1
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Otun SO, Graca R, Achilonu I. Combating Aminoglycoside Resistance: From Structural and Functional Characterisation to Therapeutic Challenges with RKAAT. Curr Protein Pept Sci 2024; 25:454-468. [PMID: 38314602 DOI: 10.2174/0113892037278814231226104509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 02/06/2024]
Abstract
A comprehensive knowledge of aminoglycoside-modifying enzymes (AMEs) and their role in bacterial resistance mechanisms is urgently required due to the rising incidence of antibiotic resistance, particularly in Klebsiella pneumoniae infections. This study explores the essential features of AMEs, including their structural and functional properties, the processes by which they contribute to antibiotic resistance, and the therapeutic importance of aminoglycosides. The study primarily examines the Recombinant Klebsiella pneumoniae Aminoglycoside Adenylyl Transferase (RKAAT), particularly emphasizing its biophysical characteristics and the sorts of resistance it imparts. Furthermore, this study examines the challenges presented by RKAAT-mediated resistance, an evaluation of treatment methods and constraints, and options for controlling infection. The analysis provides a prospective outlook on strategies to address and reduce antibiotic resistance. This extensive investigation seeks to provide vital insights into the continuing fight against bacterial resistance, directing future research efforts and medicinal approaches.
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Affiliation(s)
- Sarah Oluwatobi Otun
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Richard Graca
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
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2
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Lee E, Shrestha KL, Kang S, Ramakrishnan N, Kwon Y. Cell-Based Sensors for the Detection of EGF and EGF-Stimulated Ca 2+ Signaling. BIOSENSORS 2023; 13:383. [PMID: 36979595 PMCID: PMC10045995 DOI: 10.3390/bios13030383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Epidermal growth factor (EGF)-mediated activation of EGF receptors (EGFRs) has become an important target in drug development due to the implication of EGFR-mediated cellular signaling in cancer development. While various in vitro approaches are developed for monitoring EGF-EGFR interactions, they have several limitations. Herein, we describe a live cell-based sensor system that can be used to monitor the interaction of EGF and EGFR as well as the subsequent signaling events. The design of the EGF-detecting sensor cells is based on the split-intein-mediated conditional protein trans-cleavage reaction (CPC). CPC is triggered by the presence of the target (EGF) to activate a signal peptide that translocates the fluorescent cargo to the target cellular location (mitochondria). The developed sensor cell demonstrated excellent sensitivity with a fast response time. It was also successfully used to detect an agonist and antagonist of EGFR (transforming growth factor-α and Cetuximab, respectively), demonstrating excellent specificity and capability of screening the analytes based on their function. The usage of sensor cells was then expanded from merely detecting the presence of target to monitoring the target-mediated signaling cascade, by exploiting previously developed Ca2+-detecting sensor cells. These sensor cells provide a useful platform for monitoring EGF-EGFR interaction, for screening EGFR effectors, and for studying downstream cellular signaling cascades.
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Affiliation(s)
- Euiyeon Lee
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Keshab Lal Shrestha
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
| | - Seonhye Kang
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
| | - Neethu Ramakrishnan
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
| | - Youngeun Kwon
- Department of Biomedical Engineering, Dongguk University, Seoul 04620, Republic of Korea
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3
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Recent advances in biosensors and sequencing technologies for the detection of mutations. Microchem J 2023. [DOI: 10.1016/j.microc.2022.108306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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4
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Liu X, Zhu H, Sabó J, Lánský Z, Neužil P. Improvement of the signal to noise ratio for fluorescent imaging in microfluidic chips. Sci Rep 2022; 12:18911. [PMID: 36344576 PMCID: PMC9640556 DOI: 10.1038/s41598-022-23426-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Microfluidics systems can be fabricated in various ways using original silicon glass systems, with easy Si processing and surface modifications for subsequent applications such as cell seeding and their study. Fluorescent imaging of cells became a standard technique for the investigation of cell behavior. Unfortunately, high sensitivity fluorescent imaging, e.g., using total internal reflection fluorescence (TIRF) microscopy, is problematic in these microfluidic systems because the uneven surfaces of the silicon channels' bottoms affect light penetration through the optical filters. In this work, we study the nature of the phenomenon, finding that the problem can be rectified by using a silicon-on-insulator (SOI) substrate, defining the channel depth by the thickness of the top Si layer, and halting the etching at the buried SiO2 layer. Then the fluorescent background signal drops by = 5 times, corresponding to the limit of detection drop from = 0.05 mM to = 50 nM of fluorescein. We demonstrate the importance of a flat surface using TIRF-based single-molecule detection, improving the signal to a noise ratio more than 18 times compared to a conventional Si wafer. Overall, using very high-quality SOI substrates pays off, as it improves the fluorescence image quality due to the increase in signal-to-noise ratio. Concerning the cost of microfluidic device fabrication-design, mask fabrication, wafer processing, and device testing-the initial SOI wafer cost is marginal, and using it improves the system performance.
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Affiliation(s)
- Xiaocheng Liu
- grid.440588.50000 0001 0307 1240Department of Microsystems Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi People’s Republic of China
| | - Hanliang Zhu
- grid.440588.50000 0001 0307 1240Department of Microsystems Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi People’s Republic of China
| | - Ján Sabó
- grid.418095.10000 0001 1015 3316Institute of Biotechnology, Czech Academy of Science, Průmyslová 595, 252 50 Vestec, Czech Republic ,grid.4491.80000 0004 1937 116XDepartment of Physical Chemistry, Faculty of Science, Charles University, Hlavova 8, 12800 Prague 2, Czech Republic
| | - Zdeněk Lánský
- grid.418095.10000 0001 1015 3316Institute of Biotechnology, Czech Academy of Science, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Pavel Neužil
- grid.440588.50000 0001 0307 1240Department of Microsystems Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi’an, 710072 Shaanxi People’s Republic of China
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5
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Morris MC. A Toolbox of Fluorescent Peptide Biosensors to Highlight Protein Kinases in Complex Samples : focus on cyclin‐dependent kinases. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- May Catherine Morris
- IBMM-UMR5247 Peptide & Proteins Faculté de Pharmacie,15 Av. Charles Flahault 34093 Montpellier FRANCE
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6
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Kang C, Shrestha KL, Kwon S, Park S, Kim J, Kwon Y. Intein-Mediated Protein Engineering for Cell-Based Biosensors. BIOSENSORS 2022; 12:bios12050283. [PMID: 35624584 PMCID: PMC9138240 DOI: 10.3390/bios12050283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/21/2022]
Abstract
Cell-based sensors provide a flexible platform for screening biologically active targets and for monitoring their interactions in live cells. Their applicability extends across a vast array of biological research and clinical applications. Particularly, cell-based sensors are becoming a potent tool in drug discovery and cell-signaling studies by allowing function-based screening of targets in biologically relevant environments and enabling the in vivo visualization of cellular signals in real-time with an outstanding spatiotemporal resolution. In this review, we aim to provide a clear view of current cell-based sensor technologies, their limitations, and how the recent improvements were using intein-mediated protein engineering. We first discuss the characteristics of cell-based sensors and present several representative examples with a focus on their design strategies, which differentiate cell-based sensors from in vitro analytical biosensors. We then describe the application of intein-mediated protein engineering technology for cell-based sensor fabrication. Finally, we explain the characteristics of intein-mediated reactions and present examples of how the intein-mediated reactions are used to improve existing methods and develop new approaches in sensor cell fabrication to address the limitations of current technologies.
