1
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Beugelink JW, Sweep E, Janssen BJC, Snijder J, Pronker MF. Structural Basis for Recognition of the FLAG-tag by Anti-FLAG M2. J Mol Biol 2024; 436:168649. [PMID: 38852931 DOI: 10.1016/j.jmb.2024.168649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
The FLAG-tag/anti-FLAG system is a widely used biochemical tool for protein detection and purification. Anti-FLAG M2 is the most popular antibody against the FLAG-tag, due to its ease of use, versatility, and availability in pure form or as bead conjugate. M2 binds N-terminal, C-terminal and internal FLAG-tags and binding is calcium-independent, but the molecular basis for the FLAG-tag specificity and recognition remains unresolved. Here we present an atomic resolution (1.17 Å) structure of the FLAG peptide in complex with the Fab of anti-FLAG M2, revealing key binding determinants. Five of the eight FLAG peptide residues form direct interactions with paratope residues. The FLAG peptide adopts a 310 helix conformation in complex with the Fab. These structural insights allowed us to rationally introduce point mutations on both the peptide and antibody side. We tested these by surface plasmon resonance, leading us to propose a shorter yet equally binding version of the FLAG-tag for the M2 antibody.
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Affiliation(s)
- J Wouter Beugelink
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Els Sweep
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Bert J C Janssen
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
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2
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DeRoo J, Terry JS, Zhao N, Stasevich TJ, Snow CD, Geiss BJ. PAbFold: Linear Antibody Epitope Prediction using AlphaFold2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590298. [PMID: 38659833 PMCID: PMC11042291 DOI: 10.1101/2024.04.19.590298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Defining the binding epitopes of antibodies is essential for understanding how they bind to their antigens and perform their molecular functions. However, while determining linear epitopes of monoclonal antibodies can be accomplished utilizing well-established empirical procedures, these approaches are generally labor- and time-intensive and costly. To take advantage of the recent advances in protein structure prediction algorithms available to the scientific community, we developed a calculation pipeline based on the localColabFold implementation of AlphaFold2 that can predict linear antibody epitopes by predicting the structure of the complex between antibody heavy and light chains and target peptide sequences derived from antigens. We found that this AlphaFold2 pipeline, which we call PAbFold, was able to accurately flag known epitope sequences for several well-known antibody targets (HA / Myc) when the target sequence was broken into small overlapping linear peptides and antibody complementarity determining regions (CDRs) were grafted onto several different antibody framework regions in the single-chain antibody fragment (scFv) format. To determine if this pipeline was able to identify the epitope of a novel antibody with no structural information publicly available, we determined the epitope of a novel anti-SARS-CoV-2 nucleocapsid targeted antibody using our method and then experimentally validated our computational results using peptide competition ELISA assays. These results indicate that the AlphaFold2-based PAbFold pipeline we developed is capable of accurately identifying linear antibody epitopes in a short time using just antibody and target protein sequences. This emergent capability of the method is sensitive to methodological details such as peptide length, AlphaFold2 neural network versions, and multiple-sequence alignment database. PAbFold is available at https://github.com/jbderoo/PAbFold.
