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Sekhon H, Ha JH, Presti MF, Procopio SB, Jarvis AR, Mirsky PO, John AM, Loh SN. Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells. Nat Methods 2023; 20:1920-1929. [PMID: 37945909 PMCID: PMC11080272 DOI: 10.1038/s41592-023-02065-w] [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: 03/28/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
A grand challenge in biosensor design is to develop a single-molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Here, we created a family of adaptable, turn-on maturation (ATOM) biosensors consisting of a monobody (circularly permuted at one of two positions) or a nanobody (circularly permuted at one of three positions) inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells coexpressing cyan, yellow and red ATOM sensors detected biosensor targets that were specifically localized to various subcellular compartments. Fluorescence activation involved ligand-dependent chromophore maturation with turn-on ratios of up to 62-fold in cells and 100-fold in vitro. Endoplasmic reticulum- and mitochondria-localized ATOM sensors detected ligands that were targeted to those organelles. The ATOM design was validated with three monobodies and one nanobody inserted into distinct fluorescent proteins, suggesting that customized ATOM sensors can be generated quickly.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Spencer B Procopio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ava R Jarvis
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Paige O Mirsky
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anna M John
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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2
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Sekhon H, Ha JH, Presti MF, Procopio SB, Mirsky PO, John AM, Loh SN. Adaptable, Turn-On Monobody (ATOM) Fluorescent Biosensors for Multiplexed Detection in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534597. [PMID: 37034669 PMCID: PMC10081266 DOI: 10.1101/2023.03.28.534597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A grand challenge in biosensor design is to develop a single molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Conceptually, this can be achieved by fusing a small, antibody-like binding domain to a fluorescent protein in such a way that target binding activates fluorescence. Although this design is simple to envision, its execution is not obvious. Here, we created a family of adaptable, turn-on monobody (ATOM) biosensors consisting of a monobody, circularly permuted at one of two positions, inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells co-expressing cyan, yellow, and red ATOM sensors detected the biosensor targets (WDR5, SH2, and hRAS proteins) that were localized to the nucleus, cytoplasm, and plasma membrane, respectively, with high specificity. ER- and mitochondria-localized ATOM sensors also detected ligands that were targeted to those organelles. Fluorescence activation involved ligand-dependent chromophore maturation with fluorescence turn-on ratios of >20-fold in cells and up to 100-fold in vitro . The sensing mechanism was validated with three arbitrarily chosen monobodies inserted into jellyfish as well as anemone lineages of fluorescent proteins, suggesting that ATOM sensors with different binding specificities and additional colors can be generated relatively quickly.
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3
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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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4
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Walser M, Mayor J, Rothenberger S. Designed Ankyrin Repeat Proteins: A New Class of Viral Entry Inhibitors. Viruses 2022; 14:2242. [PMID: 36298797 PMCID: PMC9611651 DOI: 10.3390/v14102242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 08/08/2023] Open
Abstract
Designed ankyrin repeat proteins (DARPins) are engineered proteins comprising consensus designed ankyrin repeats as scaffold. Tightly packed repeats form a continuous hydrophobic core and a large groove-like solvent-accessible surface that creates a binding surface. DARPin domains recognizing a target of interest with high specificity and affinity can be generated using a synthetic combinatorial library and in vitro selection methods. They can be linked together in a single molecule to build multispecific and multifunctional proteins without affecting expression or function. The modular architecture of DARPins offers unprecedented possibilities of design and opens avenues for innovative antiviral strategies.
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Affiliation(s)
- Marcel Walser
- Molecular Partners AG, Wagistrasse 14, 8952 Zurich-Schlieren, Switzerland
| | - Jennifer Mayor
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
| | - Sylvia Rothenberger
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700 Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Rue du Bugnon 48, 1011 Lausanne, Switzerland
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5
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Rigamonti N, Veitonmäki N, Domke C, Barsin S, Jetzer S, Abdelmotaleb O, Bessey R, Lekishvili T, Malvezzi F, Gachechiladze M, Behe M, Levitsky V, Trail PA. A multispecific anti-CD40 DARPin® construct induces tumor-selective CD40 activation and tumor regression. Cancer Immunol Res 2022; 10:626-640. [PMID: 35319751 DOI: 10.1158/2326-6066.cir-21-0553] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/20/2021] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
The CD40 receptor is an attractive target for cancer immunotherapy. Although a modest pharmacodynamic effect is seen in patients following administration of CD40-targeting monoclonal antibodies (mAb), the doses that could be safely administered do not result in a meaningful clinical response, most likely due to the limited therapeutic window associated with systemic CD40 activation. To overcome this issue, we developed a multispecific DARPin® construct, α-FAPxCD40, which has conditional activity at the site of disease. α-FAPxCD40 activation of CD40 depends on binding to fibroblast activation protein (FAP), a cell surface protease overexpressed in the stroma of solid tumors. In vitro studies demonstrated that α-FAPxCD40 potently activates human antigen-presenting cells in the presence, but not in the absence, of FAP-positive cells. After intravenous injection, a murine surrogate construct (α-mFAPxCD40) accumulated in FAP-positive tumors, elicited rejection of 88% of these tumors and induced memory anti-tumor immunity. Importantly, in contrast to the mouse anti-CD40 tested in parallel, the in vivo anti-tumor activity of α-mFAPxCD40 was neither associated with elevated blood cytokines nor with hepatotoxicity, both of which contribute to the clinical dose-limiting toxicities of several CD40 mAb. This study demonstrates that α-(m)FAPxCD40 engages CD40 in an FAP-restricted manner leading to tumor eradication without signs of peripheral toxicity. This distinct preclinical profile indicates that a favorable therapeutic index may be achieved in humans. It further supports the development of α-FAPxCD40, currently tested in a first-in-human clinical study in patients with solid tumors (NCT05098405).