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7
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Shining Light on Protein Kinase Biomarkers with Fluorescent Peptide Biosensors. Life (Basel) 2022; 12:life12040516. [PMID: 35455007 PMCID: PMC9026840 DOI: 10.3390/life12040516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/23/2022] Open
Abstract
Protein kinases (PKs) are established gameplayers in biological signalling pathways, and a large body of evidence points to their dysregulation in diseases, in particular cancer, where rewiring of PK networks occurs frequently. Fluorescent biosensors constitute attractive tools for probing biomolecules and monitoring dynamic processes in complex samples. A wide variety of genetically encoded and synthetic biosensors have been tailored to report on PK activities over the last decade, enabling interrogation of their function and insight into their behaviour in physiopathological settings. These optical tools can further be used to highlight enzymatic alterations associated with the disease, thereby providing precious functional information which cannot be obtained through conventional genetic, transcriptomic or proteomic approaches. This review focuses on fluorescent peptide biosensors, recent developments and strategies that make them attractive tools to profile PK activities for biomedical and diagnostic purposes, as well as insights into the challenges and opportunities brought by this unique toolbox of chemical probes.
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8
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Nakata E, Hirose H, Gerelbaatar K, Arafiles JVV, Zhang Z, Futaki S, Morii T. A facile combinatorial approach to construct a ratiometric fluorescent sensor: application for the real-time sensing of cellular pH changes. Chem Sci 2021; 12:8231-8240. [PMID: 34194714 PMCID: PMC8208317 DOI: 10.1039/d1sc01575c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/04/2021] [Indexed: 02/02/2023] Open
Abstract
Realtime monitoring of the cellular environment, such as the intracellular pH, in a defined cellular space provides a comprehensive understanding of the dynamics processes in a living cell. Considering the limitation of spatial resolution in conventional microscopy measurements, multiple types of fluorophores assembled within that space would behave as a single fluorescent probe molecule. Such a character of microscopic measurements enables a much more flexible combinatorial design strategy in developing fluorescent probes for given targets. Nanomaterials with sizes smaller than the microscopy spatial resolution provide a scaffold to assemble several types of fluorophores with a variety of optical characteristics, therefore providing a convenient strategy for designing fluorescent pH sensors. In this study, fluorescein (CF) and tetramethylrhodamine (CR) were assembled on a DNA nanostructure with controlling the number of each type of fluorophore. By taking advantage of the different responses of CF and CR emissions to the pH environment, an appropriate assembly of both CF and CR on DNA origami enabled a controlled intensity of fluorescence emission and ratiometric pH monitoring within the space defined by DNA origami. The CF and CR-assembled DNA origami was successfully applied for monitoring the intracellular pH changes.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University Kyoto Japan
| | - Hisaaki Hirose
- Institute for Chemical Research, Kyoto University Kyoto Japan
| | | | | | | | - Shiroh Futaki
- Institute for Chemical Research, Kyoto University Kyoto Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University Kyoto Japan
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9
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Kitajima N, Takikawa K, Sekiya H, Satoh K, Asanuma D, Sakamoto H, Takahashi S, Hanaoka K, Urano Y, Namiki S, Iino M, Hirose K. Real-time in vivo imaging of extracellular ATP in the brain with a hybrid-type fluorescent sensor. eLife 2020; 9:57544. [PMID: 32648544 PMCID: PMC7398694 DOI: 10.7554/elife.57544] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
Adenosine 5' triphosphate (ATP) is a ubiquitous extracellular signaling messenger. Here, we describe a method for in-vivo imaging of extracellular ATP with high spatiotemporal resolution. We prepared a comprehensive set of cysteine-substitution mutants of ATP-binding protein, Bacillus FoF1-ATP synthase ε subunit, labeled with small-molecule fluorophores at the introduced cysteine residue. Screening revealed that the Cy3-labeled glutamine-105 mutant (Q105C-Cy3; designated ATPOS) shows a large fluorescence change in the presence of ATP, with submicromolar affinity, pH-independence, and high selectivity for ATP over ATP metabolites and other nucleotides. To enable in-vivo validation, we introduced BoNT/C-Hc for binding to neuronal plasma membrane and Alexa Fluor 488 for ratiometric measurement. The resulting ATPOS complex binds to neurons in cerebral cortex of living mice, and clearly visualized a concentrically propagating wave of extracellular ATP release in response to electrical stimulation. ATPOS should be useful to probe the extracellular ATP dynamics of diverse biological processes in vivo.
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Affiliation(s)
- Nami Kitajima
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenji Takikawa
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Sekiya
- Department of Physiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kaname Satoh
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Asanuma
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hirokazu Sakamoto
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shodai Takahashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeyuki Namiki
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masamitsu Iino
- Department of Cellular and Molecular Pharmacology, Nihon University School of Medicine, Tokyo, Japan
| | - Kenzo Hirose
- Department of Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,International Research Center for Neurointelligence, The University of Tokyo Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan
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10
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Design of fluorescent protein-based sensors through a general protection-deprotection strategy. Methods Enzymol 2020; 640:63-82. [PMID: 32560806 DOI: 10.1016/bs.mie.2020.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Engineered fluorescent proteins have been extensively used in biological research for the study of gene expression, protein function and trafficking, and protein-protein interactions. In addition, fluorescent proteins have also been engineered to act as biosensing agents to detect intracellular signaling molecules and other small-molecule metabolites. Although they have been engineered extensively to achieve novel properties, fluorescent proteins are traditionally modified using the 20 canonical amino acids. This limits the number of functional groups that are available to the design and construction of novel fluorescent proteins. The expansion of the genetic code through the incorporation of noncanonical amino acids presents an opportunity to add new functionalities with the intent of modifying chemical and physical properties of fluorescent proteins. Herein we provide a general procedure for the site-specific incorporation of noncanonical amino acids into fluorescent proteins in live cells. We will also discuss a noncanonical amino acid-containing fluorescent protein sensor that is based on a general protection-deprotection design strategy, for the selective detection and quantification of Hg2+.