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Affiliation(s)
- Jacob DeRoo
- School of Biomedical Engineering, Colorado State University, Fort Collins CO USA
| | - James S. Terry
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins CO USA
| | - Ning Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO USA
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins CO USA
| | - Christopher D. Snow
- School of Biomedical Engineering, Colorado State University, Fort Collins CO USA
- Department of Chemical & Biological Engineering, Colorado State University, Fort Collins CO USA
| | - Brian J. Geiss
- School of Biomedical Engineering, Colorado State University, Fort Collins CO USA
- Department of Microbiology, Immunology, & Pathology, Colorado State University, Fort Collins CO USA
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3
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Gruchow HM, Opdensteinen P, Buyel JF. Membrane-based inverse-transition purification facilitates a rapid isolation of various spider-silk elastin-like polypeptide fusion proteins from extracts of transgenic tobacco. Transgenic Res 2024; 33:21-33. [PMID: 38573429 PMCID: PMC11021290 DOI: 10.1007/s11248-024-00375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/05/2024] [Indexed: 04/05/2024]
Abstract
Plants can produce complex pharmaceutical and technical proteins. Spider silk proteins are one example of the latter and can be used, for example, as compounds for high-performance textiles or wound dressings. If genetically fused to elastin-like polypeptides (ELPs), the silk proteins can be reversibly precipitated from clarified plant extracts at moderate temperatures of ~ 30 °C together with salt concentrations > 1.5 M, which simplifies purification and thus reduces costs. However, the technologies developed around this mechanism rely on a repeated cycling between soluble and aggregated state to remove plant host cell impurities, which increase process time and buffer consumption. Additionally, ELPs are difficult to detect using conventional staining methods, which hinders the analysis of unit operation performance and process development. Here, we have first developed a surface plasmon resonance (SPR) spectroscopy-based assay to quantity ELP fusion proteins. Then we tested different filters to prepare clarified plant extract with > 50% recovery of spider silk ELP fusion proteins. Finally, we established a membrane-based purification method that does not require cycling between soluble and aggregated ELP state but operates similar to an ultrafiltration/diafiltration device. Using a data-driven design of experiments (DoE) approach to characterize the system of reversible ELP precipitation we found that membranes with pore sizes up to 1.2 µm and concentrations of 2-3 M sodium chloride facilitate step a recovery close to 100% and purities of > 90%. The system can thus be useful for the purification of ELP-tagged proteins produced in plants and other hosts.
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Affiliation(s)
- H M Gruchow
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - P Opdensteinen
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - J F Buyel
- Institute for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany.
- Institute of Bioprocess Science and Engineering (IBSE), Department of Biotechnology (DBT), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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4
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Russo G, Unkauf T, Meier D, Wenzel EV, Langreder N, Schneider KT, Wiesner R, Bischoff R, Stadler V, Dübel S. In vitro evolution of myc-tag antibodies: in-depth specificity and affinity analysis of Myc1-9E10 and Hyper-Myc. Biol Chem 2022; 403:479-494. [PMID: 35312243 DOI: 10.1515/hsz-2021-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/28/2022] [Indexed: 11/15/2022]
Abstract
One of the most widely used epitope tags is the myc-tag, recognized by the anti-c-Myc hybridoma antibody Myc1-9E10. Combining error-prone PCR, DNA shuffling and phage display, we generated an anti-c-Myc antibody variant (Hyper-Myc) with monovalent affinity improved to 18 nM and thermal stability increased by 37%. Quantification of capillary immunoblots and by flow cytometry demonstrated improved antigen detection by Hyper-Myc. Further, three different species variants of this antibody were generated to allow the use of either anti-human, anti-mouse or anti-rabbit Fc secondary antibodies for detection. We characterized the specificity of both antibodies in depth: individual amino acid exchange mapping demonstrated that the recognized epitope was not changed by the in vitro evolution process. A laser printed array of 29,127 different epitopes representing all human linear B-cell epitopes of the Immune Epitope Database allowing to chart unwanted reactivities with mimotopes showed these to be very low for both antibodies and not increased for Hyper-Myc despite its improved affinity. The very low background reactivity of Hyper-Myc was confirmed by staining of myc-tag transgenic zebrafish whole mounts. Hyper-Myc retains the very high specificity of Myc1-9E10 while allowing myc-tag detection at lower concentrations and with either anti-mouse, anti-rabbit or anti human secondary antibodies.
