1
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Chan A, Haley RM, Najar MA, Gonzalez-Martinez D, Bugaj LJ, Burslem GM, Mitchell MJ, Tsourkas A. Lipid-mediated intracellular delivery of recombinant bioPROTACs for the rapid degradation of undruggable proteins. Nat Commun 2024; 15:5808. [PMID: 38987546 PMCID: PMC11237011 DOI: 10.1038/s41467-024-50235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
Recently, targeted degradation has emerged as a powerful therapeutic modality. Relying on "event-driven" pharmacology, proteolysis targeting chimeras (PROTACs) can degrade targets and are superior to conventional inhibitors against undruggable proteins. Unfortunately, PROTAC discovery is limited by warhead scarcity and laborious optimization campaigns. To address these shortcomings, analogous protein-based heterobifunctional degraders, known as bioPROTACs, have been developed. Compared to small-molecule PROTACs, bioPROTACs have higher success rates and are subject to fewer design constraints. However, the membrane impermeability of proteins severely restricts bioPROTAC deployment as a generalized therapeutic modality. Here, we present an engineered bioPROTAC template able to complex with cationic and ionizable lipids via electrostatic interactions for cytosolic delivery. When delivered by biocompatible lipid nanoparticles, these modified bioPROTACs can rapidly degrade intracellular proteins, exhibiting near-complete elimination (up to 95% clearance) of targets within hours of treatment. Our bioPROTAC format can degrade proteins localized to various subcellular compartments including the mitochondria, nucleus, cytosol, and membrane. Moreover, substrate specificity can be easily reprogrammed, allowing modular design and targeting of clinically-relevant proteins such as Ras, Jnk, and Erk. In summary, this work introduces an inexpensive, flexible, and scalable platform for efficient intracellular degradation of proteins that may elude chemical inhibition.
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Affiliation(s)
- Alexander Chan
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca M Haley
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohd Altaf Najar
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Gonzalez-Martinez
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J Mitchell
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Ivanova JR, Benk AS, Schaefer JV, Dreier B, Hermann LO, Plückthun A, Missirlis D, Spatz JP. Designed Ankyrin Repeat Proteins as Actin Labels of Distinct Cytoskeletal Structures in Living Cells. ACS NANO 2024; 18:8919-8933. [PMID: 38489155 DOI: 10.1021/acsnano.3c12265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
The orchestrated assembly of actin and actin-binding proteins into cytoskeletal structures coordinates cell morphology changes during migration, cytokinesis, and adaptation to external stimuli. The accurate and unbiased visualization of the diverse actin assemblies within cells is an ongoing challenge. We describe here the identification and use of designed ankyrin repeat proteins (DARPins) as synthetic actin binders. Actin-binding DARPins were identified through ribosome display and validated biochemically. When introduced or expressed inside living cells, fluorescently labeled DARPins accumulated at actin filaments, validated through phalloidin colocalization on fixed cells. Nevertheless, different DARPins displayed different actin labeling patterns: some DARPins labeled efficiently dynamic structures, such as filopodia, lamellipodia, and blebs, while others accumulated primarily in stress fibers. This differential intracellular distribution correlated with DARPin-actin binding kinetics, as measured by fluorescence recovery after photobleaching experiments. Moreover, the rapid arrest of actin dynamics induced by pharmacological treatment led to the fast relocalization of DARPins. Our data support the hypothesis that the localization of actin probes depends on the inherent dynamic movement of the actin cytoskeleton. Compared to the widely used LifeAct probe, one DARPin exhibited enhanced signal-to-background ratio while retaining a similar ability to label stress fibers. In summary, we propose DARPins as promising actin-binding proteins for labeling or manipulation in living cells.
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Affiliation(s)
- Julia R Ivanova
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
- Heidelberg University, Faculty of Biosciences, 69120 Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Amelie S Benk
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- CSL Behring AG, 3014 Bern, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Leon O Hermann
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Dimitris Missirlis
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, D-69120 Heidelberg, Germany
| | - Joachim P Spatz
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, D-69120 Heidelberg, Germany
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
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3
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Gee M, Atai K, Coller HA, Yeates TO, Castells-Graells R. Designed fluorescent protein cages as fiducial markers for targeted cell imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582585. [PMID: 38464160 PMCID: PMC10925312 DOI: 10.1101/2024.02.28.582585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Understanding how proteins function within their cellular environments is essential for cellular biology and biomedical research. However, current imaging techniques exhibit limitations, particularly in the study of small complexes and individual proteins within cells. Previously, protein cages have been employed as imaging scaffolds to study purified small proteins using cryo-electron microscopy (cryo-EM). Here we demonstrate an approach to deliver designed protein cages - endowed with fluorescence and targeted binding properties - into cells, thereby serving as fiducial markers for cellular imaging. We used protein cages with anti-GFP DARPin domains to target a mitochondrial protein (MFN1) expressed in mammalian cells, which was genetically fused to GFP. We demonstrate that the protein cages can penetrate cells, are directed to specific subcellular locations, and are detectable with confocal microscopy. This innovation represents a milestone in developing tools for in-depth cellular exploration, especially in conjunction with methods such as cryo-correlative light and electron microscopy (cryo-CLEM).
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Affiliation(s)
- Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
| | - Kaiser Atai
- Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA 90095
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA 90095
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA 90095
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4
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Lee EJ, Gladkov N, Miller JE, Yeates TO. Design of Ligand-Operable Protein-Cages That Open Upon Specific Protein Binding. ACS Synth Biol 2024; 13:157-167. [PMID: 38133598 DOI: 10.1021/acssynbio.3c00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Protein nanocages have diverse applications in medicine and biotechnology, including molecular delivery. However, although numerous studies have demonstrated the ability of protein nanocages to encapsulate various molecular species, limited methods are available for subsequently opening a nanocage for cargo release under specific conditions. A modular platform with a specific protein-target-based mechanism of nanocage opening is notably lacking. To address this important technology gap, we present a new class of designed protein cages, the Ligand-Operable Cage (LOC). LOCs primarily comprise a protein nanocage core and a fused surface binding adaptor. The geometry of the LOC is designed so that binding of a target protein ligand (or multiple copies thereof) to the surface binder is sterically incompatible with retention of the assembled state of the cage. Therefore, the tight binding of a target ligand drives cage disassembly by mass action, subsequently exposing the encapsulated cargo. LOCs are modular; direct substitution of the surface binder sequence can reprogram the nanocage to open in response to any target protein ligand of interest. We demonstrate these design principles using both a natural and a designed protein cage as the core, with different proteins acting as the triggering ligand and with different reporter readouts─fluorescence unquenching and luminescence─for cage disassembly. These developments advance the critical problem of targeted molecular delivery and detection.
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Affiliation(s)
- Eric J Lee
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Nika Gladkov
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Justin E Miller
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States
- Molecular Biology Institute, UCLA, Los Angeles, California 90095, United States
- UCLA-DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095, United States
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5
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Leka O, Wu Y, Zanetti G, Furler S, Reinberg T, Marinho J, Schaefer JV, Plückthun A, Li X, Pirazzini M, Kammerer RA. A DARPin promotes faster onset of botulinum neurotoxin A1 action. Nat Commun 2023; 14:8317. [PMID: 38110403 PMCID: PMC10728214 DOI: 10.1038/s41467-023-44102-4] [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: 12/24/2022] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
In this study, we characterize Designed Ankyrin Repeat Proteins (DARPins) as investigative tools to probe botulinum neurotoxin A1 (BoNT/A1) structure and function. We identify DARPin-F5 that completely blocks SNAP25 substrate cleavage by BoNT/A1 in vitro. X-ray crystallography reveals that DARPin-F5 inhibits BoNT/A1 activity by interacting with a substrate-binding region between the α- and β-exosite. This DARPin does not block substrate cleavage of BoNT/A3, indicating that DARPin-F5 is a subtype-specific inhibitor. BoNT/A1 Glu-171 plays a critical role in the interaction with DARPin-F5 and its mutation to Asp, the residue found in BoNT/A3, results in a loss of inhibition of substrate cleavage. In contrast to the in vitro results, DARPin-F5 promotes faster substrate cleavage of BoNT/A1 in primary neurons and muscle tissue by increasing toxin translocation. Our findings could have important implications for the application of BoNT/A1 in therapeutic areas requiring faster onset of toxin action combined with long persistence.
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Affiliation(s)
- Oneda Leka
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland
| | - Yufan Wu
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland
| | - Giulia Zanetti
- Department of Biomedical Sciences, University of Padova, 35121, Padova, Italy
| | - Sven Furler
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Joana Marinho
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Xiaodan Li
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland
| | - Marco Pirazzini
- Department of Biomedical Sciences, University of Padova, 35121, Padova, Italy
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland.
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6
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Corno A, Cordeiro MH, Allan LA, Lim Q, Harrington E, Smith RJ, Saurin AT. A bifunctional kinase-phosphatase module balances mitotic checkpoint strength and kinetochore-microtubule attachment stability. EMBO J 2023; 42:e112630. [PMID: 37712330 PMCID: PMC10577578 DOI: 10.15252/embj.2022112630] [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: 09/16/2022] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
Two major mechanisms safeguard genome stability during mitosis: the mitotic checkpoint delays mitosis until all chromosomes have attached to microtubules, and the kinetochore-microtubule error-correction pathway keeps this attachment process free from errors. We demonstrate here that the optimal strength and dynamics of these processes are set by a kinase-phosphatase pair (PLK1-PP2A) that engage in negative feedback from adjacent phospho-binding motifs on the BUB complex. Uncoupling this feedback to skew the balance towards PLK1 produces a strong checkpoint, hypostable microtubule attachments and mitotic delays. Conversely, skewing the balance towards PP2A causes a weak checkpoint, hyperstable microtubule attachments and chromosome segregation errors. These phenotypes are associated with altered BUB complex recruitment to KNL1-MELT motifs, implicating PLK1-PP2A in controlling auto-amplification of MELT phosphorylation. In support, KNL1-BUB disassembly becomes contingent on PLK1 inhibition when KNL1 is engineered to contain excess MELT motifs. This elevates BUB-PLK1/PP2A complex levels on metaphase kinetochores, stabilises kinetochore-microtubule attachments, induces chromosome segregation defects and prevents KNL1-BUB disassembly at anaphase. Together, these data demonstrate how a bifunctional PLK1/PP2A module has evolved together with the MELT motifs to optimise BUB complex dynamics and ensure accurate chromosome segregation.
