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Radom F, Vonrhein C, Mittl PRE, Plückthun A. Crystal structures of HER3 extracellular domain 4 in complex with the designed ankyrin-repeat protein D5. Acta Crystallogr F Struct Biol Commun 2021; 77:192-201. [PMID: 34196609 PMCID: PMC8248824 DOI: 10.1107/s2053230x21006002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/09/2021] [Indexed: 11/10/2022] Open
Abstract
The members of the human epidermal growth factor receptor (HER) family are among the most intensely studied oncological targets. HER3 (ErbB3), which had long been neglected, has emerged as a key oncogene, regulating the activity of other receptors and being involved in progression and tumor escape in multiple types of cancer. Designed ankyrin-repeat proteins (DARPins) serve as antibody mimetics that have proven to be useful in the clinic, in diagnostics and in research. DARPins have previously been selected against EGFR (HER1), HER2 and HER4. In particular, their combination into bivalent binders that separate or lock receptors in their inactive conformation has proved to be a promising strategy for the design of potent anticancer therapeutics. Here, the selection of DARPins targeting extracellular domain 4 of HER3 (HER3d4) is described. One of the selected DARPins, D5, in complex with HER3d4 crystallized in two closely related crystal forms that diffracted to 2.3 and 2.0 Å resolution, respectively. The DARPin D5 epitope comprises HER3d4 residues 568-577. These residues also contribute to interactions within the tethered (inactive) and extended (active) conformations of the extracellular domain of HER3.
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Affiliation(s)
- Filip Radom
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Clemens Vonrhein
- Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX, United Kingdom
| | - Peer R. E. Mittl
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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2
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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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3
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Tušar L, Usenik A, Turk B, Turk D. Mechanisms Applied by Protein Inhibitors to Inhibit Cysteine Proteases. Int J Mol Sci 2021; 22:997. [PMID: 33498210 PMCID: PMC7863939 DOI: 10.3390/ijms22030997] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 02/07/2023] Open
Abstract
Protein inhibitors of proteases are an important tool of nature to regulate and control proteolysis in living organisms under physiological and pathological conditions. In this review, we analyzed the mechanisms of inhibition of cysteine proteases on the basis of structural information and compiled kinetic data. The gathered structural data indicate that the protein fold is not a major obstacle for the evolution of a protease inhibitor. It appears that nature can convert almost any starting fold into an inhibitor of a protease. In addition, there appears to be no general rule governing the inhibitory mechanism. The structural data make it clear that the "lock and key" mechanism is a historical concept with limited validity. However, the analysis suggests that the shape of the active site cleft of proteases imposes some restraints. When the S1 binding site is shaped as a pocket buried in the structure of protease, inhibitors can apply substrate-like binding mechanisms. In contrast, when the S1 binding site is in part exposed to solvent, the substrate-like inhibition cannot be employed. It appears that all proteases, with the exception of papain-like proteases, belong to the first group of proteases. Finally, we show a number of examples and provide hints on how to engineer protein inhibitors.
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Affiliation(s)
- Livija Tušar
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Aleksandra Usenik
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Faculty of Chemistry, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
- Institute of Regenerative Medicine, I.M. Sechenov First Moscow State Medical University, Bol’shaya Pirogovskaya Ulitsa, 19c1, 119146 Moscow, Russia
| | - Dušan Turk
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; (L.T.); (A.U.); (B.T.)
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova cesta 39, 1000 Ljubljana, Slovenia
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4
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Pham B, Eron SJ, Hill ME, Li X, Fahie MA, Hardy JA, Chen M. A Nanopore Approach for Analysis of Caspase-7 Activity in Cell Lysates. Biophys J 2019; 117:844-855. [PMID: 31427065 PMCID: PMC6731459 DOI: 10.1016/j.bpj.2019.07.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 07/02/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
Caspases are an important protease family that coordinate inflammation and programmed cell death. Two closely related caspases, caspase-3 and caspase-7, exhibit largely overlapping substrate specificities. Assessing their proteolytic activities individually has therefore proven extremely challenging. Here, we constructed an outer membrane protein G (OmpG) nanopore with a caspase substrate sequence DEVDG grafted into one of the OmpG loops. Cleavage of the substrate sequence in the nanopore by caspase-7 generated a characteristic signal in the current recording of the OmpG nanopore that allowed the determination of the activity of caspase-7 in Escherichia coli cell lysates. Our approach may provide a framework for the activity-based profiling of proteases that share highly similar substrate specificity spectrums.