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11
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Weng C, Fan N, Xu T, Chen H, Li Z, Li Y, Tan H, Fu Q, Ding M. FRET-based polymer materials for detection of cellular microenvironments. CHINESE CHEM LETT 2020. [DOI: 10.1016/j.cclet.2019.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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Better together: building protein oligomers naturally and by design. Biochem Soc Trans 2020; 47:1773-1780. [PMID: 31803901 PMCID: PMC6925524 DOI: 10.1042/bst20190283] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022]
Abstract
Protein oligomers are more common in nature than monomers, with dimers being the most prevalent final structural state observed in known structures. From a biological perspective, this makes sense as it conserves vital molecular resources that may be wasted simply by generating larger single polypeptide units, and allows new features such as cooperativity to emerge. Taking inspiration from nature, protein designers and engineers are now building artificial oligomeric complexes using a variety of approaches to generate new and useful supramolecular protein structures. Oligomerisation is thus offering a new approach to sample structure and function space not accessible through simply tinkering with monomeric proteins.
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13
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Sakamoto S, Kiyonaka S, Hamachi I. Construction of ligand assay systems by protein-based semisynthetic biosensors. Curr Opin Chem Biol 2019; 50:10-18. [PMID: 30875618 DOI: 10.1016/j.cbpa.2019.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 01/14/2023]
Abstract
Proteins as causative agents of diseases such as cancers, diabetes and neurological disorders are attractive drug targets. For developing chemicals selectively acting on key disease-causing proteins, one useful concept is the direct conversion of such target proteins into biosensors. This approach provides ligand-binding assay systems based on protein-based biosensors, which can quantitatively evaluate interactions between the protein and a specific ligand in many environments. Site-specific chemical modifications are used widely for the creation of protein-based semisynthetic biosensors in vitro. Notably, a few bio-orthogonal approaches capable of selectively modifying drug-targets have been developed, allowing conversion of specific target proteins into semisynthetic biosensors in live cells. These biosensors can be used for quantitative drug binding analyses in native environments. In this review, we discuss recent efforts for the construction of ligand assay systems using semisynthetic protein-based biosensors and their application to quantitative analysis and high-throughput screening of small molecules for drug discovery.
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Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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14
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Tamura T, Hamachi I. Chemistry for Covalent Modification of Endogenous/Native Proteins: From Test Tubes to Complex Biological Systems. J Am Chem Soc 2018; 141:2782-2799. [DOI: 10.1021/jacs.8b11747] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomonori Tamura
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- ERATO, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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15
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Jeon H, Lee E, Kim D, Lee M, Ryu J, Kang C, Kim S, Kwon Y. Cell-Based Biosensors Based on Intein-Mediated Protein Engineering for Detection of Biologically Active Signaling Molecules. Anal Chem 2018; 90:9779-9786. [PMID: 30028129 DOI: 10.1021/acs.analchem.8b01481] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Live-cell-based biosensors have emerged as a useful tool for biotechnology and chemical biology. Genetically encoded sensor cells often use bimolecular fluorescence complementation or fluorescence resonance energy transfer to build a reporter unit that suffers from nonspecific signal activation at high concentrations. Here, we designed genetically encoded sensor cells that can report the presence of biologically active molecules via fluorescence-translocation based on split intein-mediated conditional protein trans-splicing (PTS) and conditional protein trans-cleavage (PTC) reactions. In this work, the target molecules or the external stimuli activated intein-mediated reactions, which resulted in activation of the fluorophore-conjugated signal peptide. This approach fully valued the bond-making and bond-breaking features of intein-mediated reactions in sensor construction and thus eliminated the interference of false-positive signals resulting from the mere binding of fragmented reporters. We could also avoid the necessity of designing split reporters to refold into active structures upon reconstitution. These live-cell-based sensors were able to detect biologically active signaling molecules, such as Ca2+ and cortisol, as well as relevant biological stimuli, such as histamine-induced Ca2+ stimuli and the glucocorticoid receptor agonist, dexamethasone. These live-cell-based sensing systems hold large potential for applications such as drug screening and toxicology studies, which require functional information about targets.
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Affiliation(s)
- Hyunjin Jeon
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Euiyeon Lee
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Dahee Kim
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Minhyung Lee
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Jeahee Ryu
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Chungwon Kang
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Soyoun Kim
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
| | - Youngeun Kwon
- Department of Biomedical Engineering (BK21 plus) , Dongguk University , Seoul 04620 , Korea
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16
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Abstract
Chemically constructed biosensors consisting of a protein scaffold and an artificial small molecule have recently been recognized as attractive analytical tools for the specific detection and real-time monitoring of various biological substances or events in cells. Conventionally, such semisynthetic biosensors have been prepared in test tubes and then introduced into cells using invasive methods. With the impressive advances seen in bioorthogonal protein conjugation methodologies, however, it is now becoming feasible to directly construct semisynthetic biosensors in living cells, providing unprecedented tools for life-science research. We discuss here recent efforts regarding the in situ construction of protein-based semisynthetic biosensors and highlight their uses in the visualization and quantification of biomolecules and events in multimolecular and crowded cellular systems.
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Affiliation(s)
- Tsuyoshi Ueda
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomonori Tamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- CREST(Core Research for Evolutional Science and Technology, JST), Sanbancho, Chiyodaku, Tokyo, 102-0075, Japan
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17
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Nakano S, Tamura T, Das RK, Nakata E, Chang YT, Morii T. A Diversity-Oriented Library of Fluorophore-Modified Receptors Constructed from a Chemical Library of Synthetic Fluorophores. Chembiochem 2017; 18:2212-2216. [PMID: 28879678 DOI: 10.1002/cbic.201700403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/16/2022]
Abstract
The practical application of biosensors can be determined by evaluating the sensing ability of fluorophore-modified derivatives of a receptor with appropriate recognition characteristics for target molecules. One of the key determinants for successfully obtaining a useful biosensor is wide variation in the fluorophores attached to a given receptor. Thus, using a larger fluorophore-modified receptor library provides a higher probability of obtaining a practically useful biosensor. However, no effective method has yet been developed for constructing such a diverse library of fluorophore-modified receptors. Herein, we report a method for constructing fluorophore-modified receptors by using a chemical library of synthetic fluorophores with a thiol-reactive group. This library was converted into a library of fluorophore-modified adenosine-binding ribonucleopeptide (RNP) receptors by introducing the fluorophores to the Rev peptide of the RNP complex by alkylation of the thiol group. This method enabled the construction of 263 fluorophore-modified ATP-binding RNP receptors and allowed the selection of suitable receptor-based fluorescent sensors that target ATP.