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Affiliation(s)
- Giulio Russo
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.,Abcalis GmbH, Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Tobias Unkauf
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
| | - Doris Meier
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
| | - Esther Veronika Wenzel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.,Abcalis GmbH, Inhoffenstr. 7, D-38124 Braunschweig, Germany
| | - Nora Langreder
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany.,iTUBS mbH, Wilhelmsgarten 3, D-38100 Braunschweig, Germany
| | - Kai-Thomas Schneider
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
| | - Rebecca Wiesner
- Technische Universität Braunschweig, Institut für Medizinische und Pharmazeutische Chemie, Beethovenstr. 55, D-38106 Braunschweig, Germany
| | - Ralf Bischoff
- Division of Functional Genome Analysis, Research Program "Functional and Structural Genomics", German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Volker Stadler
- Pepperprint GmbH, Rischerstrasse 12, D-69123 Heidelberg, Germany
| | - Stefan Dübel
- Department of Biotechnology, Technische Universität Braunschweig, Spielmannstr. 7, D-38106 Braunschweig, Germany
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5
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Pao PJ, Hsu MF, Chiang MH, Chen CT, Lee CC, Wang AHJ. Structural basis of an epitope tagging system derived from Haloarcula marismortui bacteriorhodopsin I D94N and its monoclonal antibody GD-26. FEBS J 2021; 289:730-747. [PMID: 34499806 PMCID: PMC9292375 DOI: 10.1111/febs.16184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 07/12/2021] [Accepted: 09/06/2021] [Indexed: 02/05/2023]
Abstract
Specific antibody interactions with short peptides have made epitope tagging systems a vital tool employed in virtually all fields of biological research. Here, we present a novel epitope tagging system comprised of a monoclonal antibody named GD‐26, which recognises the TD peptide (GTGATPADD) derived from Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant. The crystal structure of the antigen‐binding fragment (Fab) of GD‐26 complexed with the TD peptide was determined to a resolution of 1.45 Å. The TD peptide was found to adopt a 310 helix conformation within the binding cleft, providing a characteristic peptide structure for recognition by GD‐26 Fab. Based on the structure information, polar and nonpolar forces collectively contribute to the strong binding. Attempts to engineer the TD peptide show that the proline residue is crucial for the formation of the 310 helix in order to fit into the binding cleft. Isothermal calorimetry (ITC) reported a dissociation constant KD of 12 ± 2.8 nm, indicating a strong interaction between the TD peptide and GD‐26 Fab. High specificity of GD‐26 IgG to the TD peptide was demonstrated by western blotting, ELISA and immunofluorescence as only TD‐tagged proteins were detected, suggesting the effectiveness of the GD‐26/TD peptide tagging system. In addition to already‐existing epitope tags such as the FLAG tag and the ALFA tag adopting either extended or α‐helix conformations, the unique 310 helix conformation of the TD peptide together with the corresponding monoclonal antibody GD‐26 offers a novel tagging option for research.
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Affiliation(s)
- Po-Jung Pao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Min-Feng Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ming-Hui Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chun-Ting Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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6
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Wakasa A, Kaneko MK, Kato Y, Takagi J, Arimori T. Site-specific epitope insertion into recombinant proteins using the MAP tag system. J Biochem 2021; 168:375-384. [PMID: 32386302 PMCID: PMC7585734 DOI: 10.1093/jb/mvaa054] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/24/2020] [Indexed: 01/17/2023] Open
Abstract
The MAP tag system comprises a 14-residue peptide derived from mouse podoplanin and its high-affinity monoclonal antibody PMab-1. We determined the crystal structure of PMab-1 complexed with the MAP tag peptide and found that the recognition required only the N-terminal 8 residues of MAP tag sequence, enabling the shortening of the tag length without losing the affinity for PMab-1. Furthermore, the structure illustrated that the MAP tag adopts a U-shaped conformation when bound by PMab-1, suggesting that loop-inserted MAP tag would assume conformation compatible with the PMab-1 binding. We inserted the 8-residue MAP tag into multiple loop regions in various proteins including fibronectin type III domain and G-protein-coupled receptors and tested if they maintain PMab-1 reactivity. Despite the conformational restraints forced by the insertion position, all MAP-inserted mutants were expressed well in mammalian cells at levels comparable to the non-tagged proteins. Furthermore, the binding by PMab-1 was fully maintained even for the mutant where MAP tag was inserted at a structurally restricted β-hairpin, indicating that the MAP tag system has unique feature that allows placement in the middle of protein domain at desired locations. Our results indicate the versatile utility of the MAP tag system in 'site-specific epitope insertion' application.
