O, Fdh-N, and Fdh-H, are the only proteins in Escherichia coli that incorporate selenocysteine at a specific position by decoding a UGA codon. However, an excess of selenium can lead to toxicity through misincorporation of selenocysteine into proteins. To determine whether selenocysteine substitutes for cysteine, we grew Escherichia coli in the presence of excess sodium selenite. The respiratory Fdh-N and Fdh-O enzymes, along with nitrate reductase (Nar) were co-purified from wild type strain MC4100 after anaerobic growth with nitrate and either 2 µM or 100 µM selenite. Mass spectrometric analysis of the catalytic subunits of both Fdhs identified the UGA-specified selenocysteine residue and revealed incorporation of additional, ‘non-specific’ selenocysteinyl residues, which always replaced particular cysteinyl residues. Although variable, their incorporation was not random and was independent of the selenite concentration used. Notably, these cysteines are likely to be non-essential for catalysis and they do not coordinate the iron-sulfur cluster. The remaining cysteinyl residues that could be identified were never substituted by selenocysteine. Selenomethionine was never observed in our analyses. Non-random substitution of particular cysteinyl residues was also noted in the electron-transferring subunit of both Fdhs as well as in the subunits of the Nar enzyme. Nar isolated from an E. coli selC mutant also showed a similar selenocysteine incorporation pattern to the wild-type indicating that non-specific selenocysteine incorporation was independent of the specific selenocysteine pathway. Thus, selenide replaces sulfide in the biosynthesis of cysteine and misacylated selenocysteyl-tRNACys decodes either UGU or UGC codons, which usually specify cysteine. Nevertheless, not every UGU or UGC codon was decoded as selenocysteine. Together, our results suggest that a degree of misincorporation of selenocysteine into enzymes through replacement of particular, non-essential cysteines, is tolerated and this might act as a buffering system to cope with excessive intracellular selenium.
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Affiliation(s)
- Michael Zorn
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Ralph Golbik
- Institute of Biochemistry, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - R. Gary Sawers
- Institute of Microbiology, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (RGS); (AS)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
- * E-mail: (RGS); (AS)
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Abstract
The combination of chemical cross-linking and high-resolution mass spectrometry is an emerging technique for monitoring conformational changes in proteins induced by drug binding. In this chapter, we describe this approach for gaining insights into the conformational changes of the peroxisome proliferator-activated receptor alpha after binding of low-molecular weight ligands. Our strategy provides a basis to efficiently characterize target protein-drug interactions.
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Affiliation(s)
- Mathias Q Müller
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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Kölbel K, Ihling CH, Sinz A. Analyse von Sekundärstrukturen in Peptiden mithilfe photoaktivierbarer Aminosäureanaloga. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kölbel K, Ihling CH, Sinz A. Analysis of Peptide Secondary Structures by Photoactivatable Amino Acid Analogues. Angew Chem Int Ed Engl 2012; 51:12602-5. [DOI: 10.1002/anie.201205308] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Indexed: 11/09/2022]
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Pettelkau J, Schröder T, Ihling CH, Olausson BES, Kölbel K, Lange C, Sinz A. Structural Insights into Retinal Guanylylcyclase–GCAP-2 Interaction Determined by Cross-Linking and Mass Spectrometry. Biochemistry 2012; 51:4932-49. [DOI: 10.1021/bi300064v] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jens Pettelkau
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, D-06120 Halle (Saale), Germany
| | - Thomas Schröder
- Department of Technical Biochemistry, Institute of Biochemistry and
Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, D-06120 Halle (Saale), Germany
| | - Björn E. S. Olausson
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, D-06120 Halle (Saale), Germany