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Affiliation(s)
| | | | - Clara Domke
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | - Sophie Barsin
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | - Sarah Jetzer
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | - Ralph Bessey
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | | | | | - Martin Behe
- Paul Scherrer Institute, Villigen, Switzerland
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6
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Chang MP, Huang W, Mai DJ. Monomer‐scale design of functional protein polymers using consensus repeat sequences. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Marina P. Chang
- Department of Materials Science and Engineering Stanford University Stanford California USA
| | - Winnie Huang
- Department of Chemical Engineering Stanford University Stanford California USA
| | - Danielle J. Mai
- Department of Chemical Engineering Stanford University Stanford California USA
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7
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Protein-Protein Interactions: Insight from Molecular Dynamics Simulations and Nanoparticle Tracking Analysis. Molecules 2021; 26:molecules26185696. [PMID: 34577167 PMCID: PMC8472368 DOI: 10.3390/molecules26185696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interaction plays an essential role in almost all cellular processes and biological functions. Coupling molecular dynamics (MD) simulations and nanoparticle tracking analysis (NTA) assay offered a simple, rapid, and direct approach in monitoring the protein-protein binding process and predicting the binding affinity. Our case study of designed ankyrin repeats proteins (DARPins)—AnkGAG1D4 and the single point mutated AnkGAG1D4-Y56A for HIV-1 capsid protein (CA) were investigated. As reported, AnkGAG1D4 bound with CA for inhibitory activity; however, it lost its inhibitory strength when tyrosine at residue 56 AnkGAG1D4, the most key residue was replaced by alanine (AnkGAG1D4-Y56A). Through NTA, the binding of DARPins and CA was measured by monitoring the increment of the hydrodynamic radius of the AnkGAG1D4-gold conjugated nanoparticles (AnkGAG1D4-GNP) and AnkGAG1D4-Y56A-GNP upon interaction with CA in buffer solution. The size of the AnkGAG1D4-GNP increased when it interacted with CA but not AnkGAG1D4-Y56A-GNP. In addition, a much higher binding free energy (∆GB) of AnkGAG1D4-Y56A (−31 kcal/mol) obtained from MD further suggested affinity for CA completely reduced compared to AnkGAG1D4 (−60 kcal/mol). The possible mechanism of the protein-protein binding was explored in detail by decomposing the binding free energy for crucial residues identification and hydrogen bond analysis.
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8
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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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9
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Caputi AP, Navarra P. Beyond antibodies: ankyrins and DARPins. From basic research to drug approval. Curr Opin Pharmacol 2020; 51:93-101. [PMID: 32674998 DOI: 10.1016/j.coph.2020.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/23/2022]
Abstract
This Pharmacological Perspective describes the pathway that, starting from the deep understanding of ankyrins - a family of proteins with high variability-binding and high specificity-binding characteristics - led to the development of a new class of recombinant-binding proteins, the DARPins (designed ankyrin repeat proteins). These are envisaged as alternatives to mAbs and related biologics, with the potential to overcome certain shortcomings of mAbs. DARPins have relatively low molecular weights (14-21kDas) and more favorable PK profiles than mAbs, are stable proteins that can be easily produced in Escherichia coli and can be used in their monovalent form or conjugated to other moieties, for example, polyethylene glycol (PEG) to enhance their half-life. DARPins can also be engineered to produce bi-specific or tri-specific compounds that bind different epitopes of the same target or two different targets. Abicipar, a first-in-class anti-VEGF-A DARPin had similar efficacy compared to anti-VEGF biologics (bevacizumab, ranibizumab) in preclinical studies and was not inferior to ranibizumab in the treatment of age-related macular degeneration (AMD) with a reduced number of intravitreal injections. Abicipar has recently been submitted for regulatory approval for use in AMD.
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Affiliation(s)
| | - Pierluigi Navarra
- Dept. of Healthcare Surveillance and Bioethics, Section of Pharmacology, Fondazione Policlinico Universitario A, Gemelli IRCCS, Roma -Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.
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10
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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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11
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A Novel Nanobody Scaffold Optimized for Bacterial Expression and Suitable for the Construction of Ribosome Display Libraries. Mol Biotechnol 2019; 62:43-55. [DOI: 10.1007/s12033-019-00224-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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12
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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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13
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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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14
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Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It works entirely in vitro, and this has two important consequences. First, since no transformation of any cells is required, libraries with much greater diversity can be handled than with most other techniques. Second, since a library does not have to be cloned and transformed, it is very convenient to introduce random errors in the library by PCR-based methods and select improved binders. Thus, a true directed evolution, an iteration between randomization and selection over several generations, can be conveniently carried out, e.g., for affinity maturation, either on a given clone or on the whole library. Ribosome display has been successfully applied to antibody single-chain Fv fragments (scFv), which can be selected not only for specificity but also for stability and catalytic activity. High-affinity binders with new target specificity can be obtained from highly diverse libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
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15
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Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system. Proc Natl Acad Sci U S A 2018; 115:3362-3367. [PMID: 29507202 DOI: 10.1073/pnas.1718825115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Current single-particle cryo-electron microscopy (cryo-EM) techniques can produce images of large protein assemblies and macromolecular complexes at atomic level detail without the need for crystal growth. However, proteins of smaller size, typical of those found throughout the cell, are not presently amenable to detailed structural elucidation by cryo-EM. Here we use protein design to create a modular, symmetrical scaffolding system to make protein molecules of typical size suitable for cryo-EM. Using a rigid continuous alpha helical linker, we connect a small 17-kDa protein (DARPin) to a protein subunit that was designed to self-assemble into a cage with cubic symmetry. We show that the resulting construct is amenable to structural analysis by single-particle cryo-EM, allowing us to identify and solve the structure of the attached small protein at near-atomic detail, ranging from 3.5- to 5-Å resolution. The result demonstrates that proteins considerably smaller than the theoretical limit of 50 kDa for cryo-EM can be visualized clearly when arrayed in a rigid fashion on a symmetric designed protein scaffold. Furthermore, because the amino acid sequence of a DARPin can be chosen to confer tight binding to various other protein or nucleic acid molecules, the system provides a future route for imaging diverse macromolecules, potentially broadening the application of cryo-EM to proteins of typical size in the cell.
