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Ohmuro-Matsuyama Y, Gomi K, Shimoda T, Yamaji H, Ueda H. Improving the Stability of Protein-Protein Interaction Assay FlimPIA Using a Thermostabilized Firefly Luciferase. Front Bioeng Biotechnol 2021; 9:778120. [PMID: 34858964 PMCID: PMC8631863 DOI: 10.3389/fbioe.2021.778120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/27/2021] [Indexed: 11/13/2022] Open
Abstract
The protein–protein interaction assay is a key technology in various fields, being applicable in drug screening as well as in diagnosis and inspection, wherein the stability of assays is important. In a previous study, we developed a unique protein–protein interaction assay “FlimPIA” based on the functional complementation of mutant firefly luciferases (Fluc). The catalytic step of Fluc was divided into two half steps: D-luciferin was adenylated in the first step, while adenylated luciferin was oxidized in the second step. We constructed two mutants of Fluc from Photinus pyralis (Ppy); one mutant named Donor is defective in the second half reaction, while the other mutant named Acceptor exhibited low activity in the first half reaction. To date, Ppy has been used in the system; however, its thermostability is low. In this study, to improve the stability of the system, we applied Fluc from thermostabilized Luciola lateralis to FlimPIA. We screened suitable mutants as probes for FlimPIA and obtained Acceptor and Donor candidates. We detected the interaction of FKBP12-FRB with FlimPIA using these candidates. Furthermore, after the incubation of the probes at 37°C for 1 h, the luminescence signal of the new system was 2.4-fold higher than that of the previous system, showing significant improvement in the stability of the assay.
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Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.,Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | | | - Takuya Shimoda
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hideki Yamaji
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hiroshi Ueda
- Laboratory of Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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2
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Blaszczak E, Lazarewicz N, Sudevan A, Wysocki R, Rabut G. Protein-fragment complementation assays for large-scale analysis of protein-protein interactions. Biochem Soc Trans 2021; 49:1337-1348. [PMID: 34156434 PMCID: PMC8286835 DOI: 10.1042/bst20201058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 12/25/2022]
Abstract
Protein-protein interactions (PPIs) orchestrate nearly all biological processes. They are also considered attractive drug targets for treating many human diseases, including cancers and neurodegenerative disorders. Protein-fragment complementation assays (PCAs) provide a direct and straightforward way to study PPIs in living cells or multicellular organisms. Importantly, PCAs can be used to detect the interaction of proteins expressed at endogenous levels in their native cellular environment. In this review, we present the principle of PCAs and discuss some of their advantages and limitations. We describe their application in large-scale experiments to investigate PPI networks and to screen or profile PPI targeting compounds.
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Affiliation(s)
- Ewa Blaszczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
- Univ Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes) – UMR 6290, F-35000 Rennes, France
| | - Aswani Sudevan
- Univ Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes) – UMR 6290, F-35000 Rennes, France
| | - Robert Wysocki
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, Kanonia 6/8, 50-328 Wroclaw, Poland
| | - Gwenaël Rabut
- Univ Rennes, CNRS, IGDR (Institute of Genetics and Development of Rennes) – UMR 6290, F-35000 Rennes, France
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3
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Krasitskaya VV, Bashmakova EE, Frank LA. Coelenterazine-Dependent Luciferases as a Powerful Analytical Tool for Research and Biomedical Applications. Int J Mol Sci 2020; 21:E7465. [PMID: 33050422 PMCID: PMC7590018 DOI: 10.3390/ijms21207465] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022] Open
Abstract
: The functioning of bioluminescent systems in most of the known marine organisms is based on the oxidation reaction of the same substrate-coelenterazine (CTZ), catalyzed by luciferase. Despite the diversity in structures and the functioning mechanisms, these enzymes can be united into a common group called CTZ-dependent luciferases. Among these, there are two sharply different types of the system organization-Ca2+-regulated photoproteins and luciferases themselves that function in accordance with the classical enzyme-substrate kinetics. Along with deep and comprehensive fundamental research on these systems, approaches and methods of their practical use as highly sensitive reporters in analytics have been developed. The research aiming at the creation of artificial luciferases and synthetic CTZ analogues with new unique properties has led to the development of new experimental analytical methods based on them. The commercial availability of many ready-to-use assay systems based on CTZ-dependent luciferases is also important when choosing them by first-time-users. The development of analytical methods based on these bioluminescent systems is currently booming. The bioluminescent systems under consideration were successfully applied in various biological research areas, which confirms them to be a powerful analytical tool. In this review, we consider the main directions, results, and achievements in research involving these luciferases.