| | - Knut Kölbel
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, D-06120 Halle (Saale), Germany
| | - Christian Lange
- Department of Technical Biochemistry, Institute of Biochemistry and
Biotechnology, Martin-Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Andrea Sinz
- Department
of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Straße
4, D-06120 Halle (Saale), Germany
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Fritzsche R, Ihling CH, Götze M, Sinz A. Optimizing the enrichment of cross-linked products for mass spectrometric protein analysis. Rapid Commun Mass Spectrom 2012; 26:653-8. [PMID: 22328219 DOI: 10.1002/rcm.6150] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
RATIONALE Chemical cross-linking in combination with a mass spectrometric analysis of the created cross-linked products is an area of growing interest for deriving low-resolution structural information of proteins and protein complexes. One of the greatest challenges is the complexity of the created cross-linking mixtures, which can be met by a charge-based enrichment of cross-linked peptides after proteolytic digestion using strong cation-exchange (SCX) chromatography. METHODS SCX chromatography was used for the enrichment of cross-linked peptides with the N-hydroxysuccinimide ester bis(sulfosuccinimidyl)succinate (BS(3)) prior to a mass spectrometric analysis by nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS. Bovine serum albumin (BSA) and glutathione S-transferase (GST) were employed as model proteins. RESULTS Conditions for SCX enrichment were optimized for obtaining as many interpeptide cross-linked peptides as possible in order to maximize the amount of structural information from a single experiment. With an SCX-based enrichment step of cross-linked products within BSA using the cross-linker BS(3), 154 interpeptidal cross-linking products were identified during nano-HPLC/nano-ESI-MS/MS analyses, whereas analyses without a prior SCX enrichment allowed the identification of merely 20 cross-linked products. The application of the SCX enrichment strategy for the analysis of cross-linked products of GST with BS(3) allowed the identification of 26 interpeptidal cross-linked products compared with 16 without SCX enrichment. CONCLUSIONS For both proteins investigated herein, BSA and GST, the introduction of an SCX-based enrichment step prior to nano-HPLC/nano-ESI-MS/MS of cross-linked products led to a considerable gain in structural information.
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Affiliation(s)
- Romy Fritzsche
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120, Halle (Saale), Germany
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Götze M, Pettelkau J, Schaks S, Bosse K, Ihling CH, Krauth F, Fritzsche R, Kühn U, Sinz A. StavroX--a software for analyzing crosslinked products in protein interaction studies. J Am Soc Mass Spectrom 2012; 23:76-87. [PMID: 22038510 DOI: 10.1007/s13361-011-0261-2] [Citation(s) in RCA: 241] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/19/2011] [Accepted: 09/20/2011] [Indexed: 05/03/2023]
Abstract
Chemical crosslinking in combination with mass spectrometry has matured into an alternative approach to derive low-resolution structural information of proteins and protein complexes. Yet, one of the major drawbacks of this strategy remains the lack of software that is able to handle the large MS datasets that are created after chemical crosslinking and enzymatic digestion of the crosslinking reaction mixtures. Here, we describe a software, termed StavroX, which has been specifically designed for analyzing highly complex crosslinking datasets. The StavroX software was evaluated for three diverse biological systems: (1) the complex between calmodulin and a peptide derived from Munc13, (2) an N-terminal ß-laminin fragment, and (3) the complex between guanylyl cyclase activating protein-2 and a peptide derived from retinal guanylyl cyclase. We show that the StavroX software is advantageous for analyzing crosslinked products due to its easy-to-use graphical user interface and the highly automated analysis of mass spectrometry (MS) and tandem mass spectrometry (MS/MS) data resulting in short times for analysis. StavroX is expected to give a further push to the chemical crosslinking approach as a routine technique for protein interaction studies.