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16
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Hadpech S, Nangola S, Chupradit K, Fanhchaksai K, Furnon W, Urvoas A, Valerio-Lepiniec M, Minard P, Boulanger P, Hong SS, Tayapiwatana C. Alpha-helicoidal HEAT-like Repeat Proteins (αRep) Selected as Interactors of HIV-1 Nucleocapsid Negatively Interfere with Viral Genome Packaging and Virus Maturation. Sci Rep 2017; 7:16335. [PMID: 29180782 PMCID: PMC5703948 DOI: 10.1038/s41598-017-16451-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/13/2017] [Indexed: 12/21/2022] Open
Abstract
A new generation of artificial proteins, derived from alpha-helicoidal HEAT-like repeat protein scaffolds (αRep), was previously characterized as an effective source of intracellular interfering proteins. In this work, a phage-displayed library of αRep was screened on a region of HIV-1 Gag polyprotein encompassing the C-terminal domain of the capsid, the SP1 linker and the nucleocapsid. This region is known to be essential for the late steps of HIV-1 life cycle, Gag oligomerization, viral genome packaging and the last cleavage step of Gag, leading to mature, infectious virions. Two strong αRep binders were isolated from the screen, αRep4E3 (32 kDa; 7 internal repeats) and αRep9A8 (28 kDa; 6 internal repeats). Their antiviral activity against HIV-1 was evaluated in VLP-producer cells and in human SupT1 cells challenged with HIV-1. Both αRep4E3 and αRep9A8 showed a modest but significant antiviral effects in all bioassays and cell systems tested. They did not prevent the proviral integration reaction, but negatively interfered with late steps of the HIV-1 life cycle: αRep4E3 blocked the viral genome packaging, whereas αRep9A8 altered both virus maturation and genome packaging. Interestingly, SupT1 cells stably expressing αRep9A8 acquired long-term resistance to HIV-1, implying that αRep proteins can act as antiviral restriction-like factors.
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Affiliation(s)
- Sudarat Hadpech
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Faculty of Pharmaceutical Science, Burapha University, Muang District, Chonburi Province, 20131, Thailand.,University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Sawitree Nangola
- Division of Clinical Immunology and Transfusion Sciences, School of Allied Health Sciences, University of Phayao, Phayao, 56000, Thailand
| | - Koollawat Chupradit
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Kanda Fanhchaksai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Wilhelm Furnon
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie Valerio-Lepiniec
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Philippe Minard
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Pierre Boulanger
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France
| | - Saw-See Hong
- University Lyon 1, UMR754-INRA-EPHE, Viral Infections and Comparative Pathology, 50, Avenue Tony Garnier, 69366, Lyon Cedex 07, France. .,Institut National de la Santé et de la Recherche Médicale, 101, rue de Tolbiac, 75654, Paris Cedex 13, France.
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
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17
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Kinetic characterization and molecular docking of novel allosteric inhibitors of aminoglycoside phosphotransferases. Biochim Biophys Acta Gen Subj 2017; 1861:3464-3473. [DOI: 10.1016/j.bbagen.2016.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/07/2016] [Accepted: 09/11/2016] [Indexed: 11/21/2022]
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18
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Regan L, Caballero D, Hinrichsen MR, Virrueta A, Williams DM, O'Hern CS. Protein design: Past, present, and future. Biopolymers 2016; 104:334-50. [PMID: 25784145 DOI: 10.1002/bip.22639] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/05/2015] [Accepted: 03/07/2015] [Indexed: 01/16/2023]
Abstract
Building on the pioneering work of Ho and DeGrado (J Am Chem Soc 1987, 109, 6751-6758) in the late 1980s, protein design approaches have revealed many fundamental features of protein structure and stability. We are now in the era that the early work presaged - the design of new proteins with practical applications and uses. Here we briefly survey some past milestones in protein design, in addition to highlighting recent progress and future aspirations.
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Affiliation(s)
- Lynne Regan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.,Department of Chemistry, Yale University, New Haven, CT.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT
| | - Diego Caballero
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT.,Department of Physics, Yale University, New Haven, CT
| | - Michael R Hinrichsen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Alejandro Virrueta
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT.,Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT
| | - Danielle M Williams
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Corey S O'Hern
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT.,Department of Physics, Yale University, New Haven, CT.,Department of Mechanical Engineering and Materials Science, Yale University, New Haven, CT.,Department of Applied Physics, Yale University, New Haven, CT
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19
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Aβ-Immunotherapeutic strategies: a wide range of approaches for Alzheimer's disease treatment. Expert Rev Mol Med 2016; 18:e13. [PMID: 27357999 DOI: 10.1017/erm.2016.11] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Current therapies to treat Alzheimer's disease (AD) are focused on ameliorating symptoms instead of treating the underlying causes of AD. The accumulation of amyloid β (Aβ) oligomers, whether by an increase in production or by a decrease in clearance, has been described as the seed that initiates the pathological cascade in AD. Developing therapies to target these species is a vital step in improving AD treatment. Aβ-immunotherapy, especially passive immunotherapy, is a promising approach to reduce the Aβ burden. Up to now, several monoclonal antibodies (mAbs) have been tested in clinical trials on humans, but none of them have passed Phase III. In all likelihood, these trials failed mainly because patients with mild-to-moderate AD were recruited, and thus treatment may have been too late to be effective. Therefore, many ongoing clinical trials are being conducted in patients at the prodromal stage. New structures based on antibody fragments have been engineered intending to improve efficacy and safety. This review presents the properties of this variety of developing treatments and provides a perspective on state-of-the-art of passive Aβ-immunotherapy in AD.
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20
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Regan L, Hinrichsen MR, Oi C. Protein engineering strategies with potential applications for altering clinically relevant cellular pathways at the protein level. Expert Rev Proteomics 2016; 13:481-93. [PMID: 27031866 DOI: 10.1586/14789450.2016.1172966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
All diseases can be fundamentally viewed as the result of malfunctioning cellular pathways. Protein engineering offers the potential to develop new tools that will allow these dysfunctional pathways to be better understood, in addition to potentially providing new routes to restore proper function. Here we discuss different approaches that can be used to change the intracellular activity of a protein by intervening at the protein level: targeted protein sequestration, protein recruitment, protein degradation, and selective inhibition of binding interfaces. The potential of each of these tools to be developed into effective therapeutic treatments will also be discussed, along with any major barriers that currently block their translation into the clinic.