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Affiliation(s)
- Vasilisa V. Krasitskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Eugenia E. Bashmakova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Ludmila A. Frank
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
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Blay V, Tolani B, Ho SP, Arkin MR. High-Throughput Screening: today's biochemical and cell-based approaches. Drug Discov Today 2020; 25:1807-1821. [PMID: 32801051 DOI: 10.1016/j.drudis.2020.07.024] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/01/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022]
Abstract
High-throughput screening (HTS) provides starting chemical matter in the adventure of developing a new drug. In this review, we survey several HTS methods used today for hit identification, organized in two main flavors: biochemical and cell-based assays. Biochemical assays discussed include fluorescence polarization and anisotropy, FRET, TR-FRET, and fluorescence lifetime analysis. Binding-based methods are also surveyed, including NMR, SPR, mass spectrometry, and DSF. On the other hand, cell-based assays discussed include viability, reporter gene, second messenger, and high-throughput microscopy assays. We devote some emphasis to high-content screening, which is becoming very popular. An advisable stage after hit discovery using phenotypic screens is target deconvolution, and we provide an overview of current chemical proteomics, in silico, and chemical genetics tools. Emphasis is made on recent CRISPR/dCas-based screens. Lastly, we illustrate some of the considerations that inform the choice of HTS methods and point to some areas with potential interest for future research.
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Affiliation(s)
- Vincent Blay
- Division of Biomaterials and Bioengineering, School of Dentistry, University of California San Francisco, San Francisco, CA 94143, USA; Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Sunita P Ho
- Division of Biomaterials and Bioengineering, School of Dentistry, University of California San Francisco, San Francisco, CA 94143, USA; Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA.
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5
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Advances in the strategies for designing receptor-targeted molecular imaging probes for cancer research. J Control Release 2019; 305:1-17. [DOI: 10.1016/j.jconrel.2019.04.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/09/2019] [Accepted: 04/21/2019] [Indexed: 12/24/2022]
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Dale R, Ohmuro-Matsuyama Y, Ueda H, Kato N. Non-Steady State Analysis of Enzyme Kinetics in Real Time Elucidates Substrate Association and Dissociation Rates: Demonstration with Analysis of Firefly Luciferase Mutants. Biochemistry 2019; 58:2695-2702. [PMID: 31125202 DOI: 10.1021/acs.biochem.9b00272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Firefly luciferase has been widely used in biotechnology and biophotonics due to photon emission during enzymatic activity. In the past, the effect of amino acid substitutions (mutants) on the enzymatic activity of firefly luciferase has been characterized by the Michaelis constant, KM. The KM is obtained by plotting the maximum relative luminescence units (RLU) detected for several concentrations of the substrate (luciferin or luciferyl-adenylate). The maximum RLU is used because the assay begins to violate the quasi-steady state approximation when RLU decays as a function of time. However, mutations also affect the time to reach and decay from the maximum RLU. These effects are not captured when calculating the KM. To understand changes in the RLU kinetics of firefly luciferase mutants, we used a Michaelis-Menten model with the non-steady state approximation. In this model, we do not assume that the amount of enzyme-substrate complex is at equilibrium throughout the course of the experiment. We found that one of the two mutants analyzed in this study decreases not only the dissociation rate ( koff) but also the association rate ( kon) of luciferyl-adenylate, suggesting the narrowing of the structural pocket containing the catalytic amino acids. Furthermore, comparative analysis of the nearly complete oxidation of luciferyl-adenylate with wild-type and mutant firefly luciferase reveals that the total amount of photons emitted with the mutant is 50-fold larger than that with the wild type, on average. These two results together indicate that the slow supply of luciferyl-adenylate to the enzyme increases the total number of photons emitted from the substrate, luciferyl-adenylate. Analysis with the non-steady state approximation model is generally applicable when enzymatic production kinetics are monitored in real time.
