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Koszela J, Pham NT, Shave S, St-Cyr D, Ceccarelli DF, Orlicky S, Marinier A, Sicheri F, Tyers M, Auer M. A Novel Confocal Scanning Protein-Protein Interaction Assay (PPI-CONA) Reveals Exceptional Selectivity and Specificity of CC0651, a Small Molecule Binding Enhancer of the Weak Interaction between the E2 Ubiquitin-Conjugating Enzyme CDC34A and Ubiquitin. Bioconjug Chem 2024; 35:1441-1449. [PMID: 39167708 PMCID: PMC11417995 DOI: 10.1021/acs.bioconjchem.4c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]
Abstract
Protein-protein interactions (PPIs) are some of the most challenging target classes in drug discovery. Highly sensitive detection techniques are required for the identification of chemical modulators of PPIs. Here, we introduce PPI confocal nanoscanning (PPI-CONA), a miniaturized, microbead based high-resolution fluorescence imaging assay. We demonstrate the capabilities of PPI-CONA by detecting low affinity ternary complex formation between the human CDC34A ubiquitin-conjugating (E2) enzyme, ubiquitin, and CC0651, a small molecule enhancer of the CDC34A-ubiquitin interaction. We further exemplify PPI-CONA with an E2 enzyme binding study on CC0651 and a CDC34A binding specificity study of a series of CC0651 analogues. Our results indicate that CC0651 is highly selective toward CDC34A. We further demonstrate how PPI-CONA can be applied to screening very low affinity interactions. PPI-CONA holds potential for high-throughput screening for modulators of PPI targets and characterization of their affinity, specificity, and selectivity.
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Affiliation(s)
- Joanna Koszela
- School
of Molecular Biosciences, University of
Glasgow, Glasgow G12 8QQ, U.K.
| | - Nhan T. Pham
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
- College
of Medicine and Veterinary Medicine, Institute for Regeneration and
Repair, University of Edinburgh, 4-5 Little France Drive, Edinburgh EH16 4UU, U.K.
| | - Steven Shave
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
- Edinburgh
Cancer Research, Cancer Research UK Scotland Centre, Institute of
Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, U.K.
| | - Daniel St-Cyr
- X-Chem
Inc., Montréal, Québec H4S 1Z9, Canada
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Derek F. Ceccarelli
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Steven Orlicky
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Anne Marinier
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
| | - Frank Sicheri
- Centre
for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Mike Tyers
- Institute
for Research in Immunology and Cancer, University
of Montreal, Montreal, Québec H3T 1J4, Canada
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Manfred Auer
- School
of Biological Sciences, University of Edinburgh, Edinburgh, Scotland EH9 3BF, U.K.
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Smekenov I, Alybayev S, Ayupov T, Rakhmatullaeva G, Bissenbaev A. A polyclonal antibody against a recombinantly expressed Triticum aestivum RHT-D1A protein. J Genet Eng Biotechnol 2020; 18:52. [PMID: 32936364 PMCID: PMC7494718 DOI: 10.1186/s43141-020-00072-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/08/2020] [Indexed: 02/06/2023]
Abstract
Background Reduced height-1 dwarfing alleles affect DELLA proteins belonging to a family of putative transcriptional regulators that modulate plant growth and development. The Arabidopsis thaliana genome encodes five DELLA proteins, whereas monocot plants, such as rice, barley, and wheat, each have a single DELLA protein. In wheat, wild-type Rht-B1a and Rht-D1a genes encode DELLA proteins and have many alleles that contain lesions. Among them, Rht-B1b and Rht-D1b are the most common mutant dwarfing alleles, which have played a key part in the creation of high-yielding wheat varieties. Despite their fundamental roles in plant biology, until now, DELLA proteins in wheat have been mainly researched regarding the phenotypic effect of defective Rht mutants on yield-related traits, without studies on the underlying mechanisms. The RHT-1 protein has yet to be detected in wheat tissues, owing to a lack of appropriate molecular tools for characterization of RHT function and protein interactions in signal transduction. This study is focused on the production of a polyclonal antibody to the wheat RHT-D1A protein. Results To generate the anti-RHT-D1A antibody, we expressed and purified soluble 6xHis-tagged RHT-D1A. The purified recombinant RHT-D1A was injected into New Zealand white rabbits to generate polyclonal antiserum. The polyclonal anti-RHT-D1A antibody was purified by ammonium sulfate precipitation, followed by affinity chromatography on protein A–agarose beads. The purified polyclonal antibody was demonstrated to be effective in immunoblotting, western blot hybridization, and immunoprecipitation. In wheat seedling extracts, the polyclonal antibody recognized a protein with a molecular mass close to the predicted molecular weight of the endogenous RHT-D1A protein. We also demonstrated that RHT-D1A disappears in response to exogenous and endogenous gibberellic acid. Conclusion The purified polyclonal antibody raised against the recombinant RHT-D1A protein is sufficiently specific and sensitive and could be a useful tool for future insights into upstream and downstream components of DELLA-regulatory mechanisms in wheat plants.