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Affiliation(s)
- Lynne Regan
- a Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA.,b Department of Chemistry , Yale University , New Haven , CT , USA.,c Integrated Graduate Program in Physical and Engineering Biology , Yale University , New Haven , CT , USA
| | - Michael R Hinrichsen
- a Department of Molecular Biophysics & Biochemistry , Yale University , New Haven , CT , USA
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21
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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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22
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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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23
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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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24
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Plückthun A. Designed ankyrin repeat proteins (DARPins): binding proteins for research, diagnostics, and therapy. Annu Rev Pharmacol Toxicol 2015; 55:489-511. [PMID: 25562645 DOI: 10.1146/annurev-pharmtox-010611-134654] [Citation(s) in RCA: 382] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Designed ankyrin repeat proteins (DARPins) can recognize targets with specificities and affinities that equal or surpass those of antibodies, but because of their robustness and extreme stability, they allow a multitude of more advanced formats and applications. This review highlights recent advances in DARPin design, illustrates their properties, and gives some examples of their use. In research, they have been established as intracellular, real-time sensors of protein conformations and as crystallization chaperones. For future therapies, DARPins have been developed by advanced, structure-based protein engineering to selectively induce apoptosis in tumors by uncoupling surface receptors from their signaling cascades. They have also been used successfully for retargeting viruses. In ongoing clinical trials, DARPins have shown good safety and efficacy in macular degeneration diseases. These developments all ultimately exploit the high stability, solubility, and aggregation resistance of these molecules, permitting a wide range of conjugates and fusions to be produced and purified.
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Affiliation(s)
- Andreas Plückthun
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland;
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25
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Jain D. Allosteric control of transcription in GntR family of transcription regulators: A structural overview. IUBMB Life 2015; 67:556-63. [PMID: 26172911 DOI: 10.1002/iub.1401] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 01/24/2023]
Abstract
The GntR family of transcription regulators constitutes one of the most abundant family of transcription factors. These modulators are involved in a variety of mechanisms controlling various metabolic processes. GntR family members are typically two domain proteins with a smaller N-terminus domain (NTD) with conserved architecture of winged-helix-turn-helix (wHTH) for DNA binding and a larger C-terminus domain (CTD) or the effector binding domain which is also involved in oligomerization. Interestingly, the CTD shows structural heterogeneity depending upon the type of effector molecule that it binds and displays structural homology to various classes of proteins. Binding of the effector molecule to the CTD brings about a conformational change in the transcription factor such that its affinity for its cognate DNA sequence is altered. This review summarizes the structural information available on the members of GntR family and discusses the common features of the DNA binding and operator recognition within the family. The variation in the allosteric mechanism employed by the members of this family is also discussed.
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Affiliation(s)
- Deepti Jain
- Transcription Regulation Laboratory Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
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26
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Artificial affinity proteins as ligands of immunoglobulins. Biomolecules 2015; 5:60-75. [PMID: 25647098 PMCID: PMC4384111 DOI: 10.3390/biom5010060] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/17/2022] Open
Abstract
A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized.
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27
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Brauchle M, Hansen S, Caussinus E, Lenard A, Ochoa-Espinosa A, Scholz O, Sprecher SG, Plückthun A, Affolter M. Protein interference applications in cellular and developmental biology using DARPins that recognize GFP and mCherry. Biol Open 2014; 3:1252-61. [PMID: 25416061 PMCID: PMC4265764 DOI: 10.1242/bio.201410041] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Protein–protein interactions are crucial for cellular homeostasis and play important roles in the dynamic execution of biological processes. While antibodies represent a well-established tool to study protein interactions of extracellular domains and secreted proteins, as well as in fixed and permeabilized cells, they usually cannot be functionally expressed in the cytoplasm of living cells. Non-immunoglobulin protein-binding scaffolds have been identified that also function intracellularly and are now being engineered for synthetic biology applications. Here we used the Designed Ankyrin Repeat Protein (DARPin) scaffold to generate binders to fluorescent proteins and used them to modify biological systems directly at the protein level. DARPins binding to GFP or mCherry were selected by ribosome display. For GFP, binders with KD as low as 160 pM were obtained, while for mCherry the best affinity was 6 nM. We then verified in cell culture their specific binding in a complex cellular environment and found an affinity cut-off in the mid-nanomolar region, above which binding is no longer detectable in the cell. Next, their binding properties were employed to change the localization of the respective fluorescent proteins within cells. Finally, we performed experiments in Drosophila melanogaster and Danio rerio and utilized these DARPins to either degrade or delocalize fluorescently tagged fusion proteins in developing organisms, and to phenocopy loss-of-function mutations. Specific protein binders can thus be selected in vitro and used to reprogram developmental systems in vivo directly at the protein level, thereby bypassing some limitations of approaches that function at the DNA or the RNA level.
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Affiliation(s)
- Michael Brauchle
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland Department of Zoology, University of Fribourg, Chemi du Musée 10, 1700 Fribourg, Switzerland
| | - Simon Hansen
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Emmanuel Caussinus
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Anna Lenard
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | | | - Oliver Scholz
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Simon G Sprecher
- Department of Zoology, University of Fribourg, Chemi du Musée 10, 1700 Fribourg, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Markus Affolter
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
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28
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Combined inhibition of caspase 3 and caspase 7 by two highly selective DARPins slows down cellular demise. Biochem J 2014; 461:279-90. [PMID: 24779913 DOI: 10.1042/bj20131456] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Caspases play important roles during apoptosis, inflammation and proliferation. The high homology among family members makes selective targeting of individual caspases difficult, which is necessary to precisely define the role of these enzymes. We have selected caspase-7-specific binders from a library of DARPins (designed ankyrin repeat proteins). The DARPins D7.18 and D7.43 bind specifically to procaspase 7 and active caspase 7, but not to other members of the family. Binding of the DARPins does not affect the active enzyme, but interferes with its activation by other caspases. The crystal structure of the caspase 7-D7.18 complex elucidates the high selectivity and the mode of inhibition. Combining these caspase-7-specific DARPins with the previously reported caspase-3-inhibitory DARPin D3.4S76R reduces the activity of caspase 3 and 7 in double-transfected HeLa cells during apoptosis. In addition, these cells showed less susceptibility to TRAIL (tumour-necrosis-factor-related apoptosis-inducing ligand)-induced apoptosis in living cell experiments. D7.18 and D7.43 are therefore novel tools for in vitro studies on procaspase 7 activation as well as for clarifying the role of its activation in different cellular processes. If applied in combination with D3.4S76R, they represent an excellent instrument to increase our understanding of these enzymes during various cellular processes.
