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Jung V, Roger K, Chhuon C, Pannetier L, Lipecka J, Gomez JS, Chappert P, Charbit A, Guerrera IC. BLI-MS: Combining biolayer interferometry and mass spectrometry. Proteomics 2021; 22:e2100031. [PMID: 34958708 DOI: 10.1002/pmic.202100031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 11/30/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Abstract
Biolayer Interferometry (BLI) is a technology which allows to study the affinity between two interacting macro-molecules and to visualize their kinetic of interaction in real time. In this work we combine BLI interaction measurement with mass spectrometry in order to identify the proteins interacting with the bait. We provide for the first time the proof of concept of the feasibility of BLI-MS in complex biological mixtures. Data are available via ProteomeXchange with the identifier PXD019440. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vincent Jung
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Kévin Roger
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Cerina Chhuon
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Louise Pannetier
- Université de Paris, Sorbonne Paris Cité, INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris, France
| | - Joanna Lipecka
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Josué Sulub Gomez
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Pascal Chappert
- Université de Paris, Sorbonne Paris Cité, INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris, France
- INSERM U955, Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Alain Charbit
- Université de Paris, Sorbonne Paris Cité, INSERM U1151-CNRS UMR 8253, Institut Necker-Enfants Malades, Paris, France
| | - Ida Chiara Guerrera
- Proteomics Platform Necker, Université de Paris - Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
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hSSB2 (NABP1) is required for the recruitment of RPA during the cellular response to DNA UV damage. Sci Rep 2021; 11:20256. [PMID: 34642383 PMCID: PMC8511049 DOI: 10.1038/s41598-021-99355-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 09/15/2021] [Indexed: 11/17/2022] Open
Abstract
Maintenance of genomic stability is critical to prevent diseases such as cancer. As such, eukaryotic cells have multiple pathways to efficiently detect, signal and repair DNA damage. One common form of exogenous DNA damage comes from ultraviolet B (UVB) radiation. UVB generates cyclobutane pyrimidine dimers (CPD) that must be rapidly detected and repaired to maintain the genetic code. The nucleotide excision repair (NER) pathway is the main repair system for this type of DNA damage. Here, we determined the role of the human Single-Stranded DNA Binding protein 2, hSSB2, in the response to UVB exposure. We demonstrate that hSSB2 levels increase in vitro and in vivo after UVB irradiation and that hSSB2 rapidly binds to chromatin. Depletion of hSSB2 results in significantly decreased Replication Protein A (RPA32) phosphorylation and impaired RPA32 localisation to the site of UV-induced DNA damage. Delayed recruitment of NER protein Xeroderma Pigmentosum group C (XPC) was also observed, leading to increased cellular sensitivity to UVB. Finally, hSSB2 was shown to have affinity for single-strand DNA containing a single CPD and for duplex DNA with a two-base mismatch mimicking a CPD moiety. Altogether our data demonstrate that hSSB2 is involved in the cellular response to UV exposure.
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Lawson T, El-Kamand S, Boucher D, Duong DC, Kariawasam R, Bonvin AMJJ, Richard DJ, Gamsjaeger R, Cubeddu L. The structural details of the interaction of single-stranded DNA binding protein hSSB2 (NABP1/OBFC2A) with UV-damaged DNA. Proteins 2019; 88:319-326. [PMID: 31443132 DOI: 10.1002/prot.25806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/02/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
Abstract
Single-stranded DNA-binding proteins (SSBs) are required for all known DNA metabolic events such as DNA replication, recombination and repair. While a wealth of structural and functional data is available on the essential human SSB, hSSB1 (NABP2/OBFC2B), the close homolog hSSB2 (NABP1/OBFC2A) remains relatively uncharacterized. Both SSBs possess a well-structured OB (oligonucleotide/oligosaccharide-binding) domain that is able to recognize single-stranded DNA (ssDNA) followed by a flexible carboxyl-tail implicated in the interaction with other proteins. Despite the high sequence similarity of the OB domain, several recent studies have revealed distinct functional differences between hSSB1 and hSSB2. In this study, we show that hSSB2 is able to recognize cyclobutane pyrimidine dimers (CPD) that form in cellular DNA as a consequence of UV damage. Using a combination of biolayer interferometry and NMR, we determine the molecular details of the binding of the OB domain of hSSB2 to CPD-containing ssDNA, confirming the role of four key aromatic residues in hSSB2 (W59, Y78, W82, and Y89) that are also conserved in hSSB1. Our structural data thus demonstrate that ssDNA recognition by the OB fold of hSSB2 is highly similar to hSSB1, indicating that one SSB may be able to replace the other in any initial ssDNA binding event. However, any subsequent recruitment of other repair proteins most likely depends on the divergent carboxyl-tail and as such is likely to be different between hSSB1 and hSSB2.