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Affiliation(s)
- Andrea Corno
- Cellular and Systems Medicine, School of MedicineUniversity of DundeeDundeeUK
| | - Marilia H Cordeiro
- Cellular and Systems Medicine, School of MedicineUniversity of DundeeDundeeUK
| | - Lindsey A Allan
- Cellular and Systems Medicine, School of MedicineUniversity of DundeeDundeeUK
| | - Qian‐Wei Lim
- Cellular and Systems Medicine, School of MedicineUniversity of DundeeDundeeUK
| | - Elena Harrington
- Cellular and Systems Medicine, School of MedicineUniversity of DundeeDundeeUK
| | - Richard J Smith
- Cellular and Systems Medicine, School of MedicineUniversity of DundeeDundeeUK
| | - Adrian T Saurin
- Cellular and Systems Medicine, School of MedicineUniversity of DundeeDundeeUK
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7
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Westberg M, Song D, Duong V, Fernandez D, Huang PS, Lin MZ. Photoswitchable binders enable temporal dissection of endogenous protein function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557687. [PMID: 37745504 PMCID: PMC10515898 DOI: 10.1101/2023.09.14.557687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
General methods for spatiotemporal control of specific endogenous proteins would be broadly useful for probing protein function in living cells. Synthetic protein binders that bind and inhibit endogenous protein targets can be obtained from nanobodies, designed ankyrin repeat proteins (DARPins), and other small protein scaffolds, but generalizable methods to control their binding activity are lacking. Here, we report robust single-chain photoswitchable DARPins (psDARPins) for bidirectional optical control of endogenous proteins. We created topological variants of the DARPin scaffold by computer-aided design so fusion of photodissociable dimeric Dronpa (pdDronpa) results in occlusion of target binding at baseline. Cyan light induces pdDronpa dissociation to expose the binding surface (paratope), while violet light restores pdDronpa dimerization and paratope caging. Since the DARPin redesign leaves the paratope intact, the approach was easily applied to existing DARPins for GFP, ERK, and Ras, as demonstrated by relocalizing GFP-family proteins and inhibiting endogenous ERK and Ras with optical control. Finally, a Ras-targeted psDARPin was used to determine that, following EGF-activation of EGFR, Ras is required for sustained EGFR to ERK signaling. In summary, psDARPins provide a generalizable strategy for precise spatiotemporal dissection of endogenous protein function.
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8
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Zeng Y, Woolley M, Chockalingam K, Thomas B, Arora S, Hook M, Chen Z. Click display: a rapid and efficient in vitro protein display method for directed evolution. Nucleic Acids Res 2023; 51:e89. [PMID: 37548398 PMCID: PMC10484664 DOI: 10.1093/nar/gkad643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 07/22/2023] [Indexed: 08/08/2023] Open
Abstract
We describe a novel method for in vitro protein display-click display-that does not depend on maintaining RNA integrity during biopanning and yields covalently linked protein-cDNA complexes from double-stranded input DNA within 2 h. The display is achieved in a one-pot format encompassing transcription, translation and reverse transcription reactions in series. Stable linkage between proteins and the encoding cDNA is mediated by a modified DNA linker-ML-generated via a click chemistry reaction between a puromycin-containing oligo and a cDNA synthesis primer. Biopanning of a click-displayed mock library coupled with next-generation sequencing analysis revealed >600-fold enrichment of target binders within a single round of panning. A synthetic library of Designed Ankyrin Repeat Proteins (DARPins) with ∼1012 individual members was generated using click display in a 25-μl reaction and six rounds of library panning against a model protein yielded a panel of nanomolar binders. This study establishes click display as a powerful tool for protein binder discovery/engineering and provides a convenient platform for in vitro biopanning selection even in RNase-rich environments such as on whole cells.
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Affiliation(s)
- Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Michael Woolley
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
| | - Benjamin Thomas
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
| | - Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, Houston, TX 77030, USA
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9
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Shi J, Hauschulte K, Mikicic I, Maharjan S, Arz V, Strauch T, Heidelberger JB, Schaefer JV, Dreier B, Plückthun A, Beli P, Ulrich HD, Wollscheid HP. Nuclear myosin VI maintains replication fork stability. Nat Commun 2023; 14:3787. [PMID: 37355687 PMCID: PMC10290672 DOI: 10.1038/s41467-023-39517-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 06/09/2023] [Indexed: 06/26/2023] Open
Abstract
The actin cytoskeleton is of fundamental importance for cellular structure and plasticity. However, abundance and function of filamentous actin in the nucleus are still controversial. Here we show that the actin-based molecular motor myosin VI contributes to the stabilization of stalled or reversed replication forks. In response to DNA replication stress, myosin VI associates with stalled replication intermediates and cooperates with the AAA ATPase Werner helicase interacting protein 1 (WRNIP1) in protecting these structures from DNA2-mediated nucleolytic attack. Using functionalized affinity probes to manipulate myosin VI levels in a compartment-specific manner, we provide evidence for the direct involvement of myosin VI in the nucleus and against a contribution of the abundant cytoplasmic pool during the replication stress response.
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Affiliation(s)
- Jie Shi
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Kristine Hauschulte
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Srijana Maharjan
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Mainz Biomed N.V., Robert-Koch-Str. 50, D - 55129, Mainz, Germany
| | - Valerie Arz
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
| | - Jan B Heidelberger
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Max Planck School Matter to Life, Jahnstr. 29, D - 69120, Heidelberg, Germany
| | - Jonas V Schaefer
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Birgit Dreier
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Andreas Plückthun
- University of Zurich, Department of Biochemistry, Winterthurerstr. 190, CH - 8057, Zurich, Switzerland
| | - Petra Beli
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 15, D - 55128, Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
| | - Hans-Peter Wollscheid
- Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4, D - 55128, Mainz, Germany.
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10
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Haley RM, Chan A, Billingsley MM, Gong N, Padilla MS, Kim EH, Wang HH, Yin D, Wangensteen KJ, Tsourkas A, Mitchell MJ. Lipid Nanoparticle Delivery of Small Proteins for Potent In Vivo RAS Inhibition. ACS APPLIED MATERIALS & INTERFACES 2023; 15:21877-21892. [PMID: 37115558 PMCID: PMC10727849 DOI: 10.1021/acsami.3c01501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mutated RAS proteins are potent oncogenic drivers and have long been considered "undruggable". While RAS-targeting therapies have recently shown promise, there remains a clinical need for RAS inhibitors with more diverse targets. Small proteins represent a potential new therapeutic option, including K27, a designed ankyrin repeat protein (DARPin) engineered to inhibit RAS. However, K27 functions intracellularly and is incapable of entering the cytosol on its own, currently limiting its utility. To overcome this barrier, we have engineered a lipid nanoparticle (LNP) platform for potent delivery of functional K27-D30─a charge-modified version of the protein─intracellularly in vitro and in vivo. This system efficiently encapsulates charge-modified proteins, facilitates delivery in up to 90% of cells in vitro, and maintains potency after at least 45 days of storage. In vivo, these LNPs deliver K27-D30 to the cytosol of cancerous cells in the liver, inhibiting RAS-driven growth and ultimately reducing tumor load in an HTVI-induced mouse model of hepatocellular carcinoma. This work shows that K27 holds promise as a new cancer therapeutic when delivered using this LNP platform. Furthermore, this technology has the potential to broaden the use of LNPs to include new cargo types─beyond RNA─for diverse therapeutic applications.
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Affiliation(s)
- Rebecca M. Haley
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexander Chan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Ningqiang Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Marshall S. Padilla
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Emily H. Kim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania
| | - Hejia Henry Wang
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania
| | - Dingzi Yin
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55902
| | - Kirk J. Wangensteen
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55902
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael J. Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
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11
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Blanc M, Lettl C, Guérin J, Vieille A, Furler S, Briand-Schumacher S, Dreier B, Bergé C, Plückthun A, Vadon-Le Goff S, Fronzes R, Rousselle P, Fischer W, Terradot L. Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system. PLoS Pathog 2023; 19:e1011368. [PMID: 37155700 DOI: 10.1371/journal.ppat.1011368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/18/2023] [Accepted: 04/18/2023] [Indexed: 05/10/2023] Open
Abstract
The bacterial human pathogen Helicobacter pylori produces a type IV secretion system (cagT4SS) to inject the oncoprotein CagA into gastric cells. The cagT4SS external pilus mediates attachment of the apparatus to the target cell and the delivery of CagA. While the composition of the pilus is unclear, CagI is present at the surface of the bacterium and required for pilus formation. Here, we have investigated the properties of CagI by an integrative structural biology approach. Using Alpha Fold 2 and Small Angle X-ray scattering, it was found that CagI forms elongated dimers mediated by rod-shape N-terminal domains (CagIN) prolonged by globular C-terminal domains (CagIC). Three Designed Ankyrin Repeat Proteins (DARPins) K2, K5 and K8 selected against CagI interacted with CagIC with subnanomolar affinities. The crystal structures of the CagI:K2 and CagI:K5 complexes were solved and identified the interfaces between the molecules, thereby providing a structural explanation for the difference in affinity between the two binders. Purified CagI and CagIC were found to interact with adenocarcinoma gastric (AGS) cells, induced cell spreading and the interaction was inhibited by K2. The same DARPin inhibited CagA translocation by up to 65% in AGS cells while inhibition levels were 40% and 30% with K8 and K5, respectively. Our study suggests that CagIC plays a key role in cagT4SS-mediated CagA translocation and that DARPins targeting CagI represent potent inhibitors of the cagT4SS, a crucial risk factor for gastric cancer development.