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Affiliation(s)
- Ayami Wakasa
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine.,New Industry Creation Hatchery Center, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Arimori
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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7
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Zeng J, Santos AF, Mukadam AS, Osswald M, Jacques DA, Dickson CF, McLaughlin SH, Johnson CM, Kiss L, Luptak J, Renner N, Vaysburd M, McEwan WA, Morais-de-Sá E, Clift D, James LC. Target-induced clustering activates Trim-Away of pathogens and proteins. Nat Struct Mol Biol 2021; 28:278-289. [PMID: 33633400 PMCID: PMC7611929 DOI: 10.1038/s41594-021-00560-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/13/2021] [Indexed: 01/31/2023]
Abstract
Trim-Away is a recently developed technology that exploits off-the-shelf antibodies and the RING E3 ligase and cytosolic antibody receptor TRIM21 to carry out rapid protein depletion. How TRIM21 is catalytically activated upon target engagement, either during its normal immune function or when repurposed for targeted protein degradation, is unknown. Here we show that a mechanism of target-induced clustering triggers intermolecular dimerization of the RING domain to switch on the ubiquitination activity of TRIM21 and induce virus neutralization or drive Trim-Away. We harness this mechanism for selective degradation of disease-causing huntingtin protein containing long polyglutamine tracts and expand the Trim-Away toolbox with highly active TRIM21-nanobody chimeras that can also be controlled optogenetically. This work provides a mechanism for cellular activation of TRIM RING ligases and has implications for targeted protein degradation technologies.
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Affiliation(s)
- Jingwei Zeng
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Ana Filipa Santos
- i3S - Instituto de Investigação e Inovação em Saúde and IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Aamir S. Mukadam
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mariana Osswald
- i3S - Instituto de Investigação e Inovação em Saúde and IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - David A. Jacques
- EMBL Australia Node, Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Claire F. Dickson
- EMBL Australia Node, Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, Australia
| | | | | | - Leo Kiss
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Jakub Luptak
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Nadine Renner
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - Marina Vaysburd
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK
| | - William A. McEwan
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
| | - Eurico Morais-de-Sá
- i3S - Instituto de Investigação e Inovação em Saúde and IBMC Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
| | - Dean Clift
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
| | - Leo C. James
- Medical Research Council, Laboratory of Molecular Biology, Cambridge, UK,Correspondence: William McEwan (); Eurico Morais-de-Sá (); Dean Clift (); Leo C. James ()
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8
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Schüchner S, Behm C, Mudrak I, Ogris E. The Myc tag monoclonal antibody 9E10 displays highly variable epitope recognition dependent on neighboring sequence context. Sci Signal 2020; 13:13/616/eaax9730. [PMID: 31992583 DOI: 10.1126/scisignal.aax9730] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Epitope tags are short, linear antibody recognition sequences that enable detection of tagged fusion proteins by antibodies. Epitope tag position and neighboring sequences potentially affect its recognition by antibodies, and such context-dependent differences in tag binding may have a wide-ranging effect on data interpretation. We tested by Western blotting six antibodies that recognize the c-Myc epitope tag, including monoclonal antibodies 9E10, 4A6, 9B11, and 71D10 and polyclonal antibodies 9106 and A-14. All displayed context-dependent differences in their ability to detect N- or C-terminal Myc-tagged proteins. In particular, clone 9E10, the most cited Myc-tag antibody, displayed high context-dependent detection variability, whereas others, notably 4A6 and 9B11, showed much less context sensitivity in their detection of Myc-tagged proteins. The very high context sensitivity of 9E10 was further substantiated by peptide microarray analyses. We conclude that recently developed, purpose-made monoclonal antibodies specific for Myc have much more uniform reactivity in diverse assays and are much less context sensitive than is the legacy antibody 9E10.