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Affiliation(s)
- Renee Dale
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
- Department of Experimental Statistics , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Yuki Ohmuro-Matsuyama
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Nagatsuta-cho, Yokohama , Kanagawa 226-8503 , Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Nagatsuta-cho, Yokohama , Kanagawa 226-8503 , Japan
| | - Naohiro Kato
- Department of Biological Sciences , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
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Mano H, Ikushiro S, Saito N, Kittaka A, Sakaki T. Development of a highly sensitive in vitro system to detect and discriminate between vitamin D receptor agonists and antagonists based on split-luciferase technique. J Steroid Biochem Mol Biol 2018; 178:55-59. [PMID: 29101064 DOI: 10.1016/j.jsbmb.2017.10.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/20/2017] [Accepted: 10/31/2017] [Indexed: 11/19/2022]
Abstract
Split-luciferase techniques are widely used to detect protein-protein interaction and bioactive small molecules including some hormones and vitamins. Previously, we successfully expressed chimeric proteins of luciferase and the ligand binding domain (LBD) of the vitamin D receptor (VDR), LucC-LBD-LucN in COS-7 cells. The LucC-LBD-LucN biosensor was named split-luciferase vitamin D biosensor (SLDB). This biosensor can detect and discriminate between VDR agonists and antagonists in mammalian cells. In this study, we established an in vitro screening system for VDR ligands using the SLDB proteins expressed in Escherichia coli (E. coli) cells. Our in vitro screening system using cell lysate of recombinant E. coli cells could be completed within 30min, and its activity was unchanged after 10 freeze-thaw cycles. This highly sensitive and convenient system would be quite useful to screen VDR ligands with therapeutic potential for various bone-related diseases, age-related cognitive disorders, cancer, and immune disorders. In addition, our system might be applicable to diagnostic measurement of serum concentrations of 25-hydroxyvitamin D3 and 1α,25-dihydroxyvitamin D3.
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Affiliation(s)
- Hiroki Mano
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shinichi Ikushiro
- Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Nozomi Saito
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi, Tokyo 173-8605 Japan
| | - Atsushi Kittaka
- Faculty of Pharmaceutical Sciences, Teikyo University, Itabashi, Tokyo 173-8605 Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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8
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Ohmuro-Matsuyama Y, Ueda H. Homogeneous Noncompetitive Luminescent Immunodetection of Small Molecules by Ternary Protein Fragment Complementation. Anal Chem 2018; 90:3001-3004. [PMID: 29446920 DOI: 10.1021/acs.analchem.7b05140] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The homogeneous immunological detection of small molecules at high sensitivity is still a daunting task. Here, we tried sensitive noncompetitive detection of small peptides based on the open-sandwich immunoassay principle, which was combined with a bioluminescent protein-fragment complementation assay (PCA) in vitro. Since the detection of antigen-induced approximation of the two antibody variable region fragments VH and VL by the standard Nanoluc-based PCA utilizing larger (LgBiT) and shorter (SmBiT) fragments was not successful, we decided to further split LgBiT into two, yielding smaller N-terminal derivative (LnBiT) and two C-terminal, 11 residue peptides (LcBiT and SmBiT) corresponding to consecutive beta strands, to which VH and VL were each fused and expressed in Escherichia coli cells. Through the optimization of reaction conditions and peptide sequence, the antigen osteocalcin peptide can be noncompetitively detected with a low background signal and limit of detection, yielding a high light emission of 88% compared to that of the wild-type enzyme. Since the luminescence of this open sandwich bioluminescent immunoassay (OS-BLIA) can be observed with the naked eye, it could become the foundation of many point-of-care detection systems.
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Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Yokohama , Kanagawa 226-8503 , Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , Yokohama , Kanagawa 226-8503 , Japan
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9
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Moosavi B, Mousavi B, Yang WC, Yang GF. Yeast-based assays for detecting protein-protein/drug interactions and their inhibitors. Eur J Cell Biol 2017. [PMID: 28645461 DOI: 10.1016/j.ejcb.2017.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding cellular processes at molecular levels in health and disease requires the knowledge of protein-protein interactions (PPIs). In line with this, identification of PPIs at genome-wide scale is highly valuable to understand how different cellular pathways are interconnected, and it eventually facilitates designing effective drugs against certain PPIs. Furthermore, investigating PPIs at a small laboratory scale for deciphering certain biochemical pathways has been demanded for years. In this regard, yeast two hybrid system (Y2HS) has proven an extremely useful tool to discover novel PPIs, while Y2HS derivatives and novel yeast-based assays are contributing significantly to identification of protein-drug/inhibitor interaction at both large- and small-scale set-ups. These methods have been evolving over time to provide more accurate, reproducible and quantitative results. Here we briefly describe different yeast-based assays for identification of various protein-protein/drug/inhibitor interactions and their specific applications, advantages, shortcomings, and improvements. The broad range of yeast-based assays facilitates application of the most suitable method(s) for each specific need.
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Affiliation(s)
- Behrooz Moosavi
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, PR China.
| | - Bibimaryam Mousavi
- Laboratory of Organometallics, Catalysis and Ordered Materials, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan, 430070, PR China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, PR China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079, PR China.
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10
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Creation of Antigen-Dependent β-Lactamase Fusion Protein Tethered by Circularly Permuted Antibody Variable Domains. Methods Mol Biol 2017. [PMID: 28293886 DOI: 10.1007/978-1-4939-6940-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Antibody-based molecular switches that are able to recognize a range of exogenous antigens can be highly useful as a versatile biosensor. However, regulating the catalytic activity of enzymes by antibodies is still hard to achieve. Here, we describe a design method of unique antibody variable region Fv introduced with two circular permutations, called Clampbody. By tethering the Clampbody to a circularly permuted TEM-1 β-lactamase (BLA), we successfully constructed a genetically encoded molecular switch Cbody-cpBLA that shows antigen-dependent catalytic activity.
