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Sana B, Chee SMQ, Wongsantichon J, Raghavan S, Robinson RC, Ghadessy FJ. Development and structural characterization of an engineered multi-copper oxidase reporter of protein-protein interactions. J Biol Chem 2019; 294:7002-7012. [PMID: 30770473 PMCID: PMC6497955 DOI: 10.1074/jbc.ra118.007141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/10/2019] [Indexed: 12/13/2022] Open
Abstract
Protein–protein interactions (PPIs) are ubiquitous in almost all biological processes and are often corrupted in diseased states. A detailed understanding of PPIs is therefore key to understanding cellular physiology and can yield attractive therapeutic targets. Here, we describe the development and structural characterization of novel Escherichia coli CueO multi-copper oxidase variants engineered to recapitulate protein–protein interactions with commensurate modulation of their enzymatic activities. The fully integrated single-protein sensors were developed through modular grafting of ligand-specific peptides into a highly compliant and flexible methionine-rich loop of CueO. Sensitive detection of diverse ligand classes exemplified by antibodies, an E3 ligase, MDM2 proto-oncogene (MDM2), and protease (SplB from Staphylococcus aureus) was achieved in a simple mix and measure homogeneous format with visually observable colorimetric readouts. Therapeutic antagonism of MDM2 by small molecules and peptides in clinical development for treatment of cancer patients was assayed using the MDM2-binding CueO enzyme. Structural characterization of the free and MDM2-bound CueO variant provided functional insight into signal-transducing mechanisms of the engineered enzymes and highlighted the robustness of CueO as a stable and compliant scaffold for multiple applications.
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Affiliation(s)
- Barindra Sana
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Sharon M Q Chee
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Jantana Wongsantichon
- the Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand, and.,the Institute of Molecular and Cellular Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Sarada Raghavan
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Robert C Robinson
- the Institute of Molecular and Cellular Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Farid J Ghadessy
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore,
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Tompa P. Multisteric Regulation by Structural Disorder in Modular Signaling Proteins: An Extension of the Concept of Allostery. Chem Rev 2013; 114:6715-32. [DOI: 10.1021/cr4005082] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Peter Tompa
- VIB Department of Structural
Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Institute of Enzymology, Biological Research Center, Hungarian Academy
of Sciences, Budapest H-1113, Hungary
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Nirantar SR, Yeo KS, Chee S, Lane DP, Ghadessy FJ. A generic scaffold for conversion of peptide ligands into homogenous biosensors. Biosens Bioelectron 2013; 47:421-8. [DOI: 10.1016/j.bios.2013.03.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/21/2013] [Accepted: 03/21/2013] [Indexed: 11/17/2022]
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Stratton MM, Loh SN. Converting a protein into a switch for biosensing and functional regulation. Protein Sci 2011; 20:19-29. [PMID: 21064163 DOI: 10.1002/pro.541] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins that switch conformations in response to a signaling event (e.g., ligand binding or chemical modification) present a unique solution to the design of reagent-free biosensors as well as molecules whose biological functions are regulated in useful ways. The principal roadblock in the path to develop such molecules is that the majority of natural proteins do not change conformation upon binding their cognate ligands or becoming chemically modified. Herein, we review recent protein engineering efforts to introduce switching properties into binding proteins. By co-opting natural allosteric coupling, joining proteins in creative ways and formulating altogether new switching mechanisms, researchers are learning how to coax conformational changes from proteins that previously had none. These studies are providing some answers to the challenging question: how can one convert a lock-and-key binding protein into a molecular switch?
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Affiliation(s)
- Margaret M Stratton
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 750 East Adams Street, Syracuse, New York 13210, USA
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Mukundan H, Xie H, Price D, Kubicek-Sutherland JZ, Grace WK, Anderson AS, Martinez JS, Hartman N, Swanson BI. Quantitative multiplex detection of pathogen biomarkers on multichannel waveguides. Anal Chem 2010; 82:136-44. [PMID: 20000585 DOI: 10.1021/ac901497g] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
No single biomarker can accurately predict disease. An ideal biodetection technology should be capable of the quantitative, reproducible, and sensitive detection of a limited suite of such molecules. To this end, we have developed a multiplex biomarker assay for protective antigen and lethal factor of the Bacillus anthracis lethal toxin using semiconductor quantum dots as the fluorescence reporters on our waveguide-based biosensor platform. The platform is extendable to a wide array of biomarkers, facilitating rapid, quantitative, sensitive, and multiplex detection, better than achievable by conventional immunoassay. Our assay allows for the sensitive (limit of detection 1 pM each), specific (minimal nonspecific binding), and rapid (15 min) detection of these biomarkers in complex biological samples (e.g., serum). To address the issue of reproducibility in measurement and to increase our sample throughput, we have incorporated multichannel waveguides capable of simultaneous multiplex detection of biomarkers in three samples in quadruplicate. In this paper, we present the design, fabrication, and development of multichannel waveguides for the simultaneous detection of lethal factor and protective antigen in serum. Evaluation of the multichannel waveguide shows an excellent concordance with single-channel data and effective, simultaneous, and reproducible measurement of lethal toxins in three samples.