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Affiliation(s)
- Bach Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Scott J Eron
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Maureen E Hill
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Xin Li
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Monifa A Fahie
- Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Jeanne A Hardy
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Min Chen
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts; Molecular and Cellular Biology Program, University of Massachusetts Amherst, Amherst, Massachusetts.
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5
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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: 22] [Impact Index Per Article: 4.4] [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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6
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Martin HL, Bedford R, Heseltine SJ, Tang AA, Haza KZ, Rao A, McPherson MJ, Tomlinson DC. Non-immunoglobulin scaffold proteins: Precision tools for studying protein-protein interactions in cancer. N Biotechnol 2018; 45:28-35. [DOI: 10.1016/j.nbt.2018.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/08/2018] [Accepted: 02/18/2018] [Indexed: 02/08/2023]
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7
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DeRosa JR, Moyer BS, Lumen E, Wolfe AJ, Sleeper MB, Bianchi AH, Crawford A, McGuigan C, Wortel D, Fisher C, Moody KJ, Blanden AR. RPtag as an Orally Bioavailable, Hyperstable Epitope Tag and Generalizable Protein Binding Scaffold. Biochemistry 2018; 57:3036-3049. [PMID: 29722979 DOI: 10.1021/acs.biochem.8b00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibodies are the most prolific biologics in research and clinical environments because of their ability to bind targets with high affinity and specificity. However, antibodies also carry liabilities. A significant portion of the life-science reproducibility crisis is driven by inconsistent performance of research-grade antibodies, and clinical antibodies are often unstable and require costly cold-chain management to reach their destinations in active form. In biotechnology, antibodies are also limited by difficulty integrating them in many recombinant systems due to their size and structural complexity. A switch to small, stable, sequence-verified binding scaffolds may overcome these barriers. Here we present such a scaffold, RPtag, based on a ribose-binding protein (RBP) from extremophile Caldanaerobacter subterraneus. RPtag binds an optimized peptide with pM affinity, is stable to extreme temperature, pH, and protease treatment, readily refolds after denaturation, is effective in common laboratory applications, was rationally engineered to bind bioactive PDGF-β, and was formulated as a gut-stable orally bioavailable preparation.
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Affiliation(s)
- Jennifer R DeRosa
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Brandon S Moyer
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ellie Lumen
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Aaron J Wolfe
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Meegan B Sleeper
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Anthony H Bianchi
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ashleigh Crawford
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Connor McGuigan
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Danique Wortel
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Cheyanne Fisher
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Kelsey J Moody
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Adam R Blanden
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
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8
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Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics. Methods Mol Biol 2018; 1798:307-327. [PMID: 29868969 DOI: 10.1007/978-1-4939-7893-9_23] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.
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9
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Islam Z, Nagampalli RSK, Fatima MT, Ashraf GM. New paradigm in ankyrin repeats: Beyond protein-protein interaction module. Int J Biol Macromol 2017; 109:1164-1173. [PMID: 29157912 DOI: 10.1016/j.ijbiomac.2017.11.101] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/13/2017] [Accepted: 11/16/2017] [Indexed: 01/06/2023]
Abstract
Classically, ankyrin repeat (ANK) proteins are built from tandems of two or more repeats and form curved solenoid structures that are associated with protein-protein interactions. These are short, widespread structural motif of around 33 amino acids repeats in tandem, having a canonical helix-loop-helix fold, found individually or in combination with other domains. The multiplicity of structural pattern enables it to form assemblies of diverse sizes, required for their abilities to confer multiple binding and structural roles of proteins. Three-dimensional structures of these repeats determined to date reveal a degree of structural variability that translates into the considerable functional versatility of this protein superfamily. Recent work on the ANK has proposed novel structural information, especially protein-lipid, protein-sugar and protein-protein interaction. Self-assembly of these repeats was also shown to prevent the associated protein in forming filaments. In this review, we summarize the latest findings and how the new structural information has increased our understanding of the structural determinants of ANK proteins. We discussed latest findings on how these proteins participate in various interactions to diversify the ANK roles in numerous biological processes, and explored the emerging and evolving field of designer ankyrins and its framework for protein engineering emphasizing on biotechnological applications.
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Affiliation(s)
- Zeyaul Islam
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, 13083-100, Brazil.
| | | | - Munazza Tamkeen Fatima
- Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas, SP, 13083-862, Brazil
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah, 21589, Saudi Arabia.