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11
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Guo Z, Murphy L, Stein V, Johnston WA, Alcala-Perez S, Alexandrov K. Engineered PQQ-Glucose Dehydrogenase as a Universal Biosensor Platform. J Am Chem Soc 2016; 138:10108-11. [PMID: 27463000 DOI: 10.1021/jacs.6b06342] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biosensors with direct electron output hold promise for nearly seamless integration with portable electronic devices. However, so far, they have been based on naturally occurring enzymes that significantly limit the spectrum of detectable analytes. Here, we present a novel biosensor architecture based on analyte-driven intermolecular recombination and activity reconstitution of a re-engineered component of glucometers: PQQ-glucose dehydrogenase. We demonstrate that this sensor architecture can be rapidly adopted for the detection of immunosuppressant drugs, α-amylase protein, or protease activity of thrombin and Factor Xa. The biosensors could be stored in dried form without appreciable loss of activity. We further show that ligand-induced activity of the developed biosensors could be directly monitored by chronoamperometry, enabling construction of disposable sensory electrodes. We expect that this architecture could be expanded to the detection of other biochemical activities, post-translational modifications, nucleic acids, and inorganic molecules.
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Affiliation(s)
- Zhong Guo
- Institute for Molecular Bioscience and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Lindy Murphy
- Molecular Warehouse Ltd. , 40 Occam Road, Guildford GU2 7YG, U.K
| | - Viktor Stein
- Institute for Molecular Bioscience and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Wayne A Johnston
- Institute for Molecular Bioscience and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane, QLD 4072, Australia
| | | | - Kirill Alexandrov
- Institute for Molecular Bioscience and Australian Institute for Bioengineering and Nanotechnology, The University of Queensland , Brisbane, QLD 4072, Australia
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12
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Bosmans RPG, Briels JM, Milroy LG, de Greef TFA, Merkx M, Brunsveld L. Supramolecular Control over Split-Luciferase Complementation. Angew Chem Int Ed Engl 2016; 55:8899-903. [PMID: 27356091 PMCID: PMC5113697 DOI: 10.1002/anie.201602807] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/17/2016] [Indexed: 01/18/2023]
Abstract
Supramolecular split-enzyme complementation restores enzymatic activity and allows for on-off switching. Split-luciferase fragment pairs were provided with an N-terminal FGG sequence and screened for complementation through host-guest binding to cucurbit[8]uril (Q8). Split-luciferase heterocomplex formation was induced in a Q8 concentration dependent manner, resulting in a 20-fold upregulation of luciferase activity. Supramolecular split-luciferase complementation was fully reversible, as revealed by using two types of Q8 inhibitors. Competition studies with the weak-binding FGG peptide revealed a 300-fold enhanced stability for the formation of the ternary heterocomplex compared to binding of two of the same fragments to Q8. Stochiometric binding by the potent inhibitor memantine could be used for repeated cycling of luciferase activation and deactivation in conjunction with Q8, providing a versatile module for in vitro supramolecular signaling networks.
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Affiliation(s)
- Ralph P G Bosmans
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Jeroen M Briels
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Tom F A de Greef
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.
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13
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Bosmans RPG, Briels JM, Milroy LG, de Greef TFA, Merkx M, Brunsveld L. Supramolecular Control over Split-Luciferase Complementation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602807] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ralph P. G. Bosmans
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Jeroen M. Briels
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Tom F. A. de Greef
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems, Department of Biomedical Engineering; Eindhoven University of Technology; Den Dolech 2 5612 AZ Eindhoven The Netherlands
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14
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Xing S, Wallmeroth N, Berendzen KW, Grefen C. Techniques for the Analysis of Protein-Protein Interactions in Vivo. PLANT PHYSIOLOGY 2016; 171:727-58. [PMID: 27208310 PMCID: PMC4902627 DOI: 10.1104/pp.16.00470] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 04/19/2016] [Indexed: 05/20/2023]
Abstract
Identifying key players and their interactions is fundamental for understanding biochemical mechanisms at the molecular level. The ever-increasing number of alternative ways to detect protein-protein interactions (PPIs) speaks volumes about the creativity of scientists in hunting for the optimal technique. PPIs derived from single experiments or high-throughput screens enable the decoding of binary interactions, the building of large-scale interaction maps of single organisms, and the establishment of cross-species networks. This review provides a historical view of the development of PPI technology over the past three decades, particularly focusing on in vivo PPI techniques that are inexpensive to perform and/or easy to implement in a state-of-the-art molecular biology laboratory. Special emphasis is given to their feasibility and application for plant biology as well as recent improvements or additions to these established techniques. The biology behind each method and its advantages and disadvantages are discussed in detail, as are the design, execution, and evaluation of PPI analysis. We also aim to raise awareness about the technological considerations and the inherent flaws of these methods, which may have an impact on the biological interpretation of PPIs. Ultimately, we hope this review serves as a useful reference when choosing the most suitable PPI technique.