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29
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Hanenberg M, McAfoose J, Kulic L, Welt T, Wirth F, Parizek P, Strobel L, Cattepoel S, Späni C, Derungs R, Maier M, Plückthun A, Nitsch RM. Amyloid-β peptide-specific DARPins as a novel class of potential therapeutics for Alzheimer disease. J Biol Chem 2014; 289:27080-27089. [PMID: 25118284 DOI: 10.1074/jbc.m114.564013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Passive immunization with anti-amyloid-β peptide (Aβ) antibodies is effective in animal models of Alzheimer disease. With the advent of efficient in vitro selection technologies, the novel class of designed ankyrin repeat proteins (DARPins) presents an attractive alternative to the immunoglobulin scaffold. DARPins are small and highly stable proteins with a compact modular architecture ideal for high affinity protein-protein interactions. In this report, we describe the selection, binding profile, and epitope analysis of Aβ-specific DARPins. We further showed their ability to delay Aβ aggregation and prevent Aβ-mediated neurotoxicity in vitro. To demonstrate their therapeutic potential in vivo, mono- and trivalent Aβ-specific DARPins (D23 and 3×D23) were infused intracerebroventricularly into the brains of 11-month-old Tg2576 mice over 4 weeks. Both D23 and 3×D23 treatments were shown to result in improved cognitive performance and reduced soluble Aβ levels. These findings demonstrate the therapeutic potential of Aβ-specific DARPins for the treatment of Alzheimer disease.
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Affiliation(s)
- Michael Hanenberg
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Jordan McAfoose
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Luka Kulic
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren,; Department of Neurology, University Hospital Zurich, University of Zurich, Frauenklinikstrasse 26, 8091 Zurich,; Zurich Center for Integrative Human Physiology and University of Zurich, Winterthurerstrasse 190, 8057 Zurich
| | - Tobias Welt
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Fabian Wirth
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Petra Parizek
- Institute of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, and
| | - Lisa Strobel
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Susann Cattepoel
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Claudia Späni
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Rebecca Derungs
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren
| | - Marcel Maier
- Neurimmune Holding AG, Wagistrasse 13, 8952 Schlieren, Switzerland
| | - Andreas Plückthun
- Institute of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, and
| | - Roger M Nitsch
- Division of Psychiatry Research, University of Zurich, Wagistrasse 12, 8952 Schlieren,.
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30
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Fosso MY, Li Y, Garneau-Tsodikova S. New trends in aminoglycosides use. MEDCHEMCOMM 2014; 5:1075-1091. [PMID: 25071928 PMCID: PMC4111210 DOI: 10.1039/c4md00163j] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Despite their inherent toxicity and the acquired bacterial resistance that continuously threaten their long-term clinical use, aminoglycosides (AGs) still remain valuable components of the antibiotic armamentarium. Recent literature shows that the AGs' role has been further expanded as multi-tasking players in different areas of study. This review aims at presenting some of the new trends observed in the use of AGs in the past decade, along with the current understanding of their mechanisms of action in various bacterial and eukaryotic cellular processes.
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Affiliation(s)
- Marina Y. Fosso
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Yijia Li
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
| | - Sylvie Garneau-Tsodikova
- University of Kentucky, Department of Pharmaceutical Sciences, College of Pharmacy, BioPharm Complex, Room 423, 789 South Limestone Street, Lexington, KY, 40536-0596, U.S.A
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Praditwongwan W, Chuankhayan P, Saoin S, Wisitponchai T, Lee VS, Nangola S, Hong SS, Minard P, Boulanger P, Chen CJ, Tayapiwatana C. Crystal structure of an antiviral ankyrin targeting the HIV-1 capsid and molecular modeling of the ankyrin-capsid complex. J Comput Aided Mol Des 2014; 28:869-84. [PMID: 24997121 DOI: 10.1007/s10822-014-9772-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 06/24/2014] [Indexed: 11/28/2022]
Abstract
Ankyrins are cellular repeat proteins, which can be genetically modified to randomize amino-acid residues located at defined positions in each repeat unit, and thus create a potential binding surface adaptable to macromolecular ligands. From a phage-display library of artificial ankyrins, we have isolated Ank(GAG)1D4, a trimodular ankyrin which binds to the HIV-1 capsid protein N-terminal domain (NTD(CA)) and has an antiviral effect at the late steps of the virus life cycle. In this study, the determinants of the Ank(GAG)1D4-NTD(CA) interaction were analyzed using peptide scanning in competition ELISA, capsid mutagenesis, ankyrin crystallography and molecular modeling. We determined the Ank(GAG)1D4 structure at 2.2 Å resolution, and used the crystal structure in molecular docking with a homology model of HIV-1 capsid. Our results indicated that NTD(CA) alpha-helices H1 and H7 could mediate the formation of the capsid-Ank(GAG)1D4 binary complex, but the interaction involving H7 was predicted to be more stable than with H1. Arginine-18 (R18) in H1, and R132 and R143 in H7 were found to be the key players of the Ank(GAG)1D4-NTD(CA) interaction. This was confirmed by R-to-A mutagenesis of NTD(CA), and by sequence analysis of trimodular ankyrins negative for capsid binding. In Ank(GAG)1D4, major interactors common to H1 and H7 were found to be S45, Y56, R89, K122 and K123. Collectively, our ankyrin-capsid binding analysis implied a significant degree of flexibility within the NTD(CA) domain of the HIV-1 capsid protein, and provided some clues for the design of new antivirals targeting the capsid protein and viral assembly.
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Affiliation(s)
- Warachai Praditwongwan
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
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Abstract
Protein engineering is at an exciting stage because designed protein-protein interactions are being used in many applications. For instance, three designed proteins are now in clinical trials. Although there have been many successes over the last decade, protein engineering still faces numerous challenges. Often, designs do not work as anticipated and they still require substantial redesign. The present review focuses on the successes, the challenges and the limitations of rational protein design today.