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Affiliation(s)
- Marine Blanc
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Jérémy Guérin
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Anaïs Vieille
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Sven Furler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Célia Bergé
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Sandrine Vadon-Le Goff
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Rémi Fronzes
- European Institute of Chemistry and Biology, CNRS UMR 5234 Microbiologie Fondamentale et Pathogénicité, Univ. Bordeaux, Pessac, France
| | - Patricia Rousselle
- University of Lyon, CNRS UMR5305, Tissue Biology and Therapeutic Engineering Laboratory (LBTI), Lyon, France
| | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Laurent Terradot
- UMR 5086 Molecular Microbiology and Structural Biochemistry CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, Lyon, France
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12
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Liang H, Ma Z, Wang Z, Zhong P, Li R, Jiang H, Zong X, Zhong C, Liu X, Liu P, Liu J, Zhu H, Liu R, Ding Y. Structural Insights into the Binding of Red Fluorescent Protein mCherry-Specific Nanobodies. Int J Mol Sci 2023; 24:ijms24086952. [PMID: 37108116 PMCID: PMC10138814 DOI: 10.3390/ijms24086952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Red fluorescent proteins (RFPs) have broad applications in life science research, and the manipulation of RFPs using nanobodies can expand their potential uses. However, the structural information available for nanobodies that bind with RFPs is still insufficient. In this study, we cloned, expressed, purified, and crystallized complexes formed by mCherry with LaM1, LaM3, and LaM8. Then, we analyzed the biochemical properties of the complexes using mass spectrometry (MS), fluorescence-detected size exclusion chromatography (FSEC), isothermal titration calorimetry (ITC), and bio-layer interferometry (BLI) technology. We determined the crystal structure of mCherry-LaM1, mCherry-LaM3, and mCherry-LaM8, with resolutions of 2.05 Å, 3.29 Å, and 1.31 Å, respectively. In this study, we systematically compared various parameters of several LaM series nanobodies, including LaM1, LaM3, and LaM8, with previously reported data on LaM2, LaM4, and LaM6, specifically examining their structural information. After designing multivalent tandem LaM1-LaM8 and LaM8-LaM4 nanobodies based on structural information, we characterized their properties, revealing their higher affinity and specificity to mCherry. Our research provides novel structural insights that could aid in understanding nanobodies targeting a specific target protein. This could provide a starting point for developing enhanced mCherry manipulation tools.
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Affiliation(s)
- Hui Liang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiqiang Ma
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziying Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Peiyu Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ran Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin Zong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chao Zhong
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xihuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Peng Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiayuan Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haoran Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Rui Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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13
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Kulmala A, Lappalainen M, Lamminmäki U, Huovinen T. Synonymous Codons and Hydrophobicity Optimization of Post-translational Signal Peptide PelB Increase Phage Display Efficiency of DARPins. ACS Synth Biol 2022; 11:3174-3181. [PMID: 36178799 PMCID: PMC9594773 DOI: 10.1021/acssynbio.2c00260] [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] [Indexed: 01/24/2023]
Abstract
DsbA leader peptide targets proteins for cotranslational translocation by signal recognition particle (SRP) pathway and has been the standard signal sequence for filamentous phage display of fast-folding Designed Ankyrin Repeat Proteins (DARPins). In contrast, translocation of DARPins via the post-translational pathway, for example, with the commonly used PelB leader, has been reported to be highly inefficient. In this study, two PelB signal sequence libraries were screened covering different regions of the leader peptide for identifying mutants with improved display of DARPins on phage. A PelB variant with the most favorable combination of synonymous mutations in the n-region and hydrophobic substitutions in the h-region increased the display efficiency of a DARPin library 44- and 12-fold compared to PelBWT and DsbA, respectively. Based on thioredoxin-1 (TrxA) export studies the triple valine mutant PelB DN5 V3 leader was capable of more efficient cotranslational translocation than PelBWT, but the overall display efficiency improvement over DsbA suggests that besides increased cotranslational translocation other factors contribute to the observed enhancement in DARPin display efficiency.
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Affiliation(s)
- Antti Kulmala
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Matias Lappalainen
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Urpo Lamminmäki
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Tuomas Huovinen
- Department
of Life Technologies, University of Turku Kiinamyllynkatu 10, 20520 Turku, Finland,
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14
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Lepeta K, Roubinet C, Bauer M, Vigano MA, Aguilar G, Kanca O, Ochoa-Espinosa A, Bieli D, Cabernard C, Caussinus E, Affolter M. Engineered kinases as a tool for phosphorylation of selected targets in vivo. J Cell Biol 2022; 221:213463. [PMID: 36102907 PMCID: PMC9477969 DOI: 10.1083/jcb.202106179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 05/19/2022] [Accepted: 07/27/2022] [Indexed: 11/22/2022] Open
Abstract
Reversible protein phosphorylation by kinases controls a plethora of processes essential for the proper development and homeostasis of multicellular organisms. One main obstacle in studying the role of a defined kinase–substrate interaction is that kinases form complex signaling networks and most often phosphorylate multiple substrates involved in various cellular processes. In recent years, several new approaches have been developed to control the activity of a given kinase. However, most of them fail to regulate a single protein target, likely hiding the effect of a unique kinase–substrate interaction by pleiotropic effects. To overcome this limitation, we have created protein binder-based engineered kinases that permit a direct, robust, and tissue-specific phosphorylation of fluorescent fusion proteins in vivo. We show the detailed characterization of two engineered kinases based on Rho-associated protein kinase (ROCK) and Src. Expression of synthetic kinases in the developing fly embryo resulted in phosphorylation of their respective GFP-fusion targets, providing for the first time a means to direct the phosphorylation to a chosen and tagged target in vivo. We presume that after careful optimization, the novel approach we describe here can be adapted to other kinases and targets in various eukaryotic genetic systems to regulate specific downstream effectors.
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Affiliation(s)
| | - Chantal Roubinet
- MRC Laboratory for Molecular Cell Biology, University College London, London, UK 2
| | - Milena Bauer
- Biozentrum, University of Basel, Basel, Switzerland 1
| | | | | | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 3
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15
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Nanobody-based RFP-dependent Cre recombinase for selective anterograde tracing in RFP-expressing transgenic animals. Commun Biol 2022; 5:979. [PMID: 36114373 PMCID: PMC9481622 DOI: 10.1038/s42003-022-03944-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 09/05/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractTransgenic animals expressing fluorescent proteins are widely used to label specific cells and proteins. By using a split Cre recombinase fused with mCherry-binding nanobodies or designed ankyrin repeat proteins, we created Cre recombinase dependent on red fluorescent protein (RFP) (Cre-DOR). Functional binding units for monomeric RFPs are different from those for polymeric RFPs. We confirmed selective target RFP-dependent gene expression in the mouse cerebral cortex using stereotaxic injection of adeno-associated virus vectors. In estrogen receptor-beta (Esr2)-mRFP1 mice and gastrin-releasing peptide receptor (Grpr)-mRFP1 rats, we confirmed that Cre-DOR can be used for selective tracing of the neural projection from RFP-expressing specific neurons. Cellular localization of RFPs affects recombination efficiency of Cre-DOR, and light and chemical-induced nuclear translocation of an RFP-fused protein can modulate Cre-DOR efficiency. Our results provide a method for manipulating gene expression in specific cells expressing RFPs and expand the repertory of nanobody-based genetic tools.
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16
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Wang L, Moreira EA, Kempf G, Miyake Y, Oliveira Esteves BI, Fahmi A, Schaefer JV, Dreier B, Yamauchi Y, Alves MP, Plückthun A, Matthias P. Disrupting the HDAC6-ubiquitin interaction impairs infection by influenza and Zika virus and cellular stress pathways. Cell Rep 2022; 39:110736. [PMID: 35476995 PMCID: PMC9065369 DOI: 10.1016/j.celrep.2022.110736] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 11/11/2021] [Accepted: 04/04/2022] [Indexed: 12/02/2022] Open
Abstract
The deacetylase HDAC6 has tandem catalytic domains and a zinc finger domain (ZnF) binding ubiquitin (Ub). While the catalytic domain has an antiviral effect, the ZnF facilitates influenza A virus (IAV) infection and cellular stress responses. By recruiting Ub via the ZnF, HDAC6 promotes the formation of aggresomes and stress granules (SGs), dynamic structures associated with pathologies such as neurodegeneration. IAV subverts the aggresome/HDAC6 pathway to facilitate capsid uncoating during early infection. To target this pathway, we generate designed ankyrin repeat proteins (DARPins) binding the ZnF; one of these prevents interaction with Ub in vitro and in cells. Crystallographic analysis shows that it blocks the ZnF pocket where Ub engages. Conditional expression of this DARPin reversibly impairs infection by IAV and Zika virus; moreover, SGs and aggresomes are downregulated. These results validate the HDAC6 ZnF as an attractive target for drug discovery. A small synthetic protein (DARPin) blocks interaction between HDAC6 and ubiquitin This DARPin impairs infection by influenza and Zika virus at the uncoating step Both viruses contain ubiquitin associated with their capsid The DARPin also impacts the formation of aggresomes and stress granules
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Affiliation(s)
- Longlong Wang
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland
| | - Etori Aguiar Moreira
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Yasuyuki Miyake
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK; Department of Virology, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Blandina I Oliveira Esteves
- Institute of Virology and Immunology, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Amal Fahmi
- Institute of Virology and Immunology, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zürich, 8057 Zürich Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zürich, 8057 Zürich Switzerland
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, UK
| | - Marco P Alves
- Institute of Virology and Immunology, Bern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, 8057 Zürich Switzerland
| | - Patrick Matthias
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4031 Basel, Switzerland.