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Affiliation(s)
- Shuping Xing
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
| | - Niklas Wallmeroth
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
| | - Kenneth W Berendzen
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
| | - Christopher Grefen
- University of Tübingen, ZMBP Developmental Genetics (S.X., N.W., C.G.) and ZMBP Central Facilities (K.W.B.), D-72076 Tuebingen, Germany
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15
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Iwai H, Kojima-Misaizu M, Dong J, Ueda H. Creation of a Ligand-Dependent Enzyme by Fusing Circularly Permuted Antibody Variable Region Domains. Bioconjug Chem 2016; 27:868-73. [DOI: 10.1021/acs.bioconjchem.6b00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hiroto Iwai
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Miki Kojima-Misaizu
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jinhua Dong
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroshi Ueda
- Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8503, Japan
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16
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Dixon AS, Schwinn MK, Hall MP, Zimmerman K, Otto P, Lubben TH, Butler BL, Binkowski BF, Machleidt T, Kirkland TA, Wood MG, Eggers CT, Encell LP, Wood KV. NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells. ACS Chem Biol 2016; 11:400-8. [PMID: 26569370 DOI: 10.1021/acschembio.5b00753] [Citation(s) in RCA: 806] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein-fragment complementation assays (PCAs) are widely used for investigating protein interactions. However, the fragments used are structurally compromised and have not been optimized nor thoroughly characterized for accurately assessing these interactions. We took advantage of the small size and bright luminescence of NanoLuc to engineer a new complementation reporter (NanoBiT). By design, the NanoBiT subunits (i.e., 1.3 kDa peptide, 18 kDa polypeptide) weakly associate so that their assembly into a luminescent complex is dictated by the interaction characteristics of the target proteins onto which they are appended. To ascertain their general suitability for measuring interaction affinities and kinetics, we determined that their intrinsic affinity (KD = 190 μM) and association constants (kon = 500 M(-1) s(-1), koff = 0.2 s(-1)) are outside of the ranges typical for protein interactions. The accuracy of NanoBiT was verified under defined biochemical conditions using the previously characterized interaction between SME-1 β-lactamase and a set of inhibitor binding proteins. In cells, NanoBiT fusions to FRB/FKBP produced luminescence consistent with the linear characteristics of NanoLuc. Response dynamics, evaluated using both protein kinase A and β-arrestin-2, were rapid, reversible, and robust to temperature (21-37 °C). Finally, NanoBiT provided a means to measure pharmacology of kinase inhibitors known to induce the interaction between BRAF and CRAF. Our results demonstrate that the intrinsic properties of NanoBiT allow accurate representation of protein interactions and that the reporter responds reliably and dynamically in cells.
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Affiliation(s)
- Andrew S. Dixon
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Mary P. Hall
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Kris Zimmerman
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Paul Otto
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | | | | | | | - Thomas A. Kirkland
- Promega Biosciences Incorporated, San Luis
Obispo, California 93401, United States
| | - Monika G. Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
| | | | - Lance P. Encell
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin 53711, United States
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17
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Dale R, Ohmuro-Matsuyama Y, Ueda H, Kato N. Mathematical Model of the Firefly Luciferase Complementation Assay Reveals a Non-Linear Relationship between the Detected Luminescence and the Affinity of the Protein Pair Being Analyzed. PLoS One 2016; 11:e0148256. [PMID: 26886551 PMCID: PMC4757408 DOI: 10.1371/journal.pone.0148256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/15/2016] [Indexed: 01/11/2023] Open
Abstract
The firefly luciferase complementation assay is widely used as a bioluminescent reporter technology to detect protein-protein interactions in vitro, in cellulo, and in vivo. Upon the interaction of a protein pair, complemented firefly luciferase emits light through the adenylation and oxidation of its substrate, luciferin. Although it has been suggested that kinetics of light production in the firefly luciferase complementation assay is different from that in full length luciferase, the mechanism behind this is still not understood. To quantitatively understand the different kinetics and how changes in affinity of a protein pair affect the light emission in the assay, a mathematical model of the in vitro firefly luciferase complementation assay was constructed. Analysis of the model finds that the change in kinetics is caused by rapid dissociation of the protein pair, low adenylation rate of luciferin, and increased affinity of adenylated luciferin to the enzyme. The model suggests that the affinity of the protein pair has an exponential relationship with the light detected in the assay. This relationship causes the change of affinity in a protein pair to be underestimated. This study underlines the importance of understanding the molecular mechanism of the firefly luciferase complementation assay in order to analyze protein pair affinities quantitatively.
