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Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu S, Kossiakoff A, Wells J. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Mol Cell Proteomics 2015; 14:2833-47. [PMID: 26290498 PMCID: PMC4597156 DOI: 10.1074/mcp.o115.052209] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 01/09/2023] Open
Abstract
Antibodies are key reagents in biology and medicine, but commercial sources are rarely recombinant and thus do not provide a permanent and renewable resource. Here, we describe an industrialized platform to generate antigens and validated recombinant antibodies for 346 transcription factors (TFs) and 211 epigenetic antigens. We describe an optimized automated phage display and antigen expression pipeline that in aggregate produced about 3000 sequenced Fragment antigen-binding domain that had high affinity (typically EC50<20 nm), high stability (Tm∼80 °C), good expression in E. coli (∼5 mg/L), and ability to bind antigen in complex cell lysates. We evaluated a subset of Fabs generated to homologous SCAN domains for binding specificities. These Fragment antigen-binding domains were monospecific to their target SCAN antigen except in rare cases where they cross-reacted with a few highly related antigens. Remarkably, immunofluorescence experiments in six cell lines for 270 of the TF antigens, each having multiple antibodies, show that ∼70% stain predominantly in the cytosol and ∼20% stain in the nucleus which reinforces the dominant role that translocation plays in TF biology. These cloned antibody reagents are being made available to the academic community through our web site recombinant-antibodies.org to allow a more system-wide analysis of TF and chromatin biology. We believe these platforms, infrastructure, and automated approaches will facilitate the next generation of renewable antibody reagents to the human proteome in the coming decade.
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Affiliation(s)
- Michael Hornsby
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Marcin Paduch
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Shane Miersch
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Annika Sääf
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Tet Matsuguchi
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Brian Lee
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Karolina Wypisniak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Allison Doak
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158
| | - Daniel King
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Svitlana Usatyuk
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Kimberly Perry
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Vince Lu
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - William Thomas
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Judy Luke
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jay Goodman
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Robert J Hoey
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Darson Lai
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Carly Griffin
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Zhijian Li
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Franco J Vizeacoumar
- **Saskatchewan Cancer Agency, University of Saskatchewan, Saskatoon, S7N 4H4, Canada
| | - Debbie Dong
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Elliot Campbell
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Stephen Anderson
- ‖Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
| | - Nan Zhong
- ‡‡Structural Genomics Consortium, Toronto, M5G Il7, Canada
| | | | - Shohei Koide
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637
| | - Jason Moffat
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada
| | - Sachdev Sidhu
- ¶Donnelly Center for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, Toronto, MG5 1L6, Canada;
| | - Anthony Kossiakoff
- §Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637;
| | - James Wells
- From the ‡Department of Pharmaceutical Chemistry University of California, San Francisco, California 94158;
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Pershad K, Wypisniak K, Kay BK. Directed evolution of the forkhead-associated domain to generate anti-phosphospecific reagents by phage display. J Mol Biol 2012; 424:88-103. [PMID: 22985966 DOI: 10.1016/j.jmb.2012.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Revised: 08/10/2012] [Accepted: 09/05/2012] [Indexed: 10/27/2022]
Abstract
While affinity reagents are valuable tools for monitoring protein phosphorylation and studying signaling events in cells, generating them through immunization of animals with phosphopeptides is expensive, laborious, and time-consuming. An attractive alternative is to use protein evolution techniques and isolate new anti-phosphopeptide binding specificities from a library of variants of a phosphopeptide-binding domain. To explore this strategy, we attempted to display on the surface of bacteriophage M13 the N-terminal Forkhead-associated (FHA1) domain of yeast Rad53p, which is a naturally occurring phosphothreonine (pT)-binding domain, and found it to be nonfunctional due to misfolding in the bacterial periplasm. To overcome this limitation, we constructed a library of FHA1 variants by mutagenic PCR and isolated functional variants after three rounds of affinity selection with its pT peptide ligand. A hydrophobic residue at position 34 in the β1 strand was discovered to be essential for phage display of a functional FHA1 domain. Additionally, by heating the phage library to 50°C prior to affinity selection with its cognate pT peptide, we identified a variant (G2) that was ~8°C more thermally stable than the wild-type domain. Using G2 as a scaffold, we constructed phage-displayed libraries of FHA1 variants and affinity selected for variants that bound selectively to five pT peptides. These reagents are renewable and have high protein yields (~20-25mg/L), when expressed in Escherichia coli. Thus, we have changed the specificity of the FHA1 domain and demonstrated that engineering phosphopeptide-binding domains is an attractive avenue for generating new anti-phosphopeptide binding specificities in vitro by phage display.
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Affiliation(s)
- Kritika Pershad
- Department of Biological Sciences, Laboratory for Molecular Biology (M/C 567), University of Illinois at Chicago, Molecular Biology Research Building, Chicago, IL 60607, USA.
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