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17
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Lepeta K, Bauer M, Aguilar G, Vigano MA, Matsuda S, Affolter M. Studying Protein Function Using Nanobodies and Other Protein Binders in Drosophila. Methods Mol Biol 2022; 2540:219-237. [PMID: 35980580 DOI: 10.1007/978-1-0716-2541-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The direct manipulation of proteins by nanobodies and other protein binders has become an additional and valuable approach to investigate development and homeostasis in Drosophila. In contrast to other techniques, that indirectly interfere with proteins via their nucleic acids (CRISPR, RNAi, etc.), protein binders permit direct and acute protein manipulation. Since the first use of a nanobody in Drosophila a decade ago, many different applications exploiting protein binders have been introduced. Most of these applications use nanobodies against GFP to regulate GFP fusion proteins. In order to exert specific protein manipulations, protein binders are linked to domains that confer them precise biochemical functions. Here, we reflect on the use of tools based on protein binders in Drosophila. We describe their key features and provide an overview of the available reagents. Finally, we briefly explore the future avenues that protein binders might open up and thus further contribute to better understand development and homeostasis of multicellular organisms.
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Affiliation(s)
| | - Milena Bauer
- Biozentrum der Universität Basel, Basel, Switzerland
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18
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Matsuda S, Schaefer JV, Mii Y, Hori Y, Bieli D, Taira M, Plückthun A, Affolter M. Asymmetric requirement of Dpp/BMP morphogen dispersal in the Drosophila wing disc. Nat Commun 2021; 12:6435. [PMID: 34750371 PMCID: PMC8576045 DOI: 10.1038/s41467-021-26726-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
How morphogen gradients control patterning and growth in developing tissues remains largely unknown due to lack of tools manipulating morphogen gradients. Here, we generate two membrane-tethered protein binders that manipulate different aspects of Decapentaplegic (Dpp), a morphogen required for overall patterning and growth of the Drosophila wing. One is "HA trap" based on a single-chain variable fragment (scFv) against the HA tag that traps HA-Dpp to mainly block its dispersal, the other is "Dpp trap" based on a Designed Ankyrin Repeat Protein (DARPin) against Dpp that traps Dpp to block both its dispersal and signaling. Using these tools, we found that, while posterior patterning and growth require Dpp dispersal, anterior patterning and growth largely proceed without Dpp dispersal. We show that dpp transcriptional refinement from an initially uniform to a localized expression and persistent signaling in transient dpp source cells render the anterior compartment robust against the absence of Dpp dispersal. Furthermore, despite a critical requirement of dpp for the overall wing growth, neither Dpp dispersal nor direct signaling is critical for lateral wing growth after wing pouch specification. These results challenge the long-standing dogma that Dpp dispersal is strictly required to control and coordinate overall wing patterning and growth.
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Affiliation(s)
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Yusuke Mii
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- JST PRESTO, Kawaguchi, Saitama, Japan
| | - Yutaro Hori
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | | | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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19
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Becker L, Singh Badwal J, Brandl F, Verdurmen WPR, Plückthun A. Thermodynamic Stability Is a Strong Predictor for the Delivery of DARPins to the Cytosol via Anthrax Toxin. Pharmaceutics 2021; 13:pharmaceutics13081285. [PMID: 34452246 PMCID: PMC8401532 DOI: 10.3390/pharmaceutics13081285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Anthrax toxin has evolved to translocate its toxic cargo proteins to the cytosol of cells carrying its cognate receptor. Cargo molecules need to unfold to penetrate the narrow pore formed by its membrane-spanning subunit, protective antigen (PA). Various alternative cargo molecules have previously been tested, with some showing only limited translocation efficiency, and it may be assumed that these were too stable to be unfolded before passing through the anthrax pore. In this study, we systematically and quantitatively analyzed the correlation between the translocation of various designed ankyrin repeat proteins (DARPins) and their different sizes and thermodynamic stabilities. To measure cytosolic uptake, we used biotinylation of the cargo by cytosolic BirA, and we measured cargo equilibrium stability via denaturant-induced unfolding, monitored by circular dichroism (CD). Most of the tested DARPin cargoes, including target-binding ones, were translocated to the cytosol. Those DARPins, which remained trapped in the endosome, were confirmed by CD to show a high equilibrium stability. We could pinpoint a stability threshold up to which cargo DARPins still get translocated to the cytosol. These experiments have outlined the requirements for translocatable binding proteins, relevant stability measurements to assess translocatable candidates, and guidelines to further engineer this property if needed.
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Affiliation(s)
- Lukas Becker
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland; (L.B.); (J.S.B.); (F.B.)
| | - Jasleen Singh Badwal
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland; (L.B.); (J.S.B.); (F.B.)
| | - Fabian Brandl
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland; (L.B.); (J.S.B.); (F.B.)
| | - Wouter P. R. Verdurmen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands;
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland; (L.B.); (J.S.B.); (F.B.)
- Correspondence:
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20
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Vigano MA, Ell CM, Kustermann MMM, Aguilar G, Matsuda S, Zhao N, Stasevich TJ, Affolter M, Pyrowolakis G. Protein manipulation using single copies of short peptide tags in cultured cells and in Drosophila melanogaster. Development 2021; 148:dev191700. [PMID: 33593816 PMCID: PMC7990863 DOI: 10.1242/dev.191700] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 02/09/2021] [Indexed: 01/01/2023]
Abstract
Cellular development and function rely on highly dynamic molecular interactions among proteins distributed in all cell compartments. Analysis of these interactions has been one of the main topics in cellular and developmental research, and has been mostly achieved by the manipulation of proteins of interest (POIs) at the genetic level. Although genetic strategies have significantly contributed to our current understanding, targeting specific interactions of POIs in a time- and space-controlled manner or analysing the role of POIs in dynamic cellular processes, such as cell migration or cell division, would benefit from more-direct approaches. The recent development of specific protein binders, which can be expressed and function intracellularly, along with advancement in synthetic biology, have contributed to the creation of a new toolbox for direct protein manipulations. Here, we have selected a number of short-tag epitopes for which protein binders from different scaffolds have been generated and showed that single copies of these tags allowed efficient POI binding and manipulation in living cells. Using Drosophila, we also find that single short tags can be used for POI manipulation in vivo.
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Affiliation(s)
- M Alessandra Vigano
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Clara-Maria Ell
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Manuela M M Kustermann
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Gustavo Aguilar
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Shinya Matsuda
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - George Pyrowolakis
- Institute for Biology I, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
- Center for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
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21
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Simeon RA, Zeng Y, Chonira V, Aguirre AM, Lasagna M, Baloh M, Sorg JA, Tommos C, Chen Z. Protease-stable DARPins as promising oral therapeutics. Protein Eng Des Sel 2021; 34:gzab028. [PMID: 34882774 PMCID: PMC8861517 DOI: 10.1093/protein/gzab028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/16/2021] [Accepted: 10/02/2021] [Indexed: 12/30/2022] Open
Abstract
Clostridioides difficile is an enteric bacterium whose exotoxins, TcdA and TcdB, inactivate small GTPases within the host cells, leading to bloody diarrhea. In prior work, our group engineered a panel of potent TcdB-neutralizing designed ankyrin repeat proteins (DARPin) as oral therapeutics against C. difficile infection. However, all these DARPins are highly susceptible to digestion by gut-resident proteases, i.e. trypsin and chymotrypsin. Close evaluation of the protein sequence revealed a large abundance of positively charged and aromatic residues in the DARPin scaffold. In this study, we significantly improved the protease stability of one of the DARPins, 1.4E, via protein engineering. Unlike 1.4E, whose anti-TcdB EC50 increased >83-fold after 1-hour incubation with trypsin (1 mg/ml) or chymotrypsin (0.5 mg/ml), the best progenies-T10-2 and T10b-exhibit similar anti-TcdB potency as their parent in PBS regardless of protease treatment. The superior protease stability of T10-2 and T10b is attributed to the removal of nearly all positively charged and aromatic residues except those directly engaged in target binding. Furthermore, T10-2 was found to retain significant toxin-neutralization ability in ex vivo cecum fluid and can be easily detected in mouse fecal samples upon oral administration. Both T10-2 and T10b enjoy a high thermo- and chemo-stability and can be expressed very efficiently in Escherichia coli (>100 mg/l in shaker flasks). We believe that, in additional to their potential as oral therapeutics against C. difficile infection, T10-2 and T10b can also serve as a new generation DARPin scaffold with superior protease stability.
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Affiliation(s)
- Rudo A Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
| | - Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
| | - Vikas Chonira
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
| | | | - Mauricio Lasagna
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, TX 77843, USA
| | - Marko Baloh
- Department of Biology, Texas A&M University, 424 Nagle St, College Station, TX 77840, USA
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, 424 Nagle St, College Station, TX 77840, USA
| | - Cecilia Tommos
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, TX 77843, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, 8847 Riverside Pkwy, Bryan, TX 77807, USA
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22
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Teale WD, Pasternak T, Dal Bosco C, Dovzhenko A, Kratzat K, Bildl W, Schwörer M, Falk T, Ruperti B, V Schaefer J, Shahriari M, Pilgermayer L, Li X, Lübben F, Plückthun A, Schulte U, Palme K. Flavonol-mediated stabilization of PIN efflux complexes regulates polar auxin transport. EMBO J 2021; 40:e104416. [PMID: 33185277 PMCID: PMC7780147 DOI: 10.15252/embj.2020104416] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 09/04/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023] Open
Abstract
The transport of auxin controls the rate, direction and localization of plant growth and development. The course of auxin transport is defined by the polar subcellular localization of the PIN proteins, a family of auxin efflux transporters. However, little is known about the composition and regulation of the PIN protein complex. Here, using blue-native PAGE and quantitative mass spectrometry, we identify native PIN core transport units as homo- and heteromers assembled from PIN1, PIN2, PIN3, PIN4 and PIN7 subunits only. Furthermore, we show that endogenous flavonols stabilize PIN dimers to regulate auxin efflux in the same way as does the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). This inhibitory mechanism is counteracted both by the natural auxin indole-3-acetic acid and by phosphomimetic amino acids introduced into the PIN1 cytoplasmic domain. Our results lend mechanistic insights into an endogenous control mechanism which regulates PIN function and opens the way for a deeper understanding of the protein environment and regulation of the polar auxin transport complex.