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Affiliation(s)
- Renee Dale
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Yuki Ohmuro-Matsuyama
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama, Kanagawa, Japan
| | - Hiroshi Ueda
- Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama, Kanagawa, Japan
| | - Naohiro Kato
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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18
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A Protein-Protein Interaction Assay FlimPIA Based on the Functional Complementation of Mutant Firefly Luciferases. Methods Mol Biol 2016; 1461:131-42. [PMID: 27424900 DOI: 10.1007/978-1-4939-3813-1_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
There is a significant focus on detecting and assaying protein-protein interactions (PPIs) in biology and biotechnology. Protein-fragment complementation assay (PCA) is one of the most widely used methods to detect PPI by splitting the enzyme-coding or fluorescent protein-coding polypeptide, as well as Förster resonance energy transfer (FRET). Here, we describe a novel PPI assay FlimPIA (firefly luminescent intermediate-based protein-protein interaction assay) by a unique approach of splitting the two major catalytic steps (half reactions) of firefly luciferase (FLuc).
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19
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Kurihara M, Ohmuro-Matsuyama Y, Ayabe K, Yamashita T, Yamaji H, Ueda H. Ultra sensitive firefly luciferase-based protein-protein interaction assay (FlimPIA) attained by hinge region engineering and optimized reaction conditions. Biotechnol J 2015; 11:91-9. [PMID: 26384153 DOI: 10.1002/biot.201500189] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 08/11/2015] [Accepted: 09/16/2015] [Indexed: 11/06/2022]
Abstract
Detecting and assaying protein-protein interactions are significant research procedures in biology and biotechnology. We recently reported a novel assay to detect protein-protein interaction, i.e. firefly luminescent intermediate-based protein-protein interaction assay (FlimPIA) using two mutant firefly luciferases (Flucs), which complement each other's deficient half reaction. This assay detects neighboring of two mutant Flucs, namely, a "Donor" that catalyzes the adenylation of firefly luciferin to produce a luciferyl-adenylate intermediate, and an "Acceptor" that catalyzes the subsequent light emitting reaction. However, its rather high background signal, derived from the remaining adenylation activity of the Acceptor, has limited its usefulness. To reduce this background signal, we introduced a mutation (R437K) into the hinge region of the Acceptor, while maintaining the oxidative activity. Interestingly, the signal/background (S/B) ratio of the assay was markedly improved by the addition of coenzyme A and reduction of the ATP concentration, probably due to reduced inhibition by dehydroluciferyl-adenylate formed during the catalysis and an increased ATP-based Km value of the Acceptor, respectively. As a result, a significantly improved maximal S/B ratio from 2.5 to ∼40 was attained, which promises wider use of the assay in in vitro diagnostics, drug discovery, and expanding our knowledge of various biological phenomena.
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Affiliation(s)
- Makoto Kurihara
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yuki Ohmuro-Matsuyama
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan.,The Japan Society for the Promotion of Science, Tokyo, Japan.,Department of Applied Chemistry, School of Engineering, Kobe University, Kobe, Japan
| | - Keiichi Ayabe
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Takahiro Yamashita
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Hideki Yamaji
- Department of Applied Chemistry, School of Engineering, Kobe University, Kobe, Japan
| | - Hiroshi Ueda
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan. .,Chemical Resources Laboratory, Tokyo Institute of Technology, Yokohama, Japan.
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20
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Ranallo S, Rossetti M, Plaxco KW, Vallée-Bélisle A, Ricci F. A Modular, DNA-Based Beacon for Single-Step Fluorescence Detection of Antibodies and Other Proteins. Angew Chem Int Ed Engl 2015; 54:13214-8. [PMID: 26337144 PMCID: PMC4757636 DOI: 10.1002/anie.201505179] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/20/2015] [Indexed: 12/17/2022]
Abstract
A versatile platform for the one-step fluorescence detection of both monovalent and multivalent proteins has been developed. This system is based on a conformation-switching stem-loop DNA scaffold that presents a small-molecule, polypeptide, or nucleic-acid recognition element on each of its two stem strands. The steric strain associated with the binding of one (multivalent) or two (monovalent) target molecules to these elements opens the stem, enhancing the emission of an attached fluorophore/quencher pair. The sensors respond rapidly (<10 min) and selectively, enabling the facile detection of specific proteins even in complex samples, such as blood serum. The versatility of the platform was demonstrated by detecting five bivalent proteins (four antibodies and the chemokine platelet-derived growth factor) and two monovalent proteins (a Fab fragment and the transcription factor TBP) with low nanomolar detection limits and no detectable cross-reactivity.