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Affiliation(s)
- Stefan Schüchner
- Center for Medical Biochemistry, Max Perutz Labs, Vienna BioCenter, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Christian Behm
- Center for Medical Biochemistry, Max Perutz Labs, Vienna BioCenter, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Ingrid Mudrak
- Center for Medical Biochemistry, Max Perutz Labs, Vienna BioCenter, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Egon Ogris
- Center for Medical Biochemistry, Max Perutz Labs, Vienna BioCenter, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
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9
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Abstract
Monoclonal antibodies recognize epitopes so specifically that altering a single residue can disrupt binding. In this issue of Science Signaling, Schüchner et al and Frohner et al report that flanking amino acids and an underappreciated posttranslational modification perturb epitope affinity for two groups of widely used monoclonal antibodies.
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Affiliation(s)
- Kevin A Janes
- Departments of Biomedical Engineering and Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
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10
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Mori Y, Okumura H, Watanabe T, Hohsaka T. Antigen-dependent fluorescence response of anti-c-Myc Quenchbody studied by molecular dynamics simulations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Roggenkamp E, Giersch RM, Wedeman E, Eaton M, Turnquist E, Schrock MN, Alkotami L, Jirakittisonthon T, Schluter-Pascua SE, Bayne GH, Wasko C, Halloran M, Finnigan GC. CRISPR-UnLOCK: Multipurpose Cas9-Based Strategies for Conversion of Yeast Libraries and Strains. Front Microbiol 2017; 8:1773. [PMID: 28979241 PMCID: PMC5611381 DOI: 10.3389/fmicb.2017.01773] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/31/2017] [Indexed: 11/29/2022] Open
Abstract
Saccharomyces cerevisiae continues to serve as a powerful model system for both basic biological research and industrial application. The development of genome-wide collections of individually manipulated strains (libraries) has allowed for high-throughput genetic screens and an emerging global view of this single-celled Eukaryote. The success of strain construction has relied on the innate ability of budding yeast to accept foreign DNA and perform homologous recombination, allowing for efficient plasmid construction (in vivo) and integration of desired sequences into the genome. The development of molecular toolkits and “integration cassettes” have provided fungal systems with a collection of strategies for tagging, deleting, or over-expressing target genes; typically, these consist of a C-terminal tag (epitope or fluorescent protein), a universal terminator sequence, and a selectable marker cassette to allow for convenient screening. However, there are logistical and technical obstacles to using these traditional genetic modules for complex strain construction (manipulation of many genomic targets in a single cell) or for the generation of entire genome-wide libraries. The recent introduction of the CRISPR/Cas gene editing technology has provided a powerful methodology for multiplexed editing in many biological systems including yeast. We have developed four distinct uses of the CRISPR biotechnology to generate yeast strains that utilizes the conversion of existing, commonly-used yeast libraries or strains. We present Cas9-based, marker-less methodologies for (i) N-terminal tagging, (ii) C-terminally tagging yeast genes with 18 unique fusions, (iii) conversion of fluorescently-tagged strains into newly engineered (or codon optimized) variants, and finally, (iv) use of a Cas9 “gene drive” system to rapidly achieve a homozygous state for a hypomorphic query allele in a diploid strain. These CRISPR-based methods demonstrate use of targeting universal sequences previously introduced into a genome.