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Affiliation(s)
- Shun Nakano
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Raj Kumar Das
- Bharat Petroleum Corporation Ltd., Corporate R&D Centre, Plot No. 2 A, Udyog Kendra, Surajpur Industrial Area, Greater Noida, 201 306, India
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Young-Tae Chang
- Department of Chemistry and MedChem Program of Life Sciences, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.,Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, Korea
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, 611-0011, Japan
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18
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Ruiz-Palomero C, Benítez-Martínez S, Soriano ML, Valcárcel M. Fluorescent nanocellulosic hydrogels based on graphene quantum dots for sensing laccase. Anal Chim Acta 2017; 974:93-99. [DOI: 10.1016/j.aca.2017.04.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 04/10/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022]
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19
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Abstract
Fluorescent proteins of different colors are useful probes to study protein structure and function, and to investigate cellular events and conditions. Large efforts have focused on engineering new properties into fluorescent proteins via rational design and directed evolution. In addition to applications in imaging of protein expression level and subcellular localization, fluorescent proteins have been increasingly engineered to act as biosensors to track concentrations of small-molecule metabolites, enzyme activities, and protein conformational changes in living cells. Unlike small-molecule fluorescence biosensors, fluorescent proteins are genetically encodable, and thus can be expressed inside living cells. Attachment of organelle-specific signals to the proteins allows their localization to be specified. Recently, a new class of fluorescent protein biosensors has been developed to include unnatural amino acids as the sensing element. The unique chemical and physical properties of the unnatural amino acids enable sensor designs that cannot be realized by using the standard genetic code with the 20 canonical amino acids. In this chapter, we detail the general procedure for the genetic incorporation of unnatural amino acids. We further present two protocols for the in vitro and in vivo detection of hydrogen peroxide (H2O2) using a fluorescent protein biosensor that contains an unnatural amino acid, p-boronophenylalanine.
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Affiliation(s)
- Wei Niu
- University of Nebraska-Lincoln, Lincoln, NE, United States.
| | - Jiantao Guo
- University of Nebraska-Lincoln, Lincoln, NE, United States.
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20
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Tamura T, Nakano S, Nakata E, Morii T. Construction of a library of structurally diverse ribonucleopeptides with catalytic groups. Bioorg Med Chem 2017; 25:1881-1888. [PMID: 28223024 DOI: 10.1016/j.bmc.2017.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 01/20/2023]
Abstract
Functional screening of structurally diverse libraries consisting of proteins or nucleic acids is an effective method to obtain receptors or aptamers with unique molecular recognition characteristics. However, further modification of these selected receptors to exert a newly desired function is still a challenging task. We have constructed a library of structurally diverse ribonucleopeptides (RNPs) that are modified with a catalytic group, in which the catalytic group aligns with various orientations against the ATP binding pocket of RNA subunit. As a proof-of-principle, the screening of the constructed RNP library for the catalytic reaction of ester hydrolysis was successfully carried out. The size of both the substrate-binding RNA library and the catalytic group modified peptide library are independently expandable, and thus, the size of RNPs library could be enlarged by a combination of these two subunits. We anticipate that the library of functionalized and structurally diverse RNPs would be expanded for various other catalytic reactions.
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Affiliation(s)
- Tomoki Tamura
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shun Nakano
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
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21
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Clifton BE, Whitfield JH, Sanchez-Romero I, Herde MK, Henneberger C, Janovjak H, Jackson CJ. Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors. Methods Mol Biol 2017; 1596:71-87. [PMID: 28293881 DOI: 10.1007/978-1-4939-6940-1_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Small molecule biosensors based on Förster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.
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Affiliation(s)
- Ben E Clifton
- Research School of Chemistry, The Australian National University, Building 137, Sullivans Creek Road, Canberra, ACT, 2601, Australia
| | - Jason H Whitfield
- Research School of Chemistry, The Australian National University, Building 137, Sullivans Creek Road, Canberra, ACT, 2601, Australia
| | | | - Michel K Herde
- Institute of Cellular Neurosciences, University of Bonn, Bonn, Germany
| | - Christian Henneberger
- Institute of Cellular Neurosciences, University of Bonn, Bonn, Germany
- German Centre for Neurodegenerative Diseases, Bonn, Germany
- University College of London, London, UK
| | - Harald Janovjak
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Building 137, Sullivans Creek Road, Canberra, ACT, 2601, Australia.
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22
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Anees P, Sudheesh KV, Jayamurthy P, Chandrika AR, Omkumar RV, Ajayaghosh A. A protein-dye hybrid system as a narrow range tunable intracellular pH sensor. Chem Sci 2016; 7:6808-6814. [PMID: 28042467 PMCID: PMC5134758 DOI: 10.1039/c6sc02659a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/12/2016] [Indexed: 12/14/2022] Open
Abstract
Accurate monitoring of pH variations inside cells is important for the early diagnosis of diseases such as cancer. Even though a variety of different pH sensors are available, construction of a custom-made sensor array for measuring minute variations in a narrow biological pH window, using easily available constituents, is a challenge. Here we report two-component hybrid sensors derived from a protein and organic dye nanoparticles whose sensitivity range can be tuned by choosing different ratios of the components, to monitor the minute pH variations in a given system. The dye interacts noncovalently with the protein at lower pH and covalently at higher pH, triggering two distinguishable fluorescent signals at 700 and 480 nm, respectively. The pH sensitivity region of the probe can be tuned for every unit of the pH window resulting in custom-made pH sensors. These narrow range tunable pH sensors have been used to monitor pH variations in HeLa cells using the fluorescence imaging technique.
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Affiliation(s)
- Palapuravan Anees
- Chemical Sciences and Technology Division , Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) , Thiruvananthapuram 695019 , India .
| | - Karivachery V Sudheesh
- Chemical Sciences and Technology Division , Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) , Thiruvananthapuram 695019 , India .
| | - Purushothaman Jayamurthy
- Agroprocessing and Natural Products Division , Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) , Thiruvananthapuram , 695019 , India
| | - Arunkumar R Chandrika
- Molecular Neurobiology Division , Rajiv Gandhi Centre for Biotechnology (RGCB) , Thiruvananthapuram 695 014 , India
| | - Ramakrishnapillai V Omkumar
- Molecular Neurobiology Division , Rajiv Gandhi Centre for Biotechnology (RGCB) , Thiruvananthapuram 695 014 , India
| | - Ayyappanpillai Ajayaghosh
- Chemical Sciences and Technology Division , Academy of Scientific and Innovative Research (AcSIR) , CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) , Thiruvananthapuram 695019 , India .