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Affiliation(s)
- Simona Ranallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Marianna Rossetti
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Kevin W Plaxco
- Center for Bioengineering & Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 (USA)
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre-ville, Montréal, Québec H3C 3J7 (Canada).
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy).
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21
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Ranallo S, Rossetti M, Plaxco KW, Vallée‐Bélisle A, Ricci F. A Modular, DNA‐Based Beacon for Single‐Step Fluorescence Detection of Antibodies and Other Proteins. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505179] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Simona Ranallo
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Marianna Rossetti
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
| | - Kevin W. Plaxco
- Center for Bioengineering & Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106 (USA)
| | - Alexis Vallée‐Bélisle
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, C.P. 6128, Succursale Centre‐ville, Montréal, Québec H3C 3J7 (Canada)
| | - Francesco Ricci
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome 00133 (Italy)
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22
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Janssen BMG, Engelen W, Merkx M. DNA-directed control of enzyme-inhibitor complex formation: a modular approach to reversibly switch enzyme activity. ACS Synth Biol 2015; 4:547-53. [PMID: 25216042 DOI: 10.1021/sb500278z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA-templated reversible assembly of an enzyme-inhibitor complex is presented as a new and highly modular approach to control enzyme activity. TEM1-β-lactamase and its inhibitor protein BLIP were conjugated to different oligonucleotides, resulting in enzyme inhibition in the presence of template strand. Formation of a rigid dsDNA linker upon addition of a complementary target strand disrupts the enzyme-inhibitor complex and results in the restoration of enzyme activity, enabling detection of as little as 2 fmol DNA. The noncovalent assembly of the complex allows easy tuning of target and template strands without changing the oligonucleotide-functionalized enzyme and inhibitor domains. Using a panel of eight different template sequences, restoration of enzyme activity was only observed in the presence of the target viral DNA sequence. The use of stable, well-characterized protein domains and the intrinsic modularity of our system should allow easy integration with DNA/RNA-based logic circuits for applications in biomedicine and molecular diagnostics.
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Affiliation(s)
- Brian M. G. Janssen
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
| | - Wouter Engelen
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems Eindhoven, University of Technology, Den Dolech 2, 5600
MB Eindhoven, The Netherlands
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23
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A signal-on fluorosensor based on quench-release principle for sensitive detection of antibiotic rapamycin. BIOSENSORS-BASEL 2015; 5:131-40. [PMID: 25822756 PMCID: PMC4493541 DOI: 10.3390/bios5020131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/13/2015] [Accepted: 03/20/2015] [Indexed: 11/17/2022]
Abstract
An antibiotic rapamycin is one of the most commonly used immunosuppressive drugs, and also implicated for its anti-cancer activity. Hence, the determination of its blood level after organ transplantation or tumor treatment is of great concern in medicine. Although there are several rapamycin detection methods, many of them have limited sensitivity, and/or need complicated procedures and long assay time. As a novel fluorescent biosensor for rapamycin, here we propose "Q'-body", which works on the fluorescence quench-release principle inspired by the antibody-based quenchbody (Q-body) technology. We constructed rapamycin Q'-bodies by linking the two interacting domains FKBP12 and FRB, whose association is triggered by rapamycin. The fusion proteins were each incorporated position-specifically with one of fluorescence dyes ATTO520, tetramethylrhodamine, or ATTO590 using a cell-free translation system. As a result, rapid rapamycin dose-dependent fluorescence increase derived of Q'-bodies was observed, especially for those with ATTO520 with a lowest detection limit of 0.65 nM, which indicates its utility as a novel fluorescent biosensor for rapamycin.