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Affiliation(s)
- Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Geddie ML, Matsumura I. Antibody-induced oligomerization and activation of an engineered reporter enzyme. J Mol Biol 2007; 369:1052-9. [PMID: 17467736 PMCID: PMC1995550 DOI: 10.1016/j.jmb.2007.03.076] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Revised: 03/19/2007] [Accepted: 03/27/2007] [Indexed: 11/16/2022]
Abstract
Our objective is to produce a protein biosensor (or molecular switch) that is specifically activated in solution by a monoclonal antibody. Many effector-dependent enzymes have evolved in nature, but the introduction of a novel regulatory mechanism into a normally unregulated enzyme poses a difficult design problem. We used site-saturation mutagenesis and screening to generate effector-activated variants of the reporter enzyme beta-glucuronidase (GUS). The specific activity of the purified epitope-tagged GUS variant was increased by up to approximately 500-fold by the addition of an equimolar concentration of a monoclonal antibody. This molecular switch is modular in design, so it can easily be re-engineered for the detection of other peptide-specific antibodies. Such antibody-activated reporters could someday enable point-of-care serological assays for the rapid detection of infectious diseases.
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Affiliation(s)
| | - Ichiro Matsumura
- *Corresponding author: (e-mail address: ), tele: (404) 727-5625, FAX: (404) 727-3231
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Römer L, Klein C, Dehner A, Kessler H, Buchner J. p53 – ein natürlicher Krebskiller: Einsichten in die Struktur und Therapiekonzepte. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600611] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Römer L, Klein C, Dehner A, Kessler H, Buchner J. p53—A Natural Cancer Killer: Structural Insights and Therapeutic Concepts. Angew Chem Int Ed Engl 2006; 45:6440-60. [PMID: 16983711 DOI: 10.1002/anie.200600611] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Every single day, the DNA of each cell in the human body is mutated thousands of times, even in absence of oncogenes or extreme radiation. Many of these mutations could lead to cancer and, finally, death. To fight this, multicellular organisms have evolved an efficient control system with the tumor-suppressor protein p53 as the central element. An intact p53 network ensures that DNA damage is detected early on. The importance of p53 for preventing cancer is highlighted by the fact that p53 is inactivated in more than 50 % of all human tumors. Thus, for good reason, p53 is one of the most intensively studied proteins. Despite the great effort that has been made to characterize this protein, the complex function and the structural properties of p53 are still only partially known. This review highlights basic concepts and recent progress in understanding the structure and regulation of p53, focusing on emerging new mechanistic and therapeutic concepts.
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Affiliation(s)
- Lin Römer
- Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
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Ferraz RM, Vera A, Arís A, Villaverde A. Insertional protein engineering for analytical molecular sensing. Microb Cell Fact 2006; 5:15. [PMID: 16584558 PMCID: PMC1459189 DOI: 10.1186/1475-2859-5-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 04/03/2006] [Indexed: 11/10/2022] Open
Abstract
The quantitative detection of low analyte concentrations in complex samples is becoming an urgent need in biomedical, food and environmental fields. Biosensors, being hybrid devices composed by a biological receptor and a signal transducer, represent valuable alternatives to non biological analytical instruments because of the high specificity of the biomolecular recognition. The vast range of existing protein ligands enable those macromolecules to be used as efficient receptors to cover a diversity of applications. In addition, appropriate protein engineering approaches enable further improvement of the receptor functioning such as enhancing affinity or specificity in the ligand binding. Recently, several protein-only sensors are being developed, in which either both the receptor and signal transducer are parts of the same protein, or that use the whole cell where the protein is produced as transducer. In both cases, as no further chemical coupling is required, the production process is very convenient. However, protein platforms, being rather rigid, restrict the proper signal transduction that necessarily occurs through ligand-induced conformational changes. In this context, insertional protein engineering offers the possibility to develop new devices, efficiently responding to ligand interaction by dramatic conformational changes, in which the specificity and magnitude of the sensing response can be adjusted up to a convenient level for specific analyte species. In this report we will discuss the major engineering approaches taken for the designing of such instruments as well as the relevant examples of resulting protein-only biosensors.
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Affiliation(s)
- Rosa María Ferraz
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Departament de Matemática Aplicada IV, Universitat Politècnica de Catalunya, Campus Nord, Jordi Girona, 1-3, 08034 Barcelona, Spain
| | - Andrea Vera
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Anna Arís
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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