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10
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Insight into the mechanism of action and selectivity of caspase-3 reversible inhibitors through in silico studies. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.06.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci 2017; 26:910-924. [PMID: 28249355 PMCID: PMC5405424 DOI: 10.1002/pro.3148] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/20/2023]
Abstract
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in‐depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016.,Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY, 10016
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12
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Skotte NH, Sanders SS, Singaraja RR, Ehrnhoefer DE, Vaid K, Qiu X, Kannan S, Verma C, Hayden MR. Palmitoylation of caspase-6 by HIP14 regulates its activation. Cell Death Differ 2017; 24:433-444. [PMID: 27911442 PMCID: PMC5344205 DOI: 10.1038/cdd.2016.139] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/03/2016] [Accepted: 10/25/2016] [Indexed: 02/06/2023] Open
Abstract
Caspase-6 (CASP6) has an important role in axonal degeneration during neuronal apoptosis and in the neurodegenerative diseases Alzheimer and Huntington disease. Decreasing CASP6 activity may help to restore neuronal function in these and other diseases such as stroke and ischemia, where increased CASP6 activity has been implicated. The key to finding approaches to decrease CASP6 activity is a deeper understanding of the mechanisms regulating CASP6 activation. We show that CASP6 is posttranslationally palmitoylated by the palmitoyl acyltransferase HIP14 and that the palmitoylation of CASP6 inhibits its activation. Palmitoylation of CASP6 is decreased both in Hip14-/- mice, where HIP14 is absent, and in YAC128 mice, a model of Huntington disease, where HIP14 is dysfunctional and where CASP6 activity is increased. Molecular modeling suggests that palmitoylation of CASP6 may inhibit its activation via steric blockage of the substrate-binding groove and inhibition of CASP6 dimerization, both essential for CASP6 function. Our studies identify palmitoylation as a novel CASP6 modification and as a key regulator of CASP6 activity.
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Affiliation(s)
- Niels H Skotte
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Shaun S Sanders
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Roshni R Singaraja
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Medicine at Yong Loo Lin School of Medicine, National University of Singapore, Singapore 138648, Singapore
| | - Dagmar E Ehrnhoefer
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kuljeet Vaid
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Xiaofan Qiu
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Srinivasaragavan Kannan
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science, Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
- School of Biological Sciences, Nanyang Technological University, 50 Nanyang Drive, Singapore 637551, Singapore
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Translational Laboratories in Genetic Medicine, Agency for Science, Technology and Research, Singapore, Singapore
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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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14
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Abstract
The role of caspase proteases in regulated processes such as apoptosis and inflammation has been studied for more than two decades, and the activation cascades are known in detail. Apoptotic caspases also are utilized in critical developmental processes, although it is not known how cells maintain the exquisite control over caspase activity in order to retain subthreshold levels required for a particular adaptive response while preventing entry into apoptosis. In addition to active site-directed inhibitors, caspase activity is modulated by post-translational modifications or metal binding to allosteric sites on the enzyme, which stabilize inactive states in the conformational ensemble. This review provides a comprehensive global view of the complex conformational landscape of caspases and mechanisms used to select states in the ensemble. The caspase structural database provides considerable detail on the active and inactive conformations in the ensemble, which provide the cell multiple opportunities to fine tune caspase activity. In contrast, the current database on caspase modifications is largely incomplete and thus provides only a low-resolution picture of global allosteric communications and their effects on the conformational landscape. In recent years, allosteric control has been utilized in the design of small drug compounds or other allosteric effectors to modulate caspase activity.
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Affiliation(s)
- A Clay Clark
- Department of Biology, University of Texas at Arlington , Arlington, Texas 76019, United States
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15
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Poreba M, Szalek A, Kasperkiewicz P, Rut W, Salvesen GS, Drag M. Small Molecule Active Site Directed Tools for Studying Human Caspases. Chem Rev 2015; 115:12546-629. [PMID: 26551511 DOI: 10.1021/acs.chemrev.5b00434] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Caspases are proteases of clan CD and were described for the first time more than two decades ago. They play critical roles in the control of regulated cell death pathways including apoptosis and inflammation. Due to their involvement in the development of various diseases like cancer, neurodegenerative diseases, or autoimmune disorders, caspases have been intensively investigated as potential drug targets, both in academic and industrial laboratories. This review presents a thorough, deep, and systematic assessment of all technologies developed over the years for the investigation of caspase activity and specificity using substrates and inhibitors, as well as activity based probes, which in recent years have attracted considerable interest due to their usefulness in the investigation of biological functions of this family of enzymes.