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24
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Stein V, Alexandrov K. Synthetic protein switches: design principles and applications. Trends Biotechnol 2015; 33:101-10. [DOI: 10.1016/j.tibtech.2014.11.010] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/27/2014] [Accepted: 11/29/2014] [Indexed: 12/22/2022]
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25
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Azad T, Tashakor A, Hosseinkhani S. Split-luciferase complementary assay: applications, recent developments, and future perspectives. Anal Bioanal Chem 2014; 406:5541-60. [DOI: 10.1007/s00216-014-7980-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/22/2014] [Accepted: 06/16/2014] [Indexed: 12/19/2022]
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26
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Lake MC, Aboagye EO. Luciferase fragment complementation imaging in preclinical cancer studies. Oncoscience 2014; 1:310-25. [PMID: 25594026 PMCID: PMC4278313 DOI: 10.18632/oncoscience.45] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 05/31/2014] [Indexed: 12/20/2022] Open
Abstract
The luciferase fragment complementation assay (LFCA) enables molecular events to be non-invasively imaged in live cells in vitro and in vivo in a comparatively cheap and safe manner. It is a development of previous enzyme complementation assays in which reporter genes are split into two, individually enzymatically inactive, fragments that are able to complement one another upon interaction. This complementation can be used to externally visualize cellular activities. In recent years, the number of studies which have used LFCAs to probe questions relevant to cancer have increased, and this review summarizes the most significant and interesting of these. In particular, it focuses on work conducted on the epidermal growth factor, nuclear and chemokine receptor families, and intracellular signaling pathways, including IP3, cAMP, Akt, cMyc, NRF2 and Rho GTPases. LFCAs which have been developed to image DNA methylation and detect RNA transcripts are also discussed.
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Affiliation(s)
- Madryn C. Lake
- Comprehensive Cancer Imaging Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London
| | - Eric O. Aboagye
- Comprehensive Cancer Imaging Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital, London
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27
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Application of enzyme bioluminescence for medical diagnostics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2014; 144:175-97. [PMID: 25084998 DOI: 10.1007/978-3-662-43385-0_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nowadays luciferases are effectively used as analytical instruments in a great variety of research fields. Of special interest are the studies dealing with elaboration of novel analytical systems for the purposes of medical diagnostics. The ever-expanding spectrum of clinically important analytes accounts for the increasing demand for new techniques for their detection. In this chapter we have made an attempt to summarize the results on applications of luciferases as reporters in binding assays including immunoassay, nucleic acid hybridization assay, and so on. The data over the last 15 years have been analyzed and clearly show that luciferase-based assays, due to extremely high sensitivity, low cost, and the lack of need for skilled personnel, hold much promise for clinical diagnostics.
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28
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Ohmuro-Matsuyama Y, Hara Y, Ueda H. Improved Protein–Protein Interaction Assay FlimPIA by the Entrapment of Luciferase Conformation. Anal Chem 2013; 86:2013-8. [DOI: 10.1021/ac403065v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Department
of Chemistry and Biotechnology, School of Engineering,, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
- Chemical
Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18
Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
- The Japan Society
for the Promotion of Science, 8 Ichiban-Cho, Chiyoda-ku, Tokyo, 102-8472, Japan
| | - Yuko Hara
- Department
of Chemistry and Biotechnology, School of Engineering,, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
- Chemical
Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18
Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
| | - Hiroshi Ueda
- Department
of Chemistry and Biotechnology, School of Engineering,, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-8656, Japan
- Chemical
Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18
Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan
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29
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Ohmuro-Matsuyama Y, Nakano K, Kimura A, Ayabe K, Ihara M, Wada T, Ueda H. A protein-protein interaction assay based on the functional complementation of mutant firefly luciferases. Anal Chem 2013; 85:7935-40. [PMID: 23902573 DOI: 10.1021/ac4016825] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a novel bioluminescent protein-protein interaction (PPI) assay, which is based on the functional complementation of two mutant firefly luciferases (Fluc). The chemical reaction catalyzed by Fluc is divided into two half reactions of ATP-driven luciferin adenylation and subsequent oxidative reactions. In the former adenylation half-reaction, a luciferyl-adenylate (LH2-AMP) intermediate is produced from LH2 and ATP. With this intermediate, the latter oxidative reactions produce oxyluciferin via proton abstraction at the C4 carbon of LH2-AMP. We created and optimized two Fluc mutants; one is named "Donor", which virtually lacks oxidative activity, while the other, named "Acceptor", is almost defective in the adenylation activity. Then, the two mutants are fused to interacting partners, and prepared as pure proteins. When the interaction between the partners is induced, higher efficiency of LH2-AMP transfer between the Donor and Acceptor enzymes resulted in increased luminescence. The assay was found to work both in vitro and in cultured cells with strong signals. This would be the first example of reconstituting two divided reactions of one enzyme to detect PPI, which will not only be utilized as a robust PPI assay, but also open a way to control the activity of similar enzymes in acyl/adenylate-forming enzyme superfamily.
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Affiliation(s)
- Yuki Ohmuro-Matsuyama
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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30
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Banala S, Arts R, Aper SJA, Merkx M. No washing, less waiting: engineering biomolecular reporters for single-step antibody detection in solution. Org Biomol Chem 2013; 11:7642-9. [DOI: 10.1039/c3ob41315b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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