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Affiliation(s)
- Emily Roggenkamp
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Rachael M Giersch
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Emily Wedeman
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Muriel Eaton
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Emily Turnquist
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Madison N Schrock
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Linah Alkotami
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Thitikan Jirakittisonthon
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State UniversityManhattan, KS, United States
| | | | - Gareth H Bayne
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Cory Wasko
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Megan Halloran
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
| | - Gregory C Finnigan
- Department of Biochemistry and Molecular Biophysics, Kansas State UniversityManhattan, KS, United States
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12
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Ge C, Tong D, Liang B, Lönnblom E, Schneider N, Hagert C, Viljanen J, Ayoglu B, Stawikowska R, Nilsson P, Fields GB, Skogh T, Kastbom A, Kihlberg J, Burkhardt H, Dobritzsch D, Holmdahl R. Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage. JCI Insight 2017; 2:93688. [PMID: 28679953 DOI: 10.1172/jci.insight.93688] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/23/2017] [Indexed: 12/29/2022] Open
Abstract
Today, it is known that autoimmune diseases start a long time before clinical symptoms appear. Anti-citrullinated protein antibodies (ACPAs) appear many years before the clinical onset of rheumatoid arthritis (RA). However, it is still unclear if and how ACPAs are arthritogenic. To better understand the molecular basis of pathogenicity of ACPAs, we investigated autoantibodies reactive against the C1 epitope of collagen type II (CII) and its citrullinated variants. We found that these antibodies are commonly occurring in RA. A mAb (ACC1) against citrullinated C1 was found to cross-react with several noncitrullinated epitopes on native CII, causing proteoglycan depletion of cartilage and severe arthritis in mice. Structural studies by X-ray crystallography showed that such recognition is governed by a shared structural motif "RG-TG" within all the epitopes, including electrostatic potential-controlled citrulline specificity. Overall, we have demonstrated a molecular mechanism that explains how ACPAs trigger arthritis.
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Affiliation(s)
- Changrong Ge
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Dongmei Tong
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Department of Pathophysiology, Key Lab for Shock and Microcirculation Research of Guangdong, Southern Medical University, Guangzhou, China
| | - Bibo Liang
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Department of Pathophysiology, Key Lab for Shock and Microcirculation Research of Guangdong, Southern Medical University, Guangzhou, China
| | - Erik Lönnblom
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nadine Schneider
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology, and Division of Rheumatology, University Hospital Frankfurt Goethe University, Frankfurt, Germany
| | - Cecilia Hagert
- Medicity Research Laboratory, University of Turku, Turku, Finland; National Doctoral Programme in Informational and Structural Biology, Turku, Finland
| | - Johan Viljanen
- Section of Organic Chemistry, Department of Chemistry - Biomedicinskt centrum, Uppsala University, Uppsala, Sweden
| | - Burcu Ayoglu
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Roma Stawikowska
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida, USA
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, Jupiter, Florida, USA
| | - Thomas Skogh
- Department of Rheumatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Alf Kastbom
- Department of Rheumatology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jan Kihlberg
- Section of Organic Chemistry, Department of Chemistry - Biomedicinskt centrum, Uppsala University, Uppsala, Sweden
| | - Harald Burkhardt
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology, and Division of Rheumatology, University Hospital Frankfurt Goethe University, Frankfurt, Germany
| | - Doreen Dobritzsch
- Section of Biochemistry, Department of Chemistry - Biomedicinskt centrum, Uppsala University, Uppsala, Sweden
| | - Rikard Holmdahl
- Section for Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Medicity Research Laboratory, University of Turku, Turku, Finland; National Doctoral Programme in Informational and Structural Biology, Turku, Finland.,Center for Medical Immunopharmacology Research, Southern Medical University, Guangzhou, China
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13
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Yoshikoshi K, Watanabe T, Hohsaka T. Double-Fluorescent-Labeled Single-Chain Antibodies Showing Antigen-Dependent Fluorescence Ratio Change. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20150384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kensuke Yoshikoshi
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology
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14
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Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc Natl Acad Sci U S A 2016; 113:2092-7. [PMID: 26862167 DOI: 10.1073/pnas.1522691113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. This "antigen clasping" produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody-antigen recognition and suggests a strategy for developing extremely specific antibodies.