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23
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Mehrotra P. Biosensors and their applications - A review. J Oral Biol Craniofac Res 2016; 6:153-9. [PMID: 27195214 PMCID: PMC4862100 DOI: 10.1016/j.jobcr.2015.12.002] [Citation(s) in RCA: 482] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022] Open
Abstract
The various types of biosensors such as enzyme-based, tissue-based, immunosensors, DNA biosensors, thermal and piezoelectric biosensors have been deliberated here to highlight their indispensable applications in multitudinous fields. Some of the popular fields implementing the use of biosensors are food industry to keep a check on its quality and safety, to help distinguish between the natural and artificial; in the fermentation industry and in the saccharification process to detect precise glucose concentrations; in metabolic engineering to enable in vivo monitoring of cellular metabolism. Biosensors and their role in medical science including early stage detection of human interleukin-10 causing heart diseases, rapid detection of human papilloma virus, etc. are important aspects. Fluorescent biosensors play a vital role in drug discovery and in cancer. Biosensor applications are prevalent in the plant biology sector to find out the missing links required in metabolic processes. Other applications are involved in defence, clinical sector, and for marine applications.
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24
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Zhu B, Zhang H, Pan S, Wang C, Ge J, Lee JS, Yao SQ. In Situ Proteome Profiling and Bioimaging Applications of Small-Molecule Affinity-Based Probes Derived From DOT1L Inhibitors. Chemistry 2016; 22:7824-36. [PMID: 27115831 DOI: 10.1002/chem.201600259] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Indexed: 01/01/2023]
Abstract
DOT1L is the sole protein methyltransferase that methylates histone H3 on lysine 79 (H3K79), and is a promising drug target against cancers. Small-molecule inhibitors of DOT1L such as FED1 are potential anti-cancer agents and useful tools to investigate the biological roles of DOT1L in human diseases. FED1 showed excellent in vitro inhibitory activity against DOT1L, but its cellular effect was relatively poor. In this study, we designed and synthesized photo-reactive and "clickable" affinity-based probes (AfBPs), P1 and P2, which were cell-permeable and structural mimics of FED1. The binding and inhibitory effects of these two probes against DOT1L protein were extensively investigated in vitro and in live mammalian cells (in situ). The cellular uptake and sub-cellular localization properties of the probes were subsequently studied in live-cell imaging experiments, and our results revealed that, whereas both P1 and P2 readily entered mammalian cells, most of them were not able to reach the cell nucleus where functional DOT1L resides. This offers a plausible explanation for the poor cellular activity of FED1. Finally with P1/P2, large-scale cell-based proteome profiling, followed by quantitative LC-MS/MS, was carried out to identify potential cellular off-targets of FED1. Amongst the more than 100 candidate off-targets identified, NOP2 (a putative ribosomal RNA methyltransferase) was further confirmed to be likely a genuine off-target of FED1 by preliminary validation experiments including pull-down/Western blotting (PD/WB) and cellular thermal shift assay (CETSA).
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Affiliation(s)
- Biwei Zhu
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Hailong Zhang
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Chenyu Wang
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore
| | - Jingyan Ge
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, P.R. China
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST) and Department of Biological Chemistry, University of Science & Technology, Republic of Korea
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science drive 3, Singapore, 117543, Singapore.
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25
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Huang Y, Shi J, Yuan D, Zhou N, Xu B. Length-dependent proteolytic cleavage of short oligopeptides catalyzed by matrix metalloprotease-9. Biopolymers 2016; 100:790-795. [PMID: 23520037 DOI: 10.1002/bip.22240] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/07/2013] [Accepted: 03/17/2013] [Indexed: 01/01/2023]
Abstract
Matrix metalloproteinases (MMPs), as the enzymes to degrade extracellular matrix proteins, play a major role on cell behaviors. Among them, MMP-9 usually catalyzes the degradation of proteins with the dominant cleavage at G/L site. Recent high-throughput screening suggests that S/L is a new major site for the cleavage when the substrates of MMP-9 are oligopeptides. Here we examine the cleavage sites of the N-terminal substituted short oligopeptides as the substrates of MMP-9. As the first example of such study of N-substituted small peptides, our results suggest that the substitute group at the N-terminal and the length of peptides significantly affect the position of the cleavage site on the oligopeptides, which provides a useful insight for the design of small peptide derivatives as the substrates of MMP-9.
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Affiliation(s)
- Yibing Huang
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, 2599 Qianjin St., Changchun 130012, China
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Dan Yuan
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Ning Zhou
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA
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26
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Jiao HF, Wang X, Yao K, Chen P, Jia Z, Peng Z, Li F. Self-assembly of all-conjugated block copolymer nanoparticles with tailoring size and fluorescence for live cell imaging. J Mater Chem B 2016; 4:7882-7887. [DOI: 10.1039/c6tb02211a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we describe aqueous nanoassemblies of rod–rod diblock polythiophene into core–shell nanospheres. Benefitting from their good photostability and low cytotoxicity, the nanoparticles meet the crucial requirements for cellular imaging and other biological applications.
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Affiliation(s)
- Hui-Feng Jiao
- Institute of Life Science
- Nanchang University
- Nanchang 330031
- China
| | - Xiaofeng Wang
- Department of Materials Science and Engineering
- Nanchang University
- Nanchang 330031
- China
| | - Kai Yao
- Institute of Photovoltaics
- Nanchang University
- Nanchang 330031
- China
| | - Peng Chen
- Institute of Life Science
- Nanchang University
- Nanchang 330031
- China
| | - Zhenrong Jia
- Department of Materials Science and Engineering
- Nanchang University
- Nanchang 330031
- China
| | - Zhiping Peng
- Department of Materials Science and Engineering
- Nanchang University
- Nanchang 330031
- China
| | - Fan Li
- Department of Materials Science and Engineering
- Nanchang University
- Nanchang 330031
- China
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27
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González-Vera JA, Morris MC. Fluorescent Reporters and Biosensors for Probing the Dynamic Behavior of Protein Kinases. Proteomes 2015; 3:369-410. [PMID: 28248276 PMCID: PMC5217393 DOI: 10.3390/proteomes3040369] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/30/2015] [Accepted: 10/23/2015] [Indexed: 12/20/2022] Open
Abstract
Probing the dynamic activities of protein kinases in real-time in living cells constitutes a major challenge that requires specific and sensitive tools tailored to meet the particular demands associated with cellular imaging. The development of genetically-encoded and synthetic fluorescent biosensors has provided means of monitoring protein kinase activities in a non-invasive fashion in their native cellular environment with high spatial and temporal resolution. Here, we review existing technologies to probe different dynamic features of protein kinases and discuss limitations where new developments are required to implement more performant tools, in particular with respect to infrared and near-infrared fluorescent probes and strategies which enable improved signal-to-noise ratio and controlled activation of probes.
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Affiliation(s)
- Juan A González-Vera
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
| | - May C Morris
- Cell Cycle Biosensors & Inhibitors, Department of Amino Acids, Peptides and Proteins, Institute of Biomolecules Max Mousseron (IBMM) CNRS-UMR 5247, 15 Avenue Charles Flahault, Montpellier 34093, France.
