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Farhadi SA, Restuccia A, Sorrentino A, Cruz-Sánchez A, Hudalla GA. Heterogeneous protein co-assemblies with tunable functional domain stoichiometry. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2022; 7:44-57. [PMID: 35495737 PMCID: PMC9053397 DOI: 10.1039/d1me00083g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In nature, the precise heterogeneous co-assembly of different protein domains gives rise to supramolecular machines that perform complex functions through the co-integrated activity of the individual protein subunits. A synthetic approach capable of mimicking this process would afford access to supramolecular machines with new or improved functional capabilities. Here we show that the distinct peptide strands of a heterotrimeric α-helical coiled-coil (i.e., peptides "A", "B", and "C") can be used as fusion tags for heterogeneous co-assembly of proteins into supramolecular structures with tunable subunit stoichiometry. In particular, we demonstrate that recombinant fusion of A with NanoLuc luciferase (NL-A), B with superfolder green fluorescent protein (sfGFP-B), and C with mRuby (mRuby-C) enables formation of ternary complexes capable of simultaneously emitting blue, green, and red light via sequential bioluminescence and fluorescence resonance energy transfer (BRET/FRET). Fusion of galectin-3 onto the C-terminus of NL-A, sfGFP-B, and mRuby-C endows the ternary complexes with lactose-binding affinity that can be tuned by varying the number of galectin-3 domains integrated into the complex from one to three, while maintaining BRET/FRET function. The modular nature of the fusion protein design, the precise control of domain stoichiometry, and the multiplicity afforded by the three-stranded coiled-coil scaffold provides access to a greater range of subunit combinations than what is possible with heterodimeric coiled-coils used previously. We envision that access to this expanded range of co-integrated protein domain diversity will be advantageous for future development of designer supramolecular machines for therapeutic, diagnostic, and biotechnology applications.
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Affiliation(s)
- Shaheen A. Farhadi
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Antonietta Restuccia
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Anthony Sorrentino
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Andrés Cruz-Sánchez
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Gregory A. Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, 32611, USA
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Cooke HA, Arndt J, Quan C, Shapiro RI, Wen D, Foley S, Vecchi MM, Preyer M. EFab domain substitution as a solution to the light-chain pairing problem of bispecific antibodies. MAbs 2018; 10:1248-1259. [PMID: 30215570 PMCID: PMC6284599 DOI: 10.1080/19420862.2018.1519631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bispecific antibody therapeutics can expand the functionality of a conventional monoclonal antibody drug because they can bind multiple antigens. However, their great potential is counterbalanced by the challenges faced in their production. The classic asymmetric bispecific containing an Fc requires the expression of four unique chains – two light chains and two heavy chains; each light chain must pair with its correct heavy chain, which then must heterodimerize to form the full bispecific. The light-chain pairing problem has several solutions, some of which require engineering and optimization for each bispecific pair. Here, we introduce a technology called EFab Domain Substitution, which replaces the Cϵ2 of IgE for one of the CL/CH1 domains into one arm of an asymmetric bispecific to encourage the correct pairing of the light chains. EFab Domain Substitution provides very robust correct pairing while maintaining antibody function and is effective for many variable domains. We report its effect on the biophysical properties of an antibody and the crystal structure of the EFab domain substituted into the adalimumab Fab (PDB ID 6CR1).
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Affiliation(s)
- Heather A Cooke
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
| | - Joe Arndt
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
| | - Chao Quan
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
| | - Renée I Shapiro
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
| | - Dingyi Wen
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
| | - Susan Foley
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
| | - Malgorzata M Vecchi
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
| | - Martin Preyer
- a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA
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Hou P, Zhao G, He C, Wang H, He H. Biopanning of polypeptides binding to bovine ephemeral fever virus G 1 protein from phage display peptide library. BMC Vet Res 2018; 14:3. [PMID: 29301517 PMCID: PMC5753476 DOI: 10.1186/s12917-017-1315-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 12/07/2017] [Indexed: 11/30/2022] Open
Abstract
Background The bovine ephemeral fever virus (BEFV) glycoprotein neutralization site 1 (also referred as G1 protein), is a critical protein responsible for virus infectivity and eliciting immune-protection, however, binding peptides of BEFV G1 protein are still unclear. Thus, the aim of the present study was to screen specific polypeptides, which bind BEFV G1 protein with high-affinity and inhibit BEFV replication. Methods The purified BEFV G1 was coated and then reacted with the M13-based Ph.D.-7 phage random display library. The peptides for target binding were automated sequenced after four rounds of enrichment biopanning. The amino acid sequences of polypeptide displayed on positive clones were deduced and the affinity of positive polypeptides with BEFV G1 was assayed by ELISA. Then the roles of specific G1-binding peptides in the context of BEFV infection were analyzed. Results The results showed that 27 specific peptide ligands displaying 11 different amino acid sequences were obtained, and the T18 and T25 clone had a higher affinity to G1 protein than the other clones. Then their antiviral roles of two phage clones (T25 and T18) showed that both phage polypeptide T25 and T18 exerted inhibition on BEFV replication compared to control group. Moreover, synthetic peptide based on T18 (HSIRYDF) and T25 (YSLRSDY) alone or combined use on BEFV replication showed that the synthetic peptides could effectively inhibit the formation of cytopathic plaque and significantly inhibit BEFV RNA replication in a dose-dependent manner. Conclusion Two antiviral peptide ligands binding to bovine ephemeral fever virus G1 protein from phage display peptide library were identified, which may provide a potential research tool for diagnostic reagents and novel antiviral agents. Electronic supplementary material The online version of this article (10.1186/s12917-017-1315-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peili Hou
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Disease Research Center, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan City, Shandong Province, China
| | - Guimin Zhao
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Disease Research Center, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan City, Shandong Province, China
| | - Chengqiang He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Disease Research Center, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan City, Shandong Province, China
| | - Hongmei Wang
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Disease Research Center, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan City, Shandong Province, China.