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Schilling J, Schöppe J, Plückthun A. From DARPins to LoopDARPins: novel LoopDARPin design allows the selection of low picomolar binders in a single round of ribosome display. J Mol Biol 2014; 426:691-721. [PMID: 24513107 DOI: 10.1016/j.jmb.2013.10.026] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 10/17/2013] [Accepted: 10/17/2013] [Indexed: 12/19/2022]
Abstract
Antibodies are the most versatile binding proteins in nature with six loops creating a flexible continuous interaction surface. However, in some molecular formats, antibodies are aggregation prone. Designed ankyrin repeat proteins (DARPins) were successfully created as alternative design solutions. Nevertheless, their concave shape, rigidity and incompletely randomized binding surface may limit the epitopes that can be targeted by this extremely stable scaffold. Combining conformational diversity and a continuous convex paratope found in many antibodies with the beneficial biophysical properties of DARPins, we created LoopDARPins, a next generation of DARPins with extended epitope binding properties. We employed X-ray structure determination of a LoopDARPin for design validation. Biophysical characterizations show that the introduction of an elongated loop through consensus design does not decrease the stability of the scaffold,consistent with molecular dynamics simulations. Ribosome-display selections against extracellular signal-regulated kinase 2 (ERK2) and four members of the BCL-2 family (BCL-2, BCL-XL, BCL-W and MCL-1) of anti-apoptotic regulators yielded LoopDARPins with affinities in the mid-picomolar to low nanomol arrange against all targets. The BCL-2 family binders block the interaction with their natural interaction partner and will be valuable reagents to test the apoptotic response in functional assays. With the LoopDARPin scaffold, binders for BCL-2 with an affinity of 30 pM were isolated with only a single round of ribosome display,an enrichment that has not been described for any scaffold. Identical stringent one-round selections with conventional DARPins without loop yielded no binders. The LoopDARPin scaffold may become a highly valuable tool for biotechnological high-throughput applications.
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Strategies to overcome the action of aminoglycoside-modifying enzymes for treating resistant bacterial infections. Future Med Chem 2014; 5:1285-309. [PMID: 23859208 DOI: 10.4155/fmc.13.80] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Shortly after the discovery of the first antibiotics, bacterial resistance began to emerge. Many mechanisms give rise to resistance; the most prevalent mechanism of resistance to the aminoglycoside (AG) family of antibiotics is the action of aminoglycoside-modifying enzymes (AMEs). Since the identification of these modifying enzymes, many efforts have been put forth to prevent their damaging alterations of AGs. These diverse strategies are discussed within this review, including: creating new AGs that are unaffected by AMEs; developing inhibitors of AMEs to be co-delivered with AGs; or regulating AME expression. Modern high-throughput methods as well as drug combinations and repurposing are highlighted as recent drug-discovery efforts towards fighting the increasing antibiotic resistance crisis.
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Stoevesandt O, Taussig MJ. Affinity proteomics: the role of specific binding reagents in human proteome analysis. Expert Rev Proteomics 2014; 9:401-14. [DOI: 10.1586/epr.12.34] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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36
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Seeger MA, Zbinden R, Flütsch A, Gutte PGM, Engeler S, Roschitzki-Voser H, Grütter MG. Design, construction, and characterization of a second-generation DARP in library with reduced hydrophobicity. Protein Sci 2013; 22:1239-57. [PMID: 23868333 DOI: 10.1002/pro.2312] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/24/2013] [Accepted: 06/25/2013] [Indexed: 12/18/2022]
Abstract
Designed ankyrin repeat proteins (DARPins) are well-established binding molecules based on a highly stable nonantibody scaffold. Building on 13 crystal structures of DARPin-target complexes and stability measurements of DARPin mutants, we have generated a new DARPin library containing an extended randomized surface. To counteract the enrichment of unspecific hydrophobic binders during selections against difficult targets containing hydrophobic surfaces such as membrane proteins, the frequency of apolar residues at diversified positions was drastically reduced and substituted by an increased number of tyrosines. Ribosome display selections against two human caspases and membrane transporter AcrB yielded highly enriched pools of unique and strong DARPin binders which were mainly monomeric. We noted a prominent enrichment of tryptophan residues during binder selections. A crystal structure of a representative of this library in complex with caspase-7 visualizes the key roles of both tryptophans and tyrosines in providing target contacts. These aromatic and polar side chains thus substitute the apolar residues valine, leucine, isoleucine, methionine, and phenylalanine of the original DARPins. Our work describes biophysical and structural analyses required to extend existing binder scaffolds and simplifies an existing protocol for the assembly of highly diverse synthetic binder libraries.
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Affiliation(s)
- Markus A Seeger
- Department of Biochemistry, University of Zurich, 8057, Zürich, Switzerland
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Affiliation(s)
- Scott Banta
- Department of Chemical Engineering, Columbia University, New York, NY 10027;
| | - Kevin Dooley
- Department of Chemical Engineering, Columbia University, New York, NY 10027;
| | - Oren Shur
- Department of Chemical Engineering, Columbia University, New York, NY 10027;
- Current affiliation: Boston Consulting Group, New York, NY 10022
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Parashar V, Jeffrey PD, Neiditch MB. Conformational change-induced repeat domain expansion regulates Rap phosphatase quorum-sensing signal receptors. PLoS Biol 2013; 11:e1001512. [PMID: 23526881 PMCID: PMC3601965 DOI: 10.1371/journal.pbio.1001512] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 02/07/2013] [Indexed: 11/18/2022] Open
Abstract
The large family of Gram-positive quorum-sensing receptors known as the RNPP proteins consists of receptors homologous to the Rap, NprR, PlcR, and PrgX proteins that are regulated by imported oligopeptide autoinducers. Rap proteins are phosphatases and transcriptional anti-activators, and NprR, PlcR, and PrgX proteins are DNA binding transcription factors. Despite their obvious importance, the mechanistic basis of oligopeptide receptor regulation is largely unknown. Here, we report the X-ray crystal structure of the Bacillus subtilis quorum-sensing receptor RapJ in complex with the centrally important oligopeptide autoinducer competence and sporulation factor (CSF, also termed PhrC), a member of the Phr family of quorum-sensing signals. Furthermore, we present the crystal structure of RapI. Comparison of the RapJ-PhrC, RapI, RapH-Spo0F, and RapF-ComA(C) crystal structures reveals the mechanistic basis of Phr activity. More specifically, when complexed with target proteins, Rap proteins consist of a C-terminal tetratricopeptide repeat (TPR) domain connected by a flexible helix-containing linker to an N-terminal 3-helix bundle. In the absence of a target protein or regulatory peptide, the Rap protein 3-helix bundle adopts different conformations. However, in the peptide-bound conformation, the Rap protein N-terminal 3-helix bundle and linker undergo a radical conformational change, form TPR-like folds, and merge with the existing C-terminal TPR domain. To our knowledge, this is the first example of conformational change-induced repeat domain expansion. Furthermore, upon Phr binding, the entire Rap protein is compressed along the TPR superhelical axis, generating new intramolecular contacts that lock the Rap protein in an inactive state. The fact that Rap proteins are conformationally flexible is surprising considering that it is accepted dogma that TPR proteins do not undergo large conformational changes. Repeat proteins are widely used as scaffolds for the development of designed affinity reagents, and we propose that Rap proteins could be used as scaffolds for engineering novel ligand-switchable affinity reagents.