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28
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Abstract
Nanomaterials possess unique features which make them particularly attractive for biosensing applications. In particular, carbon nanotubes (CNTs) can serve as scaffolds for immobilization of biomolecules at their surface, and combine several exceptional physical, chemical, electrical, and optical characteristics properties which make them one of the best suited materials for the transduction of signals associated with the recognition of analytes, metabolites, or disease biomarkers. Here we provide a comprehensive review on these carbon nanostructures, in which we describe their structural and physical properties, functionalization and cellular uptake, biocompatibility, and toxicity issues. We further review historical developments in the field of biosensors, and describe the different types of biosensors which have been developed over time, with specific focus on CNT-conjugates engineered for biosensing applications, and in particular detection of cancer biomarkers.
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Affiliation(s)
| | - May C. Morris
- Cell Cycle Biosensors and Inhibitors, Faculté de Pharmacie, Institut des Biomolécules Max Mousseron, Centre National de la Recherche Scientifique-UMR 5247Montpellier, France
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29
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Shrestha P, Mandal S, Mao H. Mechanochemical Sensing: A Biomimetic Sensing Strategy. Chemphyschem 2015; 16:1829-37. [PMID: 25916512 DOI: 10.1002/cphc.201500080] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Indexed: 01/14/2023]
Abstract
Existing biosensors employ two major components: analyte recognition and signal transduction. Although specificity is achieved through analyte recognition, sensitivity is usually enhanced through a chemical amplification stage that couples the two main units in a sensor. Although highly sensitive, the extra chemical amplification stage complicates the sensing protocol. In addition, it separates the two elements spatiotemporally, reducing the real-time response of the biosensor. In this review, we discuss the new mechanochemical biosensors that employ mechanochemical coupling strategies to overcome these issues. By monitoring changes in the mechanical properties of a single-molecule template upon analyte binding, single-molecule sensitivity is reached. As chemical amplification becomes unnecessary in this single-molecule mechanochemical sensing (SMMS) strategy, real-time sensing is achieved.
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Affiliation(s)
- Prakash Shrestha
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242 (USA)
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242 (USA)
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242 (USA).
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30
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Zhang S, Karaca BT, VanOosten SK, Yuca E, Mahalingam S, Edirisinghe M, Tamerler C. Coupling Infusion and Gyration for the Nanoscale Assembly of Functional Polymer Nanofibers Integrated with Genetically Engineered Proteins. Macromol Rapid Commun 2015; 36:1322-8. [PMID: 26033345 PMCID: PMC5215549 DOI: 10.1002/marc.201500174] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/22/2015] [Indexed: 12/26/2022]
Abstract
Nanofibers featuring functional nanoassemblies show great promise as enabling constituents for a diverse range of applications in areas such as tissue engineering, sensing, optoelectronics, and nanophotonics due to their controlled organization and architecture. An infusion gyration method is reported that enables the production of nanofibers with inherent biological functions by simply adjusting the flow rate of a polymer solution. Sufficient polymer chain entanglement is obtained at Berry number > 1.6 to make bead‐free fibers integrated with gold nanoparticles and proteins, in the diameter range of 117–216 nm. Integration of gold nanoparticles into the nanofiber assembly is followed using a gold‐binding peptide tag genetically conjugated to red fluorescence protein (DsRed). Fluorescence microscopy analysis corroborated with Fourier transform infrared spectroscopy (FTIR) data confirms the integration of the engineered red fluorescence protein with the nanofibers. The gold nanoparticle decorated nanofibers having red fluorescence protein as an integral part keep their biological functionality including copper‐induced fluorescence quenching of the DsRed protein due to its selective Cu+2 binding. Thus, coupling the infusion gyration method in this way offers a simple nanoscale assembly approach to integrate a diverse repertoire of protein functionalities into nanofibers to generate biohybrid materials for imaging, sensing, and biomaterial applications.
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Affiliation(s)
- Siqi Zhang
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK
| | - Banu Taktak Karaca
- Bioengineering Research Center (BERC), Department of Mechanical Engineering, University of Kansas (KU), Lawrence, KS, 66045, USA
| | - Sarah Kay VanOosten
- Bioengineering Research Center (BERC), Department of Mechanical Engineering, University of Kansas (KU), Lawrence, KS, 66045, USA
| | - Esra Yuca
- Bioengineering Research Center (BERC), Department of Mechanical Engineering, University of Kansas (KU), Lawrence, KS, 66045, USA
| | | | - Mohan Edirisinghe
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK
| | - Candan Tamerler
- Bioengineering Research Center (BERC), Department of Mechanical Engineering, University of Kansas (KU), Lawrence, KS, 66045, USA
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31
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Zhu B, Ge J, Yao SQ. Developing new chemical tools for DNA methyltransferase 1 (DNMT 1): A small-molecule activity-based probe and novel tetrazole-containing inhibitors. Bioorg Med Chem 2015; 23:2917-27. [DOI: 10.1016/j.bmc.2015.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/25/2015] [Accepted: 03/02/2015] [Indexed: 12/31/2022]
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32
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Developing a genetically encoded green fluorescent protein mutant for sensitive light-up fluorescent sensing and cellular imaging of Hg(II). Anal Chim Acta 2015; 876:77-82. [DOI: 10.1016/j.aca.2015.03.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 01/17/2023]
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33
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Takaoka Y, Nishikawa Y, Hashimoto Y, Sasaki K, Hamachi I. Ligand-directed dibromophenyl benzoate chemistry for rapid and selective acylation of intracellular natural proteins. Chem Sci 2015; 6:3217-3224. [PMID: 28706692 PMCID: PMC5490417 DOI: 10.1039/c5sc00190k] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 03/20/2015] [Indexed: 12/28/2022] Open
Abstract
A rapid and selective protein labeling method, LDBB chemistry is a useful tool for natural protein imaging in living cells.
A rapid and selective ligand-directed chemical reaction was developed for the acylation of proteins in living cells on the basis of ligand-directed chemistry. By fine tuning the reactivity and stability of the phenyl ester derivatives, we successfully identified ortho-dibromophenyl benzoate as the optimal reactive motif. It was sufficiently stable in an aqueous buffer, hydrolyzing less than 10% after 13 h of incubation, but reactive enough for efficient and selective protein labeling in living mammalian cells, as well as in vitro (referred to as ligand-directed dibromophenyl benzoate (LDBB) chemistry). Using this chemistry, various fluorophores can be tethered to the target protein directly, which allows fluorescence visualization of the labeled protein in live cells using different colored fluorophore groups (including coumarin, fluorescein and rhodamine). Furthermore, this labeling is applicable to not only an overexpressed protein (E. coli dihydrofolate reductase) but also endogenous human carbonic anhydrase II and XII under living cell conditions. LDBB chemistry is a new entry of ligand-directed protein labeling methods, and should be particularly useful for the imaging of natural proteins in living cells.