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Affiliation(s)
- Michael Götze
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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Kalkhof S, Witte K, Ihling CH, Müller MQ, Keller MV, Haehn S, Smyth N, Paulsson M, Sinz A. A Novel Disulfide Pattern in Laminin-Type Epidermal Growth Factor-like (LE) Modules of Laminin β1 and γ1 Chains. Biochemistry 2010; 49:8359-66. [DOI: 10.1021/bi101187f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefan Kalkhof
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Konstanze Witte
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Mathias Q. Müller
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Manuel V. Keller
- Center for Biochemistry and Center for Molecular Medicine, Faculty of Medicine, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), D-50931 Cologne, Germany
| | - Sebastian Haehn
- Center for Biochemistry and Center for Molecular Medicine, Faculty of Medicine, University of Cologne, D-50931 Cologne, Germany
| | - Neil Smyth
- School of Biological Sciences, University of Southampton, East Southampton SO16 7PX, United Kingdom
| | - Mats Paulsson
- Center for Biochemistry and Center for Molecular Medicine, Faculty of Medicine, University of Cologne, D-50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), D-50931 Cologne, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany
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Müller MQ, Dreiocker F, Ihling CH, Schäfer M, Sinz A. Fragmentation behavior of a thiourea-based reagent for protein structure analysis by collision-induced dissociative chemical cross-linking. J Mass Spectrom 2010; 45:880-891. [PMID: 20607845 DOI: 10.1002/jms.1775] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The fragmentation behavior of a novel thiourea-based cross-linker molecule specifically designed for collision-induced dissociation (CID) MS/MS experiments is described. The development of this cross-linker is part of our ongoing efforts to synthesize novel reagents, which create either characteristic fragment ions or indicative constant neutral losses (CNLs) during tandem mass spectrometry allowing a selective and sensitive analysis of cross-linked products. The new derivatizing reagent for chemical cross-linking solely contains a thiourea moiety that is flanked by two amine-reactive N-hydroxy succinimide (NHS) ester moieties for reaction with lysines or free N-termini in proteins. The new reagent offers simple synthetic access and easy structural variation of either length or functionalities at both ends. The thiourea moiety exhibits specifically tailored CID fragmentation capabilities--a characteristic CNL of 85 u--ensuring a reliable detection of derivatized peptides by both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry and as such possesses a versatile applicability for chemical cross-linking studies. A detailed examination of the CID behavior of the presented thiourea-based reagent reveals that slight structural variations of the reagent will be necessary to ensure its comprehensive and efficient application for chemical cross-linking of proteins.
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Affiliation(s)
- Mathias Q Müller
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, D-06120 Halle (Saale), Germany
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Müller MQ, Dreiocker F, Ihling CH, Schäfer M, Sinz A. Cleavable Cross-Linker for Protein Structure Analysis: Reliable Identification of Cross-Linking Products by Tandem MS. Anal Chem 2010; 82:6958-68. [DOI: 10.1021/ac101241t] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mathias Q. Müller
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Frank Dreiocker
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Christian H. Ihling
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Mathias Schäfer
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), and Institute for Organic Chemistry, Department of Chemistry, Universität zu Köln, Greinstrasse 4, D-50939 Cologne, Germany
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Krauth F, Ihling CH, Rüttinger HH, Sinz A. Heterobifunctional isotope-labeled amine-reactive photo-cross-linker for structural investigation of proteins by matrix-assisted laser desorption/ionization tandem time-of-flight and electrospray ionization LTQ-Orbitrap mass spectrometry. Rapid Commun Mass Spectrom 2009; 23:2811-2818. [PMID: 19653199 DOI: 10.1002/rcm.4188] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Chemical cross-linking combined with a subsequent enzymatic digestion and mass spectrometric analysis of the created cross-linked products presents an alternative approach to assess low-resolution protein structures. By covalently connecting pairs of functional groups within a protein or a protein complex a set of structurally defined interactions is built up. We synthesized the heterobifunctional amine-reactive photo-cross-linker N-succinimidyl p-benzoyldihydrocinnamate as a non-deuterated (SBC) and doubly deuterated derivative (SBDC). Applying a 1:1 mixture of SBC and SBDC for cross-linking experiments aided the identification of cross-linked amino acids in the mass spectra based on the characteristic isotope patterns of fragment ions. The cross-linker was applied to the calcium-binding protein calmodulin with a subsequent analysis of cross-linked products by nano-high-performance liquid chromatography matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (nano-HPLC/MALDI-TOF/TOF-MS) and nano-HPLC/nano-electrospray ionization (ESI)-LTQ-Orbitrap-MS.
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Affiliation(s)
- Fabian Krauth
- Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin-Luther-Universität Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, D-06120 Halle (Saale), Germany
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