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Affiliation(s)
- Marcin Poreba
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Szalek
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paulina Kasperkiewicz
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Wioletta Rut
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Guy S Salvesen
- Program in Cell Death and Survival Networks, Sanford Burnham Prebys Medical Discovery Institute , La Jolla, California 92037, United States
| | - Marcin Drag
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Technology , Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland
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16
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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: 406] [Impact Index Per Article: 45.1] [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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17
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Liao X, Rabideau AE, Pentelute BL. Delivery of antibody mimics into mammalian cells via anthrax toxin protective antigen. Chembiochem 2014; 15:2458-66. [PMID: 25250705 PMCID: PMC4498471 DOI: 10.1002/cbic.201402290] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Indexed: 11/06/2022]
Abstract
Antibody mimics have significant scientific and therapeutic utility for the disruption of protein-protein interactions inside cells; however, their delivery to the cell cytosol remains a major challenge. Here we show that protective antigen (PA), a component of anthrax toxin, efficiently transports commonly used antibody mimics to the cytosol of mammalian cells when conjugated to the N-terminal domain of LF (LFN). In contrast, a cell-penetrating peptide (CPP) was not able to deliver any of these antibody mimics into the cell cytosol. The refolding and binding of a transported tandem monobody to Bcr-Abl (its protein target) in chronic myeloid leukemia cells were confirmed by co-immunoprecipitation. We also observed inhibition of Bcr-Abl kinase activity and induction of apoptosis caused by the monobody. In a separate case, we show disruption of key interactions in the MAPK signaling pathway after PA-mediated delivery of an affibody binder that targets hRaf-1. We show for the first time that PA can deliver bioactive antibody mimics to disrupt intracellular protein-protein interactions. This technology adds a useful tool to expand the applications of these modern agents to the intracellular milieu.
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Affiliation(s)
- Xiaoli Liao
- Department of Chemistry, Massachusetts Institute of Technology77 Massachusetts Avenue 18-596, Cambridge, MA 02193 (USA) E-mail:
| | - Amy E Rabideau
- Department of Chemistry, Massachusetts Institute of Technology77 Massachusetts Avenue 18-596, Cambridge, MA 02193 (USA) E-mail:
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology77 Massachusetts Avenue 18-596, Cambridge, MA 02193 (USA) E-mail:
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18
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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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Mong SK, Vinogradov AA, Simon MD, Pentelute BL. Rapid total synthesis of DARPin pE59 and barnase. Chembiochem 2014; 15:721-33. [PMID: 24616257 DOI: 10.1002/cbic.201300797] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Indexed: 11/11/2022]
Abstract
We report the convergent total synthesis of two proteins: DARPin pE59 and Bacillus amyloliquefaciens RNase (Barnase). Leveraging our recently developed fast-flow peptide-synthesis platform, we rapidly explored numerous conditions for the assembly of long polypeptides, and were able to mitigate common side reactions, including deletion and aspartimide products. We report general strategies for improving the synthetic quality of difficult peptide sequences with our system. High-quality protein fragments produced under optimal synthetic conditions were subjected to convergent native chemical ligation, which afforded native full-length proteins after a final desulfurization step. Both DARPin and Barnase were folded and found to be as active as their recombinant analogues.
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Affiliation(s)
- Surin K Mong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
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20
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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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21
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New concepts and aids to facilitate crystallization. Curr Opin Struct Biol 2013; 23:409-16. [PMID: 23578532 DOI: 10.1016/j.sbi.2013.03.003] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 03/08/2013] [Accepted: 03/13/2013] [Indexed: 12/20/2022]
Abstract
Novel tools and technologies are required to obtain structural information of difficult to crystallize complex biological systems such as membrane proteins, multiprotein assemblies, transient conformational states and intrinsically disordered proteins. One promising approach is to select a high affinity and specificity-binding partner (crystallization chaperone), form a complex with the protein of interest and crystallize the complex. Often the chaperone reduces the conformational freedom of the target protein and additionally facilitates the formation of well-ordered crystals. This review provides an update on the recent successes in chaperone-assisted crystallography. We also stress the importance of synergistic approaches involving protein engineering, crystallization chaperones and crystallization additives. Recent examples demonstrate that investment in such approaches can be key to success.
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