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Affiliation(s)
- Yousuke Takaoka
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Yuki Nishikawa
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Yuki Hashimoto
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Kenta Sasaki
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry , Graduate School of Engineering Kyoto University , Katsura , Kyoto 615-8510 , Japan . ; ; Tel: +81-22-795-6557.,Core Research for Evolutional Science and Technology (CREST) , Japan Science and Technology Agency , 5 Sanbancho , Chiyoda-ku , Tokyo 102-0075 , Japan
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34
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Lalitha K, Nagarajan S. Strongly fluorescent organogels and self-assembled nanostructures from pyrene coupled coumarin derivatives: application in cell imaging. J Mater Chem B 2015; 3:5690-5701. [DOI: 10.1039/c5tb00694e] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present work reports facile synthesis of pyrene coupled coumarin derivatives which could form self-assembled molecular gel and nano-flakes. The nanomaterials obtained via a self-assembly process could be potentially used in fluorescence imaging applications.
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Affiliation(s)
- Krishnamoorthy Lalitha
- Organic Synthesis Group
- Department of Chemistry & The Centre for Nanotechnology and Advanced Biomaterials
- School of Chemical and Biotechnology
- SASTRA University
- Thanjavur-613401
| | - Subbiah Nagarajan
- Organic Synthesis Group
- Department of Chemistry & The Centre for Nanotechnology and Advanced Biomaterials
- School of Chemical and Biotechnology
- SASTRA University
- Thanjavur-613401
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35
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Kubota R, Hamachi I. Protein recognition using synthetic small-molecular binders toward optical protein sensing in vitro and in live cells. Chem Soc Rev 2015; 44:4454-71. [DOI: 10.1039/c4cs00381k] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review describes the recognition and sensing techniques of proteins and their building blocks by use of small synthetic binders.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Katsura
- Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Katsura
- Japan
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36
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Tamura T, Hamachi I. Recent progress in design of protein-based fluorescent biosensors and their cellular applications. ACS Chem Biol 2014; 9:2708-17. [PMID: 25317665 DOI: 10.1021/cb500661v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based fluorescent biosensors have emerged as key bioanalytical tools to visualize and quantify a wide range of biological substances and events in vitro, in cells, and even in vivo. On the basis of the construction method, the protein-based fluorescent biosensors can be principally classified into two classes: (1) genetically encoded fluorescent biosensors harnessing fluorescent proteins (FPs) and (2) semisynthetic biosensors comprised of protein scaffolds and synthetic fluorophores. Recent advances in protein engineering and chemical biology not only allowed the further optimization of conventional biosensors but also facilitated the creation of novel biosensors based on unique strategies. In this review, we survey the recent studies in the development and improvement of protein-based fluorescent biosensors and highlight the successful applications to live cell and in vivo imaging. Furthermore, we provide perspectives on possible future directions of the technique.
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Affiliation(s)
- Tomonori Tamura
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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Fluorescent biosensors for drug discovery new tools for old targets--screening for inhibitors of cyclin-dependent kinases. Eur J Med Chem 2014; 88:74-88. [PMID: 25314935 DOI: 10.1016/j.ejmech.2014.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/29/2014] [Accepted: 10/01/2014] [Indexed: 12/12/2022]
Abstract
Cyclin-dependent kinases play central roles in regulation of cell cycle progression, transcriptional regulation and other major biological processes such as neuronal differentiation and metabolism. These kinases are hyperactivated in most human cancers and constitute attractive pharmacological targets. A large number of ATP-competitive inhibitors of CDKs have been identified from natural substances, in high throughput screening assays, or through structure-guided approaches. Alternative strategies have been explored to target essential protein/protein interfaces and screen for allosteric inhibitors that trap inactive intermediates or prevent conformational activation. However this remains a major challenge given the highly conserved structural features of these kinases, and calls for new and alternative screening technologies. Fluorescent biosensors constitute powerful tools for the detection of biomolecules in complex biological samples, and are well suited to study dynamic processes and highlight molecular alterations associated with pathological disorders. They further constitute sensitive and selective tools which can be readily implemented to high throughput and high content screens in drug discovery programmes. Our group has developed fluorescent biosensors to probe cyclin-dependent kinases and gain insight into their molecular behaviour in vitro and in living cells. These tools provide a means of monitoring subtle alterations in the abundance and activity of CDK/Cyclins and can respond to compounds that interfere with the conformational dynamics of these kinases. In this review we discuss the different strategies which have been devised to target CDK/Cyclins, and describe the implementation of our CDK/Cyclin biosensors to develop HTS/HCS assays in view of identifying new classes of inhibitors for cancer therapeutics.
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Abstract
This special issue of Biotechnology Journal on fluorescent biosensors is edited by Dr. May Morris and Prof. Marc Blondel.
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Affiliation(s)
- May C Morris
- Cell Cycle Biosensors & Inhibitors, Institut des Biomolécules Max Mousseron (IBMM) - UMR5247, Faculté de Pharmacie, Montpellier, France, E-mail: .
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Van TNN, Pellerano M, Lykaso S, Morris MC. Fluorescent Protein Biosensor for Probing CDK/Cyclin Activity in vitro and in Living Cells. Chembiochem 2014; 15:2298-305. [DOI: 10.1002/cbic.201402318] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Indexed: 11/10/2022]
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40
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Tsukiji S, Hamachi I. Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications. Curr Opin Chem Biol 2014; 21:136-43. [DOI: 10.1016/j.cbpa.2014.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 07/11/2014] [Accepted: 07/14/2014] [Indexed: 11/17/2022]
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Ueda H, Dong J. From fluorescence polarization to Quenchbody: Recent progress in fluorescent reagentless biosensors based on antibody and other binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1951-1959. [PMID: 24931832 DOI: 10.1016/j.bbapap.2014.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 05/07/2014] [Accepted: 06/06/2014] [Indexed: 12/31/2022]
Abstract
Recently, antibody-based fluorescent biosensors are receiving considerable attention as a suitable biomolecule for diagnostics, namely, homogeneous immunoassay and also as an imaging probe. To date, several strategies for "reagentless biosensors" based on antibodies and natural and engineered binding proteins have been described. In this review, several approaches are introduced including a recently described fluorescent antibody-based biosensor Quenchbody, which works on the principle of fluorescence quenching of attached dye and its antigen-dependent release. The merits and possible demerits of each approach are discussed. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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Affiliation(s)
- Hiroshi Ueda
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 Japan.
| | - Jinhua Dong
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18, Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 Japan
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Morris MC. Spotlight on fluorescent biosensors-tools for diagnostics and drug discovery. ACS Med Chem Lett 2014; 5:99-101. [PMID: 24900780 DOI: 10.1021/ml400472e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Fluorescent biosensors constitute potent tools for probing biomolecules in their natural environment and for visualizing dynamic processes in complex biological samples, living cells, and organisms. They are well suited for highlighting molecular alterations associated with pathological disorders, thereby offering means of implementing sensitive and alternative technologies for diagnostic purposes. They constitute attractive tools for drug discovery programs, from high throughput screening assays to preclinical studies.