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Affiliation(s)
- William D Teale
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | - Taras Pasternak
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | | | | | | | - Wolfgang Bildl
- Institute of Physiology IIFaculty of MedicineUniversity of FreiburgFreiburgGermany
| | - Manuel Schwörer
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | - Thorsten Falk
- Institute for Computer ScienceUniversity of FreiburgFreiburgGermany
| | - Benadetto Ruperti
- Department of Agronomy, Food, Natural resources, Animals and Environment—DAFNAEUniversity of PadovaPadovaItaly
| | - Jonas V Schaefer
- High‐Throughput Binder Selection FacilityDepartment of BiochemistryUniversity of ZurichZurichSwitzerland
| | | | | | - Xugang Li
- Sino German Joint Research Center for Agricultural Biology, and State Key Laboratory of Crop BiologyCollege of Life Sciences, Shandong Agricultural UniversityTai'anChina
| | - Florian Lübben
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | - Andreas Plückthun
- High‐Throughput Binder Selection FacilityDepartment of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Uwe Schulte
- Institute of Physiology IIFaculty of MedicineUniversity of FreiburgFreiburgGermany
- Logopharm GmbHFreiburgGermany
- Signalling Research Centres BIOSS and CIBSSFreiburgGermany
| | - Klaus Palme
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
- Signalling Research Centres BIOSS and CIBSSFreiburgGermany
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23
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Zhang C, Ötjengerdes RM, Roewe J, Mejias R, Marschall ALJ. Applying Antibodies Inside Cells: Principles and Recent Advances in Neurobiology, Virology and Oncology. BioDrugs 2020; 34:435-462. [PMID: 32301049 PMCID: PMC7391400 DOI: 10.1007/s40259-020-00419-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
To interfere with cell function, many scientists rely on methods that target DNA or RNA due to the ease with which they can be applied. Proteins are usually the final executors of function but are targeted only indirectly by these methods. Recent advances in targeted degradation of proteins based on proteolysis-targeting chimaeras (PROTACs), ubiquibodies, deGradFP (degrade Green Fluorescent Protein) and other approaches have demonstrated the potential of interfering directly at the protein level for research and therapy. Proteins can be targeted directly and very specifically by antibodies, but using antibodies inside cells has so far been considered to be challenging. However, it is possible to deliver antibodies or other proteins into the cytosol using standard laboratory equipment. Physical methods such as electroporation have been demonstrated to be efficient and validated thoroughly over time. The expression of intracellular antibodies (intrabodies) inside cells is another way to interfere with intracellular targets at the protein level. Methodological strategies to target the inside of cells with antibodies, including delivered antibodies and expressed antibodies, as well as applications in the research areas of neurobiology, viral infections and oncology, are reviewed here. Antibodies have already been used to interfere with a wide range of intracellular targets. Disease-related targets included proteins associated with neurodegenerative diseases such as Parkinson's disease (α-synuclein), Alzheimer's disease (amyloid-β) or Huntington's disease (mutant huntingtin [mHtt]). The applications of intrabodies in the context of viral infections include targeting proteins associated with HIV (e.g. HIV1-TAT, Rev, Vif, gp41, gp120, gp160) and different oncoviruses such as human papillomavirus (HPV), hepatitis B virus (HBV), hepatitis C virus (HCV) and Epstein-Barr virus, and they have been used to interfere with various targets related to different processes in cancer, including oncogenic pathways, proliferation, cell cycle, apoptosis, metastasis, angiogenesis or neo-antigens (e.g. p53, human epidermal growth factor receptor-2 [HER2], signal transducer and activator of transcription 3 [STAT3], RAS-related RHO-GTPase B (RHOB), cortactin, vascular endothelial growth factor receptor 2 [VEGFR2], Ras, Bcr-Abl). Interfering at the protein level allows questions to be addressed that may remain unanswered using alternative methods. This review addresses why direct targeting of proteins allows unique insights, what is currently feasible in vitro, and how this relates to potential therapeutic applications.
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Affiliation(s)
- Congcong Zhang
- Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Frankfurt am Main, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rina M Ötjengerdes
- Hannover Medical School (MHH), Carl-Neuberg-Straße 1, 30625, Hannover, Germany
| | - Julian Roewe
- German Cancer Consortium (DKTK) Clinical Cooperation Unit (CCU) Neuroimmunology and Brain TumorImmunology (D170), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rebeca Mejias
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrea L J Marschall
- Technische Universität Braunschweig, Institute of Biochemistry, Biotechnology and Bioinformatics, Brunswick, Germany.
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24
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Salmonella-based platform for efficient delivery of functional binding proteins to the cytosol. Commun Biol 2020; 3:342. [PMID: 32620833 PMCID: PMC7335062 DOI: 10.1038/s42003-020-1072-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/11/2020] [Indexed: 12/23/2022] Open
Abstract
Protein-based affinity reagents (like antibodies or alternative binding scaffolds) offer wide-ranging applications for basic research and therapeutic approaches. However, whereas small chemical molecules efficiently reach intracellular targets, the delivery of macromolecules into the cytosol of cells remains a major challenge; thus cytosolic applications of protein-based reagents are rather limited. Some pathogenic bacteria have evolved a conserved type III secretion system (T3SS) which allows the delivery of effector proteins into eukaryotic cells. Here, we enhance the T3SS of an avirulent strain of Salmonella typhimurium to reproducibly deliver multiple classes of recombinant proteins into eukaryotic cells. The efficacy of the system is probed with both DARPins and monobodies to functionally inhibit the paradigmatic and largely undruggable RAS signaling pathway. Thus, we develop a bacterial secretion system for potent cytosolic delivery of therapeutic macromolecules. To develop a bacterial secretion system for cytosolic delivery of therapeutic macromolecules, Chabloz et al. improve an “effectorless” Salmonella strain and combine it with a plasmid modified to boost the secretion of proteins of interest. With this system, they demonstrate efficient translocation of functional DARPins and monobodies into the cytosol of different eukaryotic cells lines and successfully block the paradigmatic RAS pathway.
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25
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Ribosome Display Technology: Applications in Disease Diagnosis and Control. Antibodies (Basel) 2020; 9:antib9030028. [PMID: 32605027 PMCID: PMC7551589 DOI: 10.3390/antib9030028] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 12/28/2022] Open
Abstract
Antibody ribosome display remains one of the most successful in vitro selection technologies for antibodies fifteen years after it was developed. The unique possibility of direct generation of whole proteins, particularly single-chain antibody fragments (scFvs), has facilitated the establishment of this technology as one of the foremost antibody production methods. Ribosome display has become a vital tool for efficient and low-cost production of antibodies for diagnostics due to its advantageous ability to screen large libraries and generate binders of high affinity. The remarkable flexibility of this method enables its applicability to various platforms. This review focuses on the applications of ribosome display technology in biomedical and agricultural fields in the generation of recombinant scFvs for disease diagnostics and control.
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26
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bioPROTACs as versatile modulators of intracellular therapeutic targets including proliferating cell nuclear antigen (PCNA). Proc Natl Acad Sci U S A 2020; 117:5791-5800. [PMID: 32123106 DOI: 10.1073/pnas.1920251117] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Targeted degradation approaches such as proteolysis targeting chimeras (PROTACs) offer new ways to address disease through tackling challenging targets and with greater potency, efficacy, and specificity over traditional approaches. However, identification of high-affinity ligands to serve as PROTAC starting points remains challenging. As a complementary approach, we describe a class of molecules termed biological PROTACs (bioPROTACs)-engineered intracellular proteins consisting of a target-binding domain directly fused to an E3 ubiquitin ligase. Using GFP-tagged proteins as model substrates, we show that there is considerable flexibility in both the choice of substrate binders (binding positions, scaffold-class) and the E3 ligases. We then identified a highly effective bioPROTAC against an oncology target, proliferating cell nuclear antigen (PCNA) to elicit rapid and robust PCNA degradation and associated effects on DNA synthesis and cell cycle progression. Overall, bioPROTACs are powerful tools for interrogating degradation approaches, target biology, and potentially for making therapeutic impacts.
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27
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Küey C, Larocque G, Clarke NI, Royle SJ. Unintended perturbation of protein function using GFP nanobodies in human cells. J Cell Sci 2019; 132:jcs234955. [PMID: 31601614 PMCID: PMC6857592 DOI: 10.1242/jcs.234955] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022] Open
Abstract
Tagging a protein of interest with GFP using genome editing is a popular approach to study protein function in cell and developmental biology. To avoid re-engineering cell lines or organisms in order to introduce additional tags, functionalized nanobodies that bind GFP can be used to extend the functionality of the GFP tag. We developed functionalized nanobodies, which we termed 'dongles', that could add, for example, an FKBP tag to a GFP-tagged protein of interest, enabling knocksideways experiments in GFP knock-in cell lines. The power of knocksideways is that it allows investigators to rapidly switch the protein from an active to an inactive state. We show that dongles allow for effective knocksideways of GFP-tagged proteins in genome-edited human cells. However, we discovered that nanobody binding to dynamin-2-GFP caused inhibition of dynamin function prior to knocksideways. The function of GFP-tagged tumor protein D54 (TPD54, also known as TPD52L2) in anterograde traffic was also perturbed by dongles. While these issues potentially limit the application of dongles, we discuss strategies for their deployment as cell biological tools.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Cansu Küey
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Gabrielle Larocque
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Nicholas I Clarke
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Stephen J Royle
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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28
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Ernst P, Plückthun A, Mittl PRE. Structural analysis of biological targets by host:guest crystal lattice engineering. Sci Rep 2019; 9:15199. [PMID: 31645583 PMCID: PMC6811568 DOI: 10.1038/s41598-019-51017-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/23/2019] [Indexed: 11/17/2022] Open
Abstract
To overcome the laborious identification of crystallisation conditions for protein X-ray crystallography, we developed a method where the examined protein is immobilised as a guest molecule in a universal host lattice. We applied crystal engineering to create a generic crystalline host lattice under reproducible, predefined conditions and analysed the structures of target guest molecules of different size, namely two 15-mer peptides and green fluorescent protein (sfGFP). A fusion protein with an N-terminal endo-α-N-acetylgalactosaminidase (EngBF) domain and a C-terminal designed ankyrin repeat protein (DARPin) domain establishes the crystal lattice. The target is recruited into the host lattice, always in the same crystal form, through binding to the DARPin. The target structures can be determined rapidly from difference Fourier maps, whose quality depends on the size of the target and the orientation of the DARPin.