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Affiliation(s)
- Izat Smekenov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Sanzhar Alybayev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Temurkhan Ayupov
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Guliza Rakhmatullaeva
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040
| | - Amangeldy Bissenbaev
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040. .,Scientific Research Institute of Biology and Biotechnology Problems, al-Farabi Kazakh National University, Almaty, Kazakhstan, 050040.
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Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D, Burns KH, LaCava J. LINE-1 ORF2p expression is nearly imperceptible in human cancers. Mob DNA 2019; 11:1. [PMID: 31892958 PMCID: PMC6937734 DOI: 10.1186/s13100-019-0191-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. RESULTS We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. CONCLUSIONS Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth.
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Affiliation(s)
- Daniel Ardeljan
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Xuya Wang
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Martin S. Taylor
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - David Husband
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Jared P. Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Mikhail Gorbounov
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Brandon Sie
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - H. Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065 USA
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Zhi Li
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Wilson McKerrow
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - David Fenyö
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Kathleen H. Burns
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, 9713 AV The Netherlands
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5
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Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods 2018; 15:330-338. [PMID: 29638227 PMCID: PMC6063793 DOI: 10.1038/nmeth.4632] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 01/25/2018] [Indexed: 01/08/2023]
Abstract
A key component of efforts to address the reproducibility crisis in biomedical research is the development of rigorously validated and renewable protein-affinity reagents. As part of the US National Institutes of Health (NIH) Protein Capture Reagents Program (PCRP), we have generated a collection of 1,406 highly validated immunoprecipitation- and/or immunoblotting-grade mouse monoclonal antibodies (mAbs) to 737 human transcription factors, using an integrated production and validation pipeline. We used HuProt human protein microarrays as a primary validation tool to identify mAbs with high specificity for their cognate targets. We further validated PCRP mAbs by means of multiple experimental applications, including immunoprecipitation, immunoblotting, chromatin immunoprecipitation followed by sequencing (ChIP-seq), and immunohistochemistry. We also conducted a meta-analysis that identified critical variables that contribute to the generation of high-quality mAbs. All validation data, protocols, and links to PCRP mAb suppliers are available at http://proteincapture.org.
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Affiliation(s)
- Anand Venkataraman
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kun Yang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Paolo Mita
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zheng Kuang
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Lin Xue
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Devlina Ghosh
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shuang Liu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Sarah Keegan
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Richard Saul
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Hongyan Zhang
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Guang Song
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jessica McDade
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian S Clark
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sooyeon Yoo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seva G Khambadkone
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jimmy de Melo
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Milanka Stevanovic
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lizhi Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Atul Tandon
- NeoBiotechnologies, Inc., Union City, California, USA
| | - Elliot Campbell
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Stephen Anderson
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA.,Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Jef D Boeke
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Fenyö
- Institute for System Genetics, NYU Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York, USA
| | - Gordon Whiteley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Heng Zhu
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Center for Human Systems Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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