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Affiliation(s)
- Vijay Parashar
- Department of Microbiology and Molecular Genetics, UMDNJ–New Jersey Medical School, Newark, New Jersey, United States of America
| | - Philip D. Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Matthew B. Neiditch
- Department of Microbiology and Molecular Genetics, UMDNJ–New Jersey Medical School, Newark, New Jersey, United States of America
- * E-mail:
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39
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Conformation-dependent recognition of HIV gp120 by designed ankyrin repeat proteins provides access to novel HIV entry inhibitors. J Virol 2013; 87:5868-81. [PMID: 23487463 DOI: 10.1128/jvi.00152-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we applied the designed ankyrin repeat protein (DARPin) technology to develop novel gp120-directed binding molecules with HIV entry-inhibiting capacity. DARPins are interesting molecules for HIV envelope inhibitor design, as their high-affinity binding differs from that of antibodies. DARPins in general prefer epitopes with a defined folded structure. We probed whether this capacity favors the selection of novel gp120-reactive molecules with specificities in epitope recognition and inhibitory activity that differ from those found among neutralizing antibodies. The preference of DARPins for defined structures was notable in our selections, since of the four gp120 modifications probed as selection targets, gp120 arrested by CD4 ligation proved the most successful. Of note, all the gp120-specific DARPin clones with HIV-neutralizing activity isolated recognized their target domains in a conformation-dependent manner. This was particularly pronounced for the V3 loop-specific DARPin 5m3_D12. In stark contrast to V3-specific antibodies, 5m3_D12 preferentially recognized the V3 loop in a specific conformation, as probed by structurally arrested V3 mimetic peptides, but bound linear V3 peptides only very weakly. Most notably, this conformation-dependent V3 recognition allowed 5m3_D12 to bypass the V1V2 shielding of several tier 2 HIV isolates and to neutralize these viruses. These data provide a proof of concept that the DARPin technology holds promise for the development of HIV entry inhibitors with a unique mechanism of action.
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40
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Schroeder T, Barandun J, Flütsch A, Briand C, Mittl PRE, Grütter MG. Specific inhibition of caspase-3 by a competitive DARPin: molecular mimicry between native and designed inhibitors. Structure 2013; 21:277-89. [PMID: 23333429 DOI: 10.1016/j.str.2012.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/03/2012] [Accepted: 12/14/2012] [Indexed: 11/28/2022]
Abstract
Dysregulation of apoptosis is associated with several human diseases. The main apoptotic mediators are caspases, which propagate death signals to downstream targets. Executioner caspase-3 is responsible for the majority of cleavage events and its therapeutic potential is of high interest with to date several available active site peptide inhibitors. These molecules inhibit caspase-3, but also homologous caspases. Here, we describe caspase-3 specific inhibitors D3.4 and D3.8, which have been selected from a library of designed ankyrin repeat proteins (DARPins). The crystal structures of D3.4 and mutants thereof show how high specificity and inhibition is achieved. They also show similarities in the binding mode with that of the natural caspase inhibitor XIAP (X-linked inhibitor of apoptosis). The kinetic data reveal a competitive inhibition mechanism. D3.4 is specific for caspase-3 and does not bind the highly homologous caspase-7. D3.4 therefore is an excellent tool to define the precise role of caspase-3 in the various apoptotic pathways.
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Affiliation(s)
- Thilo Schroeder
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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41
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Parizek P, Kummer L, Rube P, Prinz A, Herberg FW, Plückthun A. Designed ankyrin repeat proteins (DARPins) as novel isoform-specific intracellular inhibitors of c-Jun N-terminal kinases. ACS Chem Biol 2012; 7:1356-66. [PMID: 22568706 DOI: 10.1021/cb3001167] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The c-Jun N-terminal kinases (JNKs) are involved in many biological processes such as proliferation, differentiation, apoptosis, and inflammation and occur in highly similar isoforms in eukaryotic cells. Isoform-specific functions and diseases have been reported for individual JNK isoforms mainly from gene-knockout studies in mice. There is, however, a high demand for intracellular inhibitors with high selectivity to improve the understanding of isoform-specific mechanisms and for use as therapeutic tools. The commonly used JNK inhibitors are based on small molecules or peptides that often target the conserved ATP binding site or docking sites and thus show only moderate selectivity. To target novel binding epitopes, we used designed ankyrin repeat proteins (DARPins) to generate alternative intracellular JNK inhibitors that discriminate two very similar isoforms, JNK1 and JNK2. DARPins are small binding proteins that are well expressed, stable, and cysteine-free, which makes them ideal candidates for applications in the reducing intracellular environment. We performed ribosome display selections against JNK1α1 and JNK2α1 using highly diverse combinatorial libraries of DARPins. The selected binders specifically recognize either JNK1 or JNK2 or both isoforms in vitro and in mammalian cells. All analyzed DARPins show affinities in the low nanomolar range and isoform-specific inhibition of JNK activation in vitro at physiological ATP concentrations. Importantly, DARPins that selectively inhibit JNK activation in human cells were also identified. These results emphasize the great potential of DARPins as a novel class of highly specific intracellular inhibitors of distinct enzyme isoforms for use in biological studies and as possible therapeutic leads.