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15
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Fujii Y, Matsunaga Y, Arimori T, Kitago Y, Ogasawara S, Kaneko MK, Kato Y, Takagi J. Tailored placement of a turn-forming PA tag into the structured domain of a protein to probe its conformational state. J Cell Sci 2016; 129:1512-22. [DOI: 10.1242/jcs.176685] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 02/10/2016] [Indexed: 11/20/2022] Open
Abstract
Placement of a tag sequence is usually limited to either terminal of the target protein, reducing the potential of epitope tags for various labeling applications. The PA tag is a dodecapeptide (GVAMPGAEDDVV) that is recognized by a high-affinity antibody NZ-1. We determined the crystal structure of the PA tag/NZ-1 complex and found that NZ-1 recognized a central segment of the PA tag peptide in a tight β-turn configuration, suggesting its compatibility with the insertion into a loop. This possibility was tested and confirmed using multiple integrin subunits and semaphorin. More specifically, the PA tag can be inserted at multiple locations within the αIIb subunit of the fibrinogen receptor αIIbβ3 integrin without affecting the structural and functional integrity, while maintaining its high affinity toward NZ-1. The large choice of the sites for "epitope grafting" enabled the placement of the PA tag at a location whose accessibility is modulated during the biological action of the receptor. Thus, we succeeded in converting a general anti-tag antibody into a special reporter/activator anti-β1 integrin antibody that can be classified as a ligand-induced binding site antibody.
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Affiliation(s)
- Yuki Fujii
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yukiko Matsunaga
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takao Arimori
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yu Kitago
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satoshi Ogasawara
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Mika K. Kaneko
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Yukinari Kato
- Department of Regional Innovation, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Junichi Takagi
- Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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16
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Chikazawa M, Otaki N, Shibata T, Yasueda T, Matsuda T, Uchida K. An apoptosis-associated mammary protein deficiency leads to enhanced production of IgM antibodies against multiple damage-associated molecules. PLoS One 2013; 8:e68468. [PMID: 23874637 PMCID: PMC3709889 DOI: 10.1371/journal.pone.0068468] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/29/2013] [Indexed: 12/21/2022] Open
Abstract
Milk fat globule epidermal growth factor 8 (MFG-E8) is a protein that binds to apoptotic cells by recognizing phosphatidylserine and enhances the engulfment of apoptotic cells by macrophages. Many apoptotic cells are left unengulfed in the germinal centers of the spleen in the MFG-E8-deficient (MFG-E8−/−) mice, and these mice develop an autoimmune disease resembling human systemic lupus erythematosus. We found that the MFG-E8 deficiency was accompanied by the increased production of immunoglobulins. Further Western blot and ELISA analyses validated the increase in the IgM levels in the MFG-E8−/− mice. It was also revealed that the sera from the MFG-E8−/− mice cross-reacted with oxidation-specific epitopes generated upon incubation of serum albumin with the peroxidized lipids. Among the modified proteins with several unsaturated aldehydes of chain lengths varying from three to nine carbons, the MFG-E8−/− mice sera exclusively cross-reacted with the protein-bound 4-oxo-2-nonenal (ONE), a highly reactive aldehyde originating from the peroxidation of ω6 polyunsaturated fatty acids. In addition, the IgM monoclonal antibodies (mAbs) that selectively cross-reacted with the ONE-modified proteins were generated from the MFG-E8−/− mice. A subset of the ONE-specific IgM mAbs significantly recognized the late apoptotic and necrotic cells and enhanced the phagocytosis by macrophages. These data demonstrate that the impairment of the phagocytic clearance of apoptotic cells through MFG-E8 can lead to the generation of natural antibodies, which may play a critical role in removing multiple damage-associated molecules, including oxidation-specific epitopes and late apoptotic/necrotic cells.