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Affiliation(s)
- Teegan Lawson
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Serene El-Kamand
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Didier Boucher
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Duc Cong Duong
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Derek J Richard
- Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Penrith, New South Wales, Australia.,School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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Xue J, Bai Y, Liu H. Hybrid methods of surface plasmon resonance coupled to mass spectrometry for biomolecular interaction analysis. Anal Bioanal Chem 2019; 411:3721-3729. [DOI: 10.1007/s00216-019-01906-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/23/2019] [Accepted: 05/08/2019] [Indexed: 01/02/2023]
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Han Y, Gao Y, He T, Wang D, Guo N, Zhang X, Chen S, Wang H. PD-1/PD-L1 inhibitor screening of caffeoylquinic acid compounds using surface plasmon resonance spectroscopy. Anal Biochem 2018; 547:52-56. [DOI: 10.1016/j.ab.2018.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/13/2018] [Accepted: 02/07/2018] [Indexed: 12/11/2022]
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Kumar PKR. Systematic screening of viral entry inhibitors using surface plasmon resonance. Rev Med Virol 2017; 27. [PMID: 29047180 DOI: 10.1002/rmv.1952] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 08/02/2017] [Accepted: 09/07/2017] [Indexed: 12/12/2022]
Abstract
Viral binding and entry into host cells for various viruses have been studied extensively, yielding a detailed understanding of the overall viral entry process. As cell entry is an essential and requisite process by which a virus initiates infection, it is an attractive target for therapeutic intervention. The advantages of targeting viral entry are an extracellular target site, relatively easy access for biological interventions, and lower toxicity. Several cell-based strategies and biophysical techniques have been used to screen compounds that block viral entry. These studies led to the discovery of inhibitors against HIV, HCV, influenza, Ebola, and RSV. In recent years, several compounds screened by fragment-based drug discovery have been approved as drugs or are in the final stages of clinical trials. Among fragment screening technologies, surface plasmon resonance has been widely used because it provides accurate information on binding kinetics, allows real-time monitoring of ligand-drug interactions, requires very small sample amounts to perform analyses, and requires no modifications to or labeling of ligands. This review focuses on surface plasmon resonance-based schemes for screening viral entry inhibitors.
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Affiliation(s)
- Penmetcha K R Kumar
- National Institute of Advanced Industrial Science and Technology, Tsukuba City, Ibaraki, Japan
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Lammirato A, Patsch K, Feiereisen F, Maly K, Nofziger C, Paulmichl M, Hackl H, Trajanoski Z, Valovka T, Huber LA, Vietor I. TIS7 induces transcriptional cascade of methylosome components required for muscle differentiation. BMC Biol 2016; 14:95. [PMID: 27782840 PMCID: PMC5080701 DOI: 10.1186/s12915-016-0318-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/14/2016] [Indexed: 02/01/2023] Open
Abstract
Background TPA Induced Sequence 7 acts as a transcriptional co-regulator controlling the expression of genes involved in differentiation of various cell types, including skeletal myoblasts. We and others have shown that TIS7 regulates adult myogenesis through MyoD, one of the essential myogenic regulatory factors. Results Here, we present data identifying ICln as the specific, novel protein downstream of TIS7 controlling myogenesis. We show that TIS7/ICln epigenetically regulate myoD expression controlling protein methyl transferase activity. In particular, ICln regulates MyoD expression via its interaction with PRMT5 by an epigenetic modification that utilizes symmetrical di-methylation of histone H3 on arginine 8. We provide multiple evidences that TIS7 directly binds DNA, which is a functional feature necessary for its role in transcriptional regulation. Conclusion We present here a molecular insight into TIS7-specific control of MyoD gene expression and thereby skeletal muscle differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0318-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Lammirato
- Division of Cell Biology, Biocenter, Medical University Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Katherin Patsch
- Division of Cell Biology, Biocenter, Medical University Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Fabien Feiereisen
- Division of Cell Biology, Biocenter, Medical University Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Karl Maly
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Charity Nofziger
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Strubergasse 21, A-5020, Salzburg, Austria
| | - Markus Paulmichl
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Strubergasse 21, A-5020, Salzburg, Austria
| | - Hubert Hackl
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Zlatko Trajanoski
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Taras Valovka
- Division of Cell Biology, Biocenter, Medical University Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Lukas A Huber
- Division of Cell Biology, Biocenter, Medical University Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Ilja Vietor
- Division of Cell Biology, Biocenter, Medical University Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria.
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Molecular mapping of α-thrombin (αT)/β2-glycoprotein I (β2GpI) interaction reveals how β2GpI affects αT functions. Biochem J 2016; 473:4629-4650. [PMID: 27760842 DOI: 10.1042/bcj20160603] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/07/2016] [Accepted: 10/14/2016] [Indexed: 01/15/2023]
Abstract
β2-Glycoprotein I (β2GpI) is the major autoantigen in the antiphospholipid syndrome, a thrombotic autoimmune disease. Nonetheless, the physiological role of β2GpI is still unclear. In a recent work, we have shown that β2GpI selectively inhibits the procoagulant functions of human α-thrombin (αT; i.e. prolongs fibrin clotting time, tc, and inhibits αT-induced platelet aggregation) without affecting the unique anticoagulant activity of the protease, i.e. the proteolytic generation of the anticoagulant protein C (PC) from the PC zymogen, which interacts with αT exclusively at the protease catalytic site. Here, we used several different biochemical/biophysical techniques and molecular probes for mapping the binding sites in the αT-β2GpI complex. Our results indicate that αT exploits the highly electropositive exosite-II, which is also responsible for anchoring αT on the platelet GpIbα (platelet receptor glycoprotein Ibα) receptor, for binding to a continuous negative region on β2GpI structure, spanning domain IV and (part of) domain V, whereas the protease active site and exosite-I (i.e. the fibrinogen-binding site) remain accessible for substrate/ligand binding. Furthermore, we provided evidence that the apparent increase in tc, previously observed with β2GpI, is more likely caused by alteration in the ensuing fibrin structure rather than by the inhibition of fibrinogen hydrolysis. Finally, we produced a theoretical docking model of αT-β2GpI interaction, which was in agreement with the experimental results. Altogether, these findings help to understand how β2GpI affects αT interactions and suggest that β2GpI may function as a scavenger of αT for binding to the GpIbα receptor, thus impairing platelet aggregation while enabling normal cleavage of fibrinogen and PC.
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Cruz C, Sousa Â, Mota É, Sousa F, Queiroz JA. Quantitative analysis of histamine- and agmatine–DNA interactions using surface plasmon resonance. Int J Biol Macromol 2014; 70:131-7. [DOI: 10.1016/j.ijbiomac.2014.06.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 10/25/2022]
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