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Affiliation(s)
- Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
| | - Peer R E Mittl
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
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29
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Aguilar G, Vigano MA, Affolter M, Matsuda S. Reflections on the use of protein binders to study protein function in developmental biology. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2019; 8:e356. [PMID: 31265212 PMCID: PMC6851689 DOI: 10.1002/wdev.356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 02/01/2023]
Abstract
Studies in the field of developmental biology aim to unravel how a fertilized egg develops into an adult organism and how proteins and other macromolecules work together during this process. With regard to protein function, most of the developmental studies have used genetic and RNA interference approaches, combined with biochemical analyses, to reach this goal. However, there always remains much room for interpretation on how a given protein functions, because proteins work together with many other molecules in complex regulatory networks and it is not easy to reveal the function of one given protein without affecting the networks. Likewise, it has remained difficult to experimentally challenge and/or validate the proposed concepts derived from mutant analyses without tools that directly manipulate protein function in a predictable manner. Recently, synthetic tools based on protein binders such as scFvs, nanobodies, DARPins, and others have been applied in developmental biology to directly manipulate target proteins in a predicted manner. Although such tools would have a great impact in filling the gap of knowledge between mutant phenotypes and protein functions, careful investigations are required when applying functionalized protein binders to fundamental questions in developmental biology. In this review, we first summarize how protein binders have been used in the field, and then reflect on possible guidelines for applying such tools to study protein functions in developmental biology. This article is categorized under: Technologies > Analysis of Proteins Establishment of Spatial and Temporal Patterns > Gradients Invertebrate Organogenesis > Flies.
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30
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Yao Q, Weaver SJ, Mock JY, Jensen GJ. Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM. Structure 2019; 27:1148-1155.e3. [PMID: 31080120 PMCID: PMC6610650 DOI: 10.1016/j.str.2019.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/04/2019] [Accepted: 04/05/2019] [Indexed: 12/21/2022]
Abstract
Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 Å resolution overall, with 5-8 Å resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.
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Affiliation(s)
- Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sara J Weaver
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Jee-Young Mock
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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31
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Simeon R, Jiang M, Chamoun-Emanuelli AM, Yu H, Zhang Y, Meng R, Peng Z, Jakana J, Zhang J, Feng H, Chen Z. Selection and characterization of ultrahigh potency designed ankyrin repeat protein inhibitors of C. difficile toxin B. PLoS Biol 2019; 17:e3000311. [PMID: 31233493 PMCID: PMC6590788 DOI: 10.1371/journal.pbio.3000311] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 05/20/2019] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile infection (CDI) is a major nosocomial disease associated with significant morbidity and mortality. The pathology of CDI stems primarily from the 2 C. difficile-secreted exotoxins-toxin A (TcdA) and toxin B (TcdB)-that disrupt the tight junctions between epithelial cells leading to the loss of colonic epithelial barrier function. Here, we report the engineering of a series of monomeric and dimeric designed ankyrin repeat proteins (DARPins) for the neutralization of TcdB. The best dimeric DARPin, DLD-4, inhibited TcdB with a half maximal effective concentration (EC50) of 4 pM in vitro, representing an approximately 330-fold higher potency than the Food and Drug Administration (FDA)-approved anti-TcdB monoclonal antibody bezlotoxumab in the same assay. DLD-4 also protected mice from a toxin challenge in vivo. Cryo-electron microscopy (cryo-EM) studies revealed that the 2 constituent DARPins of DLD-4-1.4E and U3-bind the central and C-terminal regions of the delivery domain of TcdB. Competitive enzyme-linked immunosorbent assay (ELISA) studies showed that the DARPins 1.4E and U3 interfere with the interaction between TcdB and its receptors chondroitin sulfate proteoglycan 4 (CSPG4) and frizzled class receptor 2 (FZD2), respectively. Our cryo-EM studies revealed a new conformation of TcdB (both apo- and DARPin-bound at pH 7.4) in which the combined repetitive oligopeptides (CROPS) domain points away from the delivery domain. This conformation of the CROPS domain is in stark contrast to that seen in the negative-stain electron microscopy (EM) structure of TcdA and TcdB at the same pH, in which the CROPS domain bends toward and "kisses" the delivery domain. The ultrapotent anti-TcdB molecules from this study serve as candidate starting points for CDI drug development and provide new biological tools for studying the pathogenicity of C. difficile. The structural insights regarding both the "native" conformation of TcdB and the putative sites of TcdB interaction with the FZD2 receptor, in particular, should help accelerate the development of next-generation anti-C. difficile toxin therapeutics.
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Affiliation(s)
- Rudo Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
| | - Mengqiu Jiang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ana M. Chamoun-Emanuelli
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
| | - Hua Yu
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United Sates of America
| | - Yongrong Zhang
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United Sates of America
| | - Ran Meng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Zeyu Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Hanping Feng
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United Sates of America
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
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32
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Liu Y, Huynh DT, Yeates TO. A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold. Nat Commun 2019; 10:1864. [PMID: 31015551 PMCID: PMC6478846 DOI: 10.1038/s41467-019-09836-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 04/02/2019] [Indexed: 11/15/2022] Open
Abstract
Proteins smaller than about 50 kDa are currently too small to be imaged at high resolution by cryo-electron microscopy (cryo-EM), leaving most protein molecules in the cell beyond the reach of this powerful structural technique. Here we use a designed protein scaffold to bind and symmetrically display 12 copies of a small 26 kDa protein, green fluorescent protein (GFP). We show that the bound cargo protein is held rigidly enough to visualize it at a resolution of 3.8 Å by cryo-EM, where specific structural features of the protein are visible. The designed scaffold is modular and can be modified through modest changes in its amino acid sequence to bind and display diverse proteins for imaging, thus providing a general method to break through the lower size limitation in cryo-EM.
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Affiliation(s)
- Yuxi Liu
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, 90095, USA
- UCLA Molecular Biology Institute, Los Angeles, CA, 90095, USA
| | - Duc T Huynh
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, 90095, USA
| | - Todd O Yeates
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA, 90095, USA.
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, 90095, USA.
- UCLA Molecular Biology Institute, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, Los Angeles, CA, 90095, USA.
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33
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Vallardi G, Allan LA, Crozier L, Saurin AT. Division of labour between PP2A-B56 isoforms at the centromere and kinetochore. eLife 2019; 8:e42619. [PMID: 30829571 PMCID: PMC6398977 DOI: 10.7554/elife.42619] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/03/2019] [Indexed: 11/13/2022] Open
Abstract
PP2A-B56 is a serine/threonine phosphatase complex that regulates several major mitotic processes, including sister chromatid cohesion, kinetochore-microtubule attachment and the spindle assembly checkpoint. We show here that these key functions are divided between different B56 isoforms that localise to either the centromere or kinetochore. The centromeric isoforms rely on a specific interaction with Sgo2, whereas the kinetochore isoforms bind preferentially to BubR1 and other proteins containing an LxxIxE motif. In addition to these selective binding partners, Sgo1 helps to anchor PP2A-B56 at both locations: it collaborates with BubR1 to maintain B56 at the kinetochore and it helps to preserve the Sgo2/B56 complex at the centromere. A series of chimaeras were generated to map the critical region in B56 down to a small C-terminal loop that regulates the key interactions and defines B56 localisation. Together, this study describes how different PP2A-B56 complexes utilise isoform-specific interactions to control distinct processes during mitosis.
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Affiliation(s)
- Giulia Vallardi
- Division of Cellular Medicine, School of MedicineUniversity of DundeeDundeeUnited Kingdom
| | - Lindsey A Allan
- Division of Cellular Medicine, School of MedicineUniversity of DundeeDundeeUnited Kingdom
| | - Lisa Crozier
- Division of Cellular Medicine, School of MedicineUniversity of DundeeDundeeUnited Kingdom
| | - Adrian T Saurin
- Division of Cellular Medicine, School of MedicineUniversity of DundeeDundeeUnited Kingdom
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34
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Yamaguchi N, Colak-Champollion T, Knaut H. zGrad is a nanobody-based degron system that inactivates proteins in zebrafish. eLife 2019; 8:43125. [PMID: 30735119 PMCID: PMC6384026 DOI: 10.7554/elife.43125] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/07/2019] [Indexed: 12/28/2022] Open
Abstract
The analysis of protein function is essential to modern biology. While protein function has mostly been studied through gene or RNA interference, more recent approaches to degrade proteins directly have been developed. Here, we adapted the anti-GFP nanobody-based system deGradFP from flies to zebrafish. We named this system zGrad and show that zGrad efficiently degrades transmembrane, cytosolic and nuclear GFP-tagged proteins in zebrafish in an inducible and reversible manner. Using tissue-specific and inducible promoters in combination with functional GFP-fusion proteins, we demonstrate that zGrad can inactivate transmembrane and cytosolic proteins globally, locally and temporally with different consequences. Global protein depletion results in phenotypes similar to loss of gene activity, while local and temporal protein inactivation yields more restricted and novel phenotypes. Thus, zGrad is a versatile tool to study the spatial and temporal requirement of proteins in zebrafish.