| | - Hongbin He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Disease Research Center, College of Life Sciences, Shandong Normal University, No. 88 East Wenhua Road, Jinan City, Shandong Province, China.
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Arimori T, Kitago Y, Umitsu M, Fujii Y, Asaki R, Tamura-Kawakami K, Takagi J. Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability. Structure 2017; 25:1611-1622.e4. [PMID: 28919443 DOI: 10.1016/j.str.2017.08.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/22/2017] [Accepted: 08/15/2017] [Indexed: 12/13/2022]
Abstract
Antibody fragments are frequently used as a "crystallization chaperone" to aid structural analysis of complex macromolecules that are otherwise crystallization resistant, but conventional fragment formats have not been designed for this particular application. By fusing an anti-parallel coiled-coil structure derived from the SARAH domain of human Mst1 kinase to the variable region of an antibody, we succeeded in creating a novel chimeric antibody fragment of ∼37 kDa, termed "Fv-clasp," which exhibits excellent crystallization compatibility while maintaining the binding ability of the original IgG molecule. The "clasp" and the engineered disulfide bond at the bottom of the Fv suppressed the internal mobility of the fragment and shielded hydrophobic residues, likely contributing to the high heat stability and the crystallizability of the Fv-clasp. Finally, Fv-clasp antibodies showed superior "chaperoning" activity over conventional Fab fragments, and facilitated the structure determination of an ectodomain fragment of integrin α6β1.
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Affiliation(s)
- Takao Arimori
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yu Kitago
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masataka Umitsu
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuki Fujii
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ryoko Asaki
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | | | - Junichi Takagi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
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Antibody affinity maturation through combining display of two-chain paired antibody and precision flow cytometric sorting. Appl Microbiol Biotechnol 2016; 100:5977-88. [DOI: 10.1007/s00253-016-7472-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 03/13/2016] [Accepted: 03/15/2016] [Indexed: 01/09/2023]
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The Next Generation of Biomarker Research in Spinal Cord Injury. Mol Neurobiol 2016; 54:1482-1499. [DOI: 10.1007/s12035-016-9757-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/26/2016] [Indexed: 12/14/2022]
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Antibody phage display libraries: contributions to oncology. Int J Mol Sci 2012; 13:5420-5440. [PMID: 22754305 PMCID: PMC3382779 DOI: 10.3390/ijms13055420] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 04/05/2012] [Accepted: 04/24/2012] [Indexed: 12/16/2022] Open
Abstract
Since the advent of phage display technology, dating back to 1985, antibody libraries displayed on filamentous phage surfaces have been used to identify specific binders for many different purposes, including the recognition of tumors. Phage display represents a high-throughput technique for screening billions of random fusion antibodies against virtually any target on the surface or inside cancer cells, or even soluble markers found in patient serum. Many phage display derived binders targeting important tumor markers have been identified. Selection directed to tumoral cells’ surfaces lead to the identification of unknown tumoral markers. Also the improvement of methods that require smaller amounts of cells has opened the possibility to use this approach on patient samples. Robust techniques combining an antibody library displayed on the phage surface and protein microarray allowed the identification of auto antibodies recognized by patient sera. Many Ab molecules directly or indirectly targeting angiogenesis have been identified, and one of them, ramucirumab, has been tested in 27 phase I–III clinical trials in a broad array of cancers. Examples of such antibodies will be discussed here with emphasis on those used as probes for molecular imaging and other clinical trials.
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