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Affiliation(s)
- Petra Parizek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lutz Kummer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peter Rube
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Anke Prinz
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Friedrich W. Herberg
- Department of Biochemistry, University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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42
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Structural and functional analysis of phosphorylation-specific binders of the kinase ERK from designed ankyrin repeat protein libraries. Proc Natl Acad Sci U S A 2012; 109:E2248-57. [PMID: 22843676 DOI: 10.1073/pnas.1205399109] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have selected designed ankyrin repeat proteins (DARPins) from a synthetic library by using ribosome display that selectively bind to the mitogen-activated protein kinase ERK2 (extracellular signal-regulated kinase 2) in either its nonphosphorylated (inactive) or doubly phosphorylated (active) form. They do not bind to other kinases tested. Crystal structures of complexes with two DARPins, each specific for one of the kinase forms, were obtained. The two DARPins bind to essentially the same region of the kinase, but recognize the conformational change within the activation loop and an adjacent area, which is the key structural difference that occurs upon activation. Whereas the rigid phosphorylated activation loop remains in the same form when bound by the DARPin, the more mobile unphosphorylated loop is pushed to a new position. The DARPins can be used to selectively precipitate the cognate form of the kinases from cell lysates. They can also specifically recognize the modification status of the kinase inside the cell. By fusing the kinase with Renilla luciferase and the DARPin to GFP, an energy transfer from luciferase to GFP can be observed in COS-7 cells upon intracellular complex formation. Phosphorylated ERK2 is seen to increase by incubation of the COS-7 cells with FBS and to decrease upon adding the ERK pathway inhibitor PD98509. Furthermore, the anti-ERK2 DARPin is seen to inhibit ERK phosphorylation as it blocks the target inside the cell. This strategy of creating activation-state-specific sensors and kinase-specific inhibitors may add to the repertoire to investigate intracellular signaling in real time.
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43
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Abstract
Ribosome display has proven to be a powerful in vitro selection and evolution method for generating high-affinity binders from libraries of folded proteins. It has been successfully applied to single-chain Fv fragments of antibodies and alternative scaffolds, such as Designed Ankyrin Repeat Proteins (DARPins). High-affinity binders with new target specificity can be obtained from highly diverse DARPin libraries in only a few selection rounds. In this protocol, the selection from the library and the process of affinity maturation and off-rate selection are explained in detail.
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Affiliation(s)
- Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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44
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Abstract
Ribosome display is an in vitro evolution technology for proteins. It is based on in vitro translation, but prevents the newly synthesized protein and the mRNA encoding it from leaving the ribosome. It thereby couples phenotype and genotype. Since no cells need to be transformed, very large libraries can be used directly in selections, and the in vitro amplification provides a very convenient integration of random mutagenesis that can be incorporated into the procedure. This review highlights concepts, mechanisms, and different variations of ribosome display and compares it to related methods. Applications of ribosome display are summarized, e.g., the directed evolution of proteins for higher binding affinity, for higher stability or other improved biophysical parameters and enzymatic properties. Ribosome display has developed into a robust technology used in academia and industry alike, and it has made the cell-free Darwinian evolution of proteins over multiple generations a reality.
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Affiliation(s)
- Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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45
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46
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Boersma YL, Plückthun A. DARPins and other repeat protein scaffolds: advances in engineering and applications. Curr Opin Biotechnol 2011; 22:849-57. [DOI: 10.1016/j.copbio.2011.06.004] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/27/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
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47
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Miao Z, Levi J, Cheng Z. Protein scaffold-based molecular probes for cancer molecular imaging. Amino Acids 2011; 41:1037-47. [PMID: 20174842 PMCID: PMC2914822 DOI: 10.1007/s00726-010-0503-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 01/25/2010] [Indexed: 01/18/2023]
Abstract
Protein scaffold molecules are powerful reagents for targeting various cell signal receptors, enzymes, cytokines and other cancer-related molecules. They belong to the peptide and small protein platform with distinct properties. For the purpose of development of new generation molecular probes, various protein scaffold molecules have been labeled with imaging moieties and evaluated both in vitro and in vivo. Among the evaluated probes Affibody molecules and analogs, cystine knot peptides, and nanobodies have shown especially good characteristics as protein scaffold platforms for development of in vivo molecular probes. Quantitative data obtained from positron emission tomography, single photon emission computed tomography/CT, and optical imaging together with biodistribution studies have shown high tumor uptakes and high tumor-to-blood ratios for these probes. High tumor contrast imaging has been obtained within 1 h after injection. The success of those molecular probes demonstrates the adequacy of protein scaffold strategy as a general approach in molecular probe development.
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Affiliation(s)
- Zheng Miao
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, CA 94305-5344, USA
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48
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Petrovskaya LE, Shingarova LN, Dolgikh DA, Kirpichnikov MP. Alternative scaffold proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:581-91. [DOI: 10.1134/s1068162011050141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Bradbury ARM, Sidhu S, Dübel S, McCafferty J. Beyond natural antibodies: the power of in vitro display technologies. Nat Biotechnol 2011; 29:245-54. [PMID: 21390033 PMCID: PMC3057417 DOI: 10.1038/nbt.1791] [Citation(s) in RCA: 404] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In vitro display technologies, best exemplified by phage and yeast display, were first described for the selection of antibodies some 20 years ago. Since then, many antibodies have been selected and improved upon using these methods. Although it is not widely recognized, many of the antibodies derived using in vitro display methods have properties that would be extremely difficult, if not impossible, to obtain by immunizing animals. The first antibodies derived using in vitro display methods are now in the clinic, with many more waiting in the wings. Unlike immunization, in vitro display permits the use of defined selection conditions and provides immediate availability of the sequence encoding the antibody. The amenability of in vitro display to high-throughput applications broadens the prospects for their wider use in basic and applied research.
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50
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Designed ankyrin repeat protein binders for the crystallization of AcrB: plasticity of the dominant interface. J Struct Biol 2011; 174:269-81. [PMID: 21296164 DOI: 10.1016/j.jsb.2011.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/12/2011] [Accepted: 01/31/2011] [Indexed: 11/23/2022]
Abstract
The formation of well-diffracting crystals is a major bottleneck in structural analysis of membrane proteins by X-ray crystallography. One approach to improve crystal quality is the use of DARPins as crystallization chaperones. Here, we present a detailed analysis of the interaction between DARPins and the integral membrane protein AcrB. We find that binders selected in vitro by ribosome display share a common epitope. The comparative analysis of three crystal structures of AcrB-DARPin complexes allowed us to study the plasticity of the interaction with this dominant binding site. Seemingly redundant AcrB-DARPin crystals show substantially different diffraction quality as a result of subtle differences in the binding geometry. This work exemplifies the importance to screen a number of crystallization chaperones to obtain optimal diffraction data. Crystallographic analysis is complemented by biophysical characterization of nine AcrB binders. We observe that small variations in the interface can lead to differing behavior of the DARPins with regards to affinity, stoichiometry of the complexes and specificity for their target.
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