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Affiliation(s)
- May C. Morris
- Institut des Biomolécules Max Mousseron IBMM- UMR 5247, 15 Av. Charles Flahault, 34093 Montpellier, France
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Schallmey M, Frunzke J, Eggeling L, Marienhagen J. Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. Curr Opin Biotechnol 2014; 26:148-54. [PMID: 24480185 DOI: 10.1016/j.copbio.2014.01.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 12/31/2013] [Accepted: 01/07/2014] [Indexed: 11/25/2022]
Abstract
The engineering of microbial strains for the production of small molecules of biotechnological interest is a time-consuming, laborious and expensive process. This can be mostly attributed to the fact that good producers cannot be readily obtained by high-throughput screening approaches since increased product formation usually does not confer a clear phenotype to producing strain variants. Recently, advances were made in the design and construction of genetically encoded RNA aptamer-based or transcription factor-based biosensors for detecting small molecules at the single-cell level. The first promising examples for the application of these molecular biosensors in combination with fluorescent-activated cell sorting as a high-throughput screening device demonstrated the value and potential of these new tools for microbial strain development.
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Affiliation(s)
- Marcus Schallmey
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Julia Frunzke
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Lothar Eggeling
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany
| | - Jan Marienhagen
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich D-52425, Germany.
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Nakata E, Yukimachi Y, Nazumi Y, Uwate M, Maseda H, Uto Y, Hashimoto T, Okamoto Y, Hori H, Morii T. A novel strategy to design latent ratiometric fluorescent pH probes based on self-assembled SNARF derivatives. RSC Adv 2014. [DOI: 10.1039/c3ra43928c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Prével C, Pellerano M, Van TNN, Morris MC. Fluorescent biosensors for high throughput screening of protein kinase inhibitors. Biotechnol J 2013; 9:253-65. [PMID: 24357625 DOI: 10.1002/biot.201300196] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 07/24/2013] [Accepted: 10/30/2013] [Indexed: 12/11/2022]
Abstract
High throughput screening assays aim to identify small molecules that interfere with protein function, activity, or conformation, which can serve as effective tools for chemical biology studies of targets involved in physiological processes or pathways of interest or disease models, as well as templates for development of therapeutics in medicinal chemistry. Fluorescent biosensors constitute attractive and powerful tools for drug discovery programs, from high throughput screening assays, to postscreen characterization of hits, optimization of lead compounds, and preclinical evaluation of candidate drugs. They provide a means of screening for inhibitors that selectively target enzymatic activity, conformation, and/or function in vitro. Moreover, fluorescent biosensors constitute useful tools for cell- and image-based, multiplex and multiparametric, high-content screening. Application of fluorescence-based sensors to screen large and complex libraries of compounds in vitro, in cell-based formats or whole organisms requires several levels of optimization to establish robust and reproducible assays. In this review, we describe the different fluorescent biosensor technologies which have been applied to high throughput screens, and discuss the prerequisite criteria underlying their successful application. Special emphasis is placed on protein kinase biosensors, since these enzymes constitute one of the most important classes of therapeutic targets in drug discovery.
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Affiliation(s)
- Camille Prével
- CRBM-CNRS-UMR 5237, Chemical Biology and Nanotechnology for Therapeutics, 1919 Route de Mende, 34293 Montpellier, France
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46
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Cooper D, Uhm H, Tauzin LJ, Poddar N, Landes CF. Photobleaching lifetimes of cyanine fluorophores used for single-molecule Förster resonance energy transfer in the presence of various photoprotection systems. Chembiochem 2013; 14:1075-80. [PMID: 23733413 DOI: 10.1002/cbic.201300030] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 12/19/2022]
Abstract
Lengthening smFRET lifetimes: We investigated various photoprotection system combinations to find the combination that optimally extended the photobleach lifetime of a Cy3/Cy5 smFRET pair attached to a DNA hairpin in a single-molecule environment. We found that the glucose/glucose oxygen-scavenging solution in combination with redox-based photostabilization solutions yielded the longest average photobleaching lifetimes.
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Affiliation(s)
- David Cooper
- Department of Chemistry, Rice University, 6100 Main St. Houston, TX 77005, USA
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Tamura T, Kioi Y, Miki T, Tsukiji S, Hamachi I. Fluorophore Labeling of Native FKBP12 by Ligand-Directed Tosyl Chemistry Allows Detection of Its Molecular Interactions in Vitro and in Living Cells. J Am Chem Soc 2013; 135:6782-5. [DOI: 10.1021/ja401956b] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Tomonori Tamura
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Yoshiyuki Kioi
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Takayuki Miki
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | - Shinya Tsukiji
- Top Runner Incubation Center for
Academia-Industry Fusion, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
| | - Itaru Hamachi
- Department of Synthetic
Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
- Core Research for
Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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48
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Annoni C, Nakata E, Tamura T, Liew FF, Nakano S, Gelmi ML, Morii T. Construction of ratiometric fluorescent sensors by ribonucleopeptides. Org Biomol Chem 2013; 10:8767-9. [PMID: 23069733 DOI: 10.1039/c2ob26722e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ratiometric fluorescent sensors were constructed from RNA aptamers by generating modular ribonucleopeptide complexes. Fluorescent ribonucleopeptides containing fluorophore seminaphthorhodafluor tethered to their peptide subunit revealed a dual emission property, which permitted a ratiometric fluorescent measurement of a substrate-binding event. The strategy successfully afforded ratiometric fluorescent sensors for biologically active small ligands, tetracycline, dopamine and streptomycin.
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Affiliation(s)
- Chiara Annoni
- Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Sezione Chimica Generale Organica A. Marchesini, Universita` degli Studi di Milano, via Venezian 21, 20133 Milan, Italy
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49
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Takaoka Y, Ojida A, Hamachi I. Organische Proteinchemie und ihre Anwendung für Markierungen und Engineering in Lebendzellsystemen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201207089] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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50
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Chemical tagging of a drug target using 5-sulfonyl tetrazole. Bioorg Med Chem Lett 2013; 23:1608-11. [DOI: 10.1016/j.bmcl.2013.01.092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 01/19/2013] [Accepted: 01/22/2013] [Indexed: 12/16/2022]
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