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Affiliation(s)
- Naoya Yamaguchi
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
| | - Tugba Colak-Champollion
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
| | - Holger Knaut
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, United States
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35
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Vigano MA, Bieli D, Schaefer JV, Jakob RP, Matsuda S, Maier T, Plückthun A, Affolter M. DARPins recognizing mTFP1 as novel reagents for in vitro and in vivo protein manipulations. Biol Open 2018; 7:bio.036749. [PMID: 30237292 PMCID: PMC6262872 DOI: 10.1242/bio.036749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Over the last few years, protein-based affinity reagents have proven very helpful in cell and developmental biology. While many of these versatile small proteins can be expressed both in the intracellular and extracellular milieu in cultured cells and in living organisms, they can also be functionalized by fusing them to different protein domains in order to regulate or modulate their target proteins in diverse manners. For example, protein binders have been employed to degrade, trap, localize or enzymatically modify specific target proteins. Whereas binders to many endogenous proteins or small protein tags have been generated, several affinity reagents against fluorescent proteins have also been created and used to manipulate target proteins tagged with the corresponding fluorescent protein. Both of these approaches have resulted in improved methods for cell biological and developmental studies. While binders against GFP and mCherry have been previously isolated and validated, we now report the generation and utilization of designed ankyrin repeat proteins (DARPins) against the monomeric teal fluorescent protein 1 (mTFP1). Here we use the generated DARPins to delocalize Rab proteins to the nuclear compartment, in which they cannot fulfil their regular functions anymore. In the future, such manipulations might enable the production of acute loss-of-function phenotypes in different cell types or in living organisms based on direct protein manipulation rather than on genetic loss-of-function analyses. Summary: Structural characterization of two novel DARPins (designed ankyrin repeat proteins) recognizing the monomeric teal fluorescent protein 1 (mTFP1) and their functionalization for protein manipulation strategies in cultured cells and potentially in living organisms.
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Affiliation(s)
- M Alessandra Vigano
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Dimitri Bieli
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland
| | - Roman P Jakob
- Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Shinya Matsuda
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Timm Maier
- Structural Biology and Biophysics, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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36
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Klein A, Hank S, Raulf A, Joest EF, Tissen F, Heilemann M, Wieneke R, Tampé R. Live-cell labeling of endogenous proteins with nanometer precision by transduced nanobodies. Chem Sci 2018; 9:7835-7842. [PMID: 30429993 PMCID: PMC6194584 DOI: 10.1039/c8sc02910e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 11/21/2022] Open
Abstract
Accurate labeling of endogenous proteins for advanced light microscopy in living cells remains challenging. Nanobodies have been widely used for antigen labeling, visualization of subcellular protein localization and interactions. To facilitate an expanded application, we present a scalable and high-throughput strategy to simultaneously target multiple endogenous proteins in living cells with micro- to nanometer resolution. For intracellular protein labeling, we advanced nanobodies by site-specific and stoichiometric attachment of bright organic fluorophores. Their fast and fine-tuned intracellular transfer by microfluidic cell squeezing enabled high-throughput delivery with less than 10% dead cells. This strategy allowed for the dual-color imaging of distinct endogenous cellular structures, and culminated in super-resolution imaging of native protein networks in genetically non-modified living cells. The simultaneous delivery of multiple engineered nanobodies does not only offer exciting prospects for multiplexed imaging of endogenous protein, but also holds potential for visualizing native cellular structures with unprecedented accuracy.
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Affiliation(s)
- A Klein
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - S Hank
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - A Raulf
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany
| | - E F Joest
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - F Tissen
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - M Heilemann
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany
| | - R Wieneke
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - R Tampé
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
- Cluster of Excellence - Macromolecular Complexes , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
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37
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Sacristan C, Ahmad MUD, Keller J, Fermie J, Groenewold V, Tromer E, Fish A, Melero R, Carazo JM, Klumperman J, Musacchio A, Perrakis A, Kops GJ. Dynamic kinetochore size regulation promotes microtubule capture and chromosome biorientation in mitosis. Nat Cell Biol 2018; 20:800-810. [PMID: 29915359 PMCID: PMC6485389 DOI: 10.1038/s41556-018-0130-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/22/2018] [Indexed: 01/28/2023]
Abstract
Faithful chromosome segregation depends on the ability of sister kinetochores to attach to spindle microtubules. The outer layer of kinetochores transiently expands in early mitosis to form a fibrous corona, and compacts following microtubule capture. Here we show that the dynein adaptor Spindly and the RZZ (ROD-Zwilch-ZW10) complex drive kinetochore expansion in a dynein-independent manner. C-terminal farnesylation and MPS1 kinase activity cause conformational changes of Spindly that promote oligomerization of RZZ-Spindly complexes into a filamentous meshwork in cells and in vitro. Concurrent with kinetochore expansion, Spindly potentiates kinetochore compaction by recruiting dynein via three conserved short linear motifs. Expanded kinetochores unable to compact engage in extensive, long-lived lateral microtubule interactions that persist to metaphase, and result in merotelic attachments and chromosome segregation errors in anaphase. Thus, dynamic kinetochore size regulation in mitosis is coordinated by a single, Spindly-based mechanism that promotes initial microtubule capture and subsequent correct maturation of attachments.
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Affiliation(s)
- Carlos Sacristan
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Misbha Ud Din Ahmad
- Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jenny Keller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Job Fermie
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Vincent Groenewold
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Eelco Tromer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alexander Fish
- Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roberto Melero
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Madrid, Spain
| | - José María Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), Darwin 3, Campus Universidad Autónoma, Madrid, Spain
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Anastassis Perrakis
- Department of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Geert Jpl Kops
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.
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38
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Harmansa S, Affolter M. Protein binders and their applications in developmental biology. Development 2018; 145:145/2/dev148874. [PMID: 29374062 DOI: 10.1242/dev.148874] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Developmental biology research would benefit greatly from tools that enable protein function to be regulated, both systematically and in a precise spatial and temporal manner, in vivo In recent years, functionalized protein binders have emerged as versatile tools that can be used to target and manipulate proteins. Such protein binders can be based on various scaffolds, such as nanobodies, designed ankyrin repeat proteins (DARPins) and monobodies, and can be used to block or perturb protein function in living cells. In this Primer, we provide an overview of the protein binders that are currently available and highlight recent progress made in applying protein binder-based tools in developmental and synthetic biology.
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Affiliation(s)
- Stefan Harmansa
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
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39
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Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics. Methods Mol Biol 2018; 1798:307-327. [PMID: 29868969 DOI: 10.1007/978-1-4939-7893-9_23] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.
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40
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Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity. Sci Rep 2017; 7:16292. [PMID: 29176615 PMCID: PMC5701241 DOI: 10.1038/s41598-017-15711-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/31/2017] [Indexed: 01/15/2023] Open
Abstract
Green fluorescent protein (GFP) fusions are pervasively used to study structures and processes. Specific GFP-binders are thus of great utility for detection, immobilization or manipulation of GFP-fused molecules. We determined structures of two designed ankyrin repeat proteins (DARPins), complexed with GFP, which revealed different but overlapping epitopes. Here we show a structure-guided design strategy that, by truncation and computational reengineering, led to a stable construct where both can bind simultaneously: by linkage of the two binders, fusion constructs were obtained that “wrap around” GFP, have very high affinities of about 10–30 pM, and extremely slow off-rates. They can be natively produced in E. coli in very large amounts, and show excellent biophysical properties. Their very high stability and affinity, facile site-directed functionalization at introduced unique lysines or cysteines facilitate many applications. As examples, we present them as tight yet reversible immobilization reagents for surface plasmon resonance, as fluorescently labelled monomeric detection reagents in flow cytometry, as pull-down ligands to selectively enrich GFP fusion proteins from cell extracts, and as affinity column ligands for inexpensive large-scale protein purification. We have thus described a general design strategy to create a “clamp” from two different high-affinity repeat proteins, even if their epitopes overlap.
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41
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Hughes DJ, Tiede C, Penswick N, Tang AAS, Trinh CH, Mandal U, Zajac KZ, Gaule T, Howell G, Edwards TA, Duan J, Feyfant E, McPherson MJ, Tomlinson DC, Whitehouse A. Generation of specific inhibitors of SUMO-1- and SUMO-2/3-mediated protein-protein interactions using Affimer (Adhiron) technology. Sci Signal 2017; 10:10/505/eaaj2005. [PMID: 29138295 DOI: 10.1126/scisignal.aaj2005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Because protein-protein interactions underpin most biological processes, developing tools that target them to understand their function or to inform the development of therapeutics is an important task. SUMOylation is the posttranslational covalent attachment of proteins in the SUMO family (SUMO-1, SUMO-2, or SUMO-3), and it regulates numerous cellular pathways. SUMOylated proteins are recognized by proteins with SUMO-interaction motifs (SIMs) that facilitate noncovalent interactions with SUMO. We describe the use of the Affimer system of peptide display for the rapid isolation of synthetic binding proteins that inhibit SUMO-dependent protein-protein interactions mediated by SIMs both in vitro and in cells. Crucially, these synthetic proteins did not prevent SUMO conjugation either in vitro or in cell-based systems, enabling the specific analysis of SUMO-mediated protein-protein interactions. Furthermore, through structural analysis and molecular modeling, we explored the molecular mechanisms that may underlie their specificity in interfering with either SUMO-1-mediated interactions or interactions mediated by either SUMO-2 or SUMO-3. Not only will these reagents enable investigation of the biological roles of SUMOylation, but the Affimer technology used to generate these synthetic binding proteins could also be exploited to design or validate reagents or therapeutics that target other protein-protein interactions.