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Affiliation(s)
- Miho Chikazawa
- Laboratory of Food and Biodynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Natsuki Otaki
- Laboratory of Food and Biodynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takahiro Shibata
- Laboratory of Food and Biodynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takehiko Yasueda
- Laboratory of Molecular Bioregulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tsukasa Matsuda
- Laboratory of Molecular Bioregulation, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Koji Uchida
- Laboratory of Food and Biodynamics, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- * E-mail:
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17
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Sherwood LJ, Hayhurst A. Hapten mediated display and pairing of recombinant antibodies accelerates assay assembly for biothreat countermeasures. Sci Rep 2012; 2:807. [PMID: 23150778 PMCID: PMC3495282 DOI: 10.1038/srep00807] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/17/2012] [Indexed: 11/14/2022] Open
Abstract
A bottle-neck in recombinant antibody sandwich immunoassay development is pairing, demanding protein purification and modification to distinguish captor from tracer. We developed a simple pairing scheme using microliter amounts of E. coli osmotic shockates bearing site-specific biotinylated antibodies and demonstrated proof of principle with a single domain antibody (sdAb) that is both captor and tracer for polyvalent Marburgvirus nucleoprotein. The system could also host pairs of different sdAb specific for the 7 botulinum neurotoxin (BoNT) serotypes, enabling recognition of the cognate serotype. Inducible supE co-expression enabled sdAb populations to be propagated as either phage for more panning from repertoires or expressed as soluble sdAb for screening within a single host strain. When combined with streptavidin-g3p fusions, a novel transdisplay system was formulated to retrofit a semi-synthetic sdAb library which was mined for an anti-Ebolavirus sdAb which was immediately immunoassay ready, thereby speeding up the recombinant antibody discovery and utilization processes.
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Affiliation(s)
- Laura J. Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
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18
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Calcium stabilizes the von Willebrand factor A2 domain by promoting refolding. Proc Natl Acad Sci U S A 2012; 109:3742-7. [PMID: 22357761 DOI: 10.1073/pnas.1121261109] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Von Willebrand factor (VWF) is a large, multimeric plasma glycoprotein that critically mediates hemostasis at sites of vascular injury. Very large VWF multimers have the greatest thrombogenic activity, which is attenuated by cleavage in the A2 domain by the metalloproteinase ADAMTS13. ADAMTS13 proteolysis requires mechanical force to expose the scissile bond and is regulated by a calcium-binding site within A2. In this study, we characterized the interaction between VWF A2 and calcium by examining the effect of calcium on VWF A2 stability and mechanical unfolding and refolding. Isothermal calorimetry yielded a calcium binding K(d) = 3.8 ± 1.0 μM and reversible thermal denaturation showed that 5 mM calcium stabilized the unfolding transition from 56.7 ± 0.1 to 69.1 ± 0.1 °C. Using optical tweezers to apply tensile force to single domains, we found that calcium did not affect VWF A2 unfolding, but rather enhanced refolding kinetics fivefold, resulting in a 0.9 kcal/mol stabilization in the folding activation energy in the presence of calcium. Taken together, our data demonstrate that VWF binds calcium at physiologic calcium concentrations and that calcium stabilizes VWF A2 by accelerating refolding.
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19
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Huang J, Nagy SS, Koide A, Rock RS, Koide S. A peptide tag system for facile purification and single-molecule immobilization. Biochemistry 2010; 48:11834-6. [PMID: 19928925 DOI: 10.1021/bi901756n] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A peptide fusion tag and accompanying recombinant capture reagents have been developed on the basis of the peptide-PDZ domain interaction and affinity clamps, a new class of affinity reagent. This system allows for single-step purification under mild conditions and stable capture of a tagged protein. The subnanomolar affinity, high force resistance (>30 pN), small size ( approximately 25 kDa, approximately one-sixth of the size of IgG), and monomeric nature of the affinity clamp are all superior features for many applications, in particular single-molecule measurements.
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Affiliation(s)
- Jin Huang
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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20
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Sonneson GJ, Horn JR. Hapten-Induced Dimerization of a Single-Domain VHH Camelid Antibody. Biochemistry 2009; 48:6693-5. [DOI: 10.1021/bi900862r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gregory J. Sonneson
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115
| | - James R. Horn
- Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, Illinois 60115
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