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Affiliation(s)
- David J Hughes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews KY16 9ST, UK
| | - Christian Tiede
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Natalie Penswick
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Anna Ah-San Tang
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Chi H Trinh
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Upasana Mandal
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Katarzyna Z Zajac
- BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thembaninskosi Gaule
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Gareth Howell
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Thomas A Edwards
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | | | - Michael J McPherson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Darren C Tomlinson
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,BioScreening Technology Group, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK. .,Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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42
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Rigidly connected multispecific artificial binders with adjustable geometries. Sci Rep 2017; 7:11217. [PMID: 28894181 PMCID: PMC5593856 DOI: 10.1038/s41598-017-11472-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/24/2017] [Indexed: 11/09/2022] Open
Abstract
Multivalent binding proteins can gain biological activities beyond what is inherent in the individual binders, by bringing together different target molecules, restricting their conformational flexibility or changing their subcellular localization. In this study, we demonstrate a method to build up rigid multivalent and multispecific scaffolds by exploiting the modular nature of a repeat protein scaffold and avoiding flexible linkers. We use DARPins (Designed Ankyrin Repeat Proteins), synthetic binding proteins based on the Ankyrin-repeat protein scaffold, as binding units. Their ease of in vitro selection, high production yield and stability make them ideal specificity-conferring building blocks for the design of more complex constructs. C- and N-terminal DARPin capping repeats were re-designed to be joined by a shared helix in such a way that rigid connector modules are formed. This allows us to join two or more DARPins in predefined geometries without compromising their binding affinities and specificities. Nine connector modules with distinct geometries were designed; for eight of these we were able to confirm the structure by X-ray crystallography, while only one did not crystallize. The bispecific constructs were all able to bind both target proteins simultaneously.
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43
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Harmansa S, Alborelli I, Bieli D, Caussinus E, Affolter M. A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila. eLife 2017; 6. [PMID: 28395731 PMCID: PMC5388529 DOI: 10.7554/elife.22549] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 03/14/2017] [Indexed: 12/26/2022] Open
Abstract
The role of protein localization along the apical-basal axis of polarized cells is difficult to investigate in vivo, partially due to lack of suitable tools. Here, we present the GrabFP system, a collection of four nanobody-based GFP-traps that localize to defined positions along the apical-basal axis. We show that the localization preference of the GrabFP traps can impose a novel localization on GFP-tagged target proteins and results in their controlled mislocalization. These new tools were used to mislocalize transmembrane and cytoplasmic GFP fusion proteins in the Drosophila wing disc epithelium and to investigate the effect of protein mislocalization. Furthermore, we used the GrabFP system as a tool to study the extracellular dispersal of the Decapentaplegic (Dpp) protein and show that the Dpp gradient forming in the lateral plane of the Drosophila wing disc epithelium is essential for patterning of the wing imaginal disc.
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Affiliation(s)
- Stefan Harmansa
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland
| | - Ilaria Alborelli
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland
| | - Dimitri Bieli
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland
| | - Emmanuel Caussinus
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland.,Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, Basel, Switzerland
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44
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Pratt SE, Speltz EB, Mochrie SGJ, Regan L. Designed Proteins as Novel Imaging Reagents in Living Escherichia coli. Chembiochem 2016; 17:1652-7. [PMID: 27304706 DOI: 10.1002/cbic.201600252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/06/2022]
Abstract
Fluorescence imaging is a powerful tool to study protein function in living cells. Here, we introduce a novel imaging strategy that is fully genetically encodable, does not require the use of exogenous substrates, and adds a minimally disruptive tag to the protein of interest (POI). Our method was based on a set of designed tetratricopeptide repeat affinity proteins (TRAPs) that specifically and reversibly interact with a short, extended peptide tag. We co-expressed the TRAPs fused to fluorescent proteins (FPs) and the peptide tags fused to the POIs. We illustrated the method using the Escherichia coli protein FtsZ and showed that our system could track distinct FtsZ structures under both low and high expression conditions in live cells. We anticipate that our imaging strategy will be a useful tool for imaging the subcellular localization of many proteins, especially those recalcitrant to imaging by direct tagging with FPs.
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Affiliation(s)
- Susan E Pratt
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Elizabeth B Speltz
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA
| | - Simon G J Mochrie
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, 06511, USA. .,Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Applied Physics, Yale University, 15 Prospect Street, New Haven, CT, 06511, USA.
| | - Lynne Regan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT, 06511, USA. .,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.
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45
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DARPin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography. J Mol Biol 2016; 428:1574-88. [DOI: 10.1016/j.jmb.2016.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/28/2016] [Accepted: 03/02/2016] [Indexed: 11/21/2022]
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46
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BMP morphogen gradients in flies. Cytokine Growth Factor Rev 2016; 27:119-27. [DOI: 10.1016/j.cytogfr.2015.11.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022]
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47
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Nicholes N, Date A, Beaujean P, Hauk P, Kanwar M, Ostermeier M. Modular protein switches derived from antibody mimetic proteins. Protein Eng Des Sel 2016; 29:77-85. [PMID: 26637825 PMCID: PMC4757927 DOI: 10.1093/protein/gzv062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 12/21/2022] Open
Abstract
Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms.
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Affiliation(s)
- N Nicholes
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
| | - A Date
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
| | - P Beaujean
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
| | - P Hauk
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
| | - M Kanwar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
| | - M Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21218, USA
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Generation of Fluorogen-Activating Designed Ankyrin Repeat Proteins (FADAs) as Versatile Sensor Tools. J Mol Biol 2016; 428:1272-1289. [PMID: 26812208 DOI: 10.1016/j.jmb.2016.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/12/2016] [Accepted: 01/15/2016] [Indexed: 11/21/2022]
Abstract
Fluorescent probes constitute a valuable toolbox to address a variety of biological questions and they have become irreplaceable for imaging methods. Commonly, such probes consist of fluorescent proteins or small organic fluorophores coupled to biological molecules of interest. Recently, a novel class of fluorescence-based probes, fluorogen-activating proteins (FAPs), has been reported. These binding proteins are based on antibody single-chain variable fragments and activate fluorogenic dyes, which only become fluorescent upon activation and do not fluoresce when free in solution. Here we present a novel class of fluorogen activators, termed FADAs, based on the very robust designed ankyrin repeat protein scaffold, which also readily folds in the reducing environment of the cytoplasm. The FADA generated in this study was obtained by combined selections with ribosome display and yeast surface display. It enhances the fluorescence of malachite green (MG) dyes by a factor of more than 11,000 and thus activates MG to a similar extent as FAPs based on single-chain variable fragments. As shown by structure determination and in vitro measurements, this FADA was evolved to form a homodimer for the activation of MG dyes. Exploiting the favorable properties of the designed ankyrin repeat protein scaffold, we created a FADA biosensor suitable for imaging of proteins on the cell surface, as well as in the cytosol. Moreover, based on the requirement of dimerization for strong fluorogen activation, a prototype FADA biosensor for in situ detection of a target protein and protein-protein interactions was developed. Therefore, FADAs are versatile fluorescent probes that are easily produced and suitable for diverse applications and thus extend the FAP technology.
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Bieli D, Alborelli I, Harmansa S, Matsuda S, Caussinus E, Affolter M. Development and Application of Functionalized Protein Binders in Multicellular Organisms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:181-213. [DOI: 10.1016/bs.ircmb.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Huet S, Gorre H, Perrocheau A, Picot J, Cinier M. Use of the Nanofitin Alternative Scaffold as a GFP-Ready Fusion Tag. PLoS One 2015; 10:e0142304. [PMID: 26539718 PMCID: PMC4634965 DOI: 10.1371/journal.pone.0142304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 10/19/2015] [Indexed: 11/26/2022] Open
Abstract
With the continuous diversification of recombinant DNA technologies, the possibilities for new tailor-made protein engineering have extended on an on-going basis. Among these strategies, the use of the green fluorescent protein (GFP) as a fusion domain has been widely adopted for cellular imaging and protein localization. Following the lead of the direct head-to-tail fusion of GFP, we proposed to provide additional features to recombinant proteins by genetic fusion of artificially derived binders. Thus, we reported a GFP-ready fusion tag consisting of a small and robust fusion-friendly anti-GFP Nanofitin binding domain as a proof-of-concept. While limiting steric effects on the carrier, the GFP-ready tag allows the capture of GFP or its blue (BFP), cyan (CFP) and yellow (YFP) alternatives. Here, we described the generation of the GFP-ready tag from the selection of a Nanofitin variant binding to the GFP and its spectral variants with a nanomolar affinity, while displaying a remarkable folding stability, as demonstrated by its full resistance upon thermal sterilization process or the full chemical synthesis of Nanofitins. To illustrate the potential of the Nanofitin-based tag as a fusion partner, we compared the expression level in Escherichia coli and activity profile of recombinant human tumor necrosis factor alpha (TNFα) constructs, fused to a SUMO or GFP-ready tag. Very similar expression levels were found with the two fusion technologies. Both domains of the GFP-ready tagged TNFα were proved fully active in ELISA and interferometry binding assays, allowing the simultaneous capture by an anti-TNFα antibody and binding to the GFP, and its spectral mutants. The GFP-ready tag was also shown inert in a L929 cell based assay, demonstrating the potent TNFα mediated apoptosis induction by the GFP-ready tagged TNFα. Eventually, we proposed the GFP-ready tag as a versatile capture and labeling system in addition to expected applications of anti-GFP Nanofitins (as illustrated with previously described state-of-the-art anti-GFP binders applied to living cells and in vitro applications). Through a single fusion domain, the GFP-ready tagged proteins benefit from subsequent customization within a wide range of fluorescence spectra upon indirect binding of a chosen GFP variant.
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