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Ahmed WS, Geethakumari AM, Sultana A, Fatima A, Philip AM, Uddin SMN, Biswas KH. A slow but steady nanoLuc: R162A mutation results in a decreased, but stable, nanoLuc activity. Int J Biol Macromol 2024; 269:131864. [PMID: 38692549 DOI: 10.1016/j.ijbiomac.2024.131864] [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: 11/04/2023] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
NanoLuc (NLuc) luciferase has found extensive application in designing a range of biological assays, including gene expression analysis, protein-protein interaction, and protein conformational changes due to its enhanced brightness and small size. However, questions related to its mechanism of interaction with the substrate, furimazine, as well as bioluminescence activity remain elusive. Here, we combined molecular dynamics (MD) simulation and mutational analysis to show that the R162A mutation results in a decreased but stable bioluminescence activity of NLuc in living cells and in vitro. Specifically, we performed multiple, all-atom, explicit solvent MD simulations of the apo and furimazine-docked (holo) NLuc structures revealing differential dynamics of the protein in the absence and presence of the ligand. Further, analysis of trajectories for hydrogen bonds (H-bonds) formed between NLuc and furimazine revealed substantial H-bond interaction between R162 and Q32 residues. Mutation of the two residues in NLuc revealed a decreased but stable activity of the R162A, but not Q32A, mutant NLuc in live cell and in vitro assays performed using lysates prepared from cells expressing the proteins and with the furimazine substrate. In addition to highlighting the role of the R162 residue in NLuc activity, we believe that the mutant NLuc will find wide application in designing in vitro assays requiring extended monitoring of NLuc bioluminescence activity. SIGNIFICANCE: Bioluminescence has been extensively utilized in developing a variety of biological and biomedical assays. In this regard, engineering of brighter bioluminescent proteins, i.e. luciferases, has played a significant role. This is acutely exemplified by the engineering of the NLuc luciferase, which is small in size and displays much enhanced bioluminescence and thermal stability compared to previously available luciferases. While enhanced bioluminescent activity is desirable in a multitude of biological and biomedical assays, it would also be useful to develop variants of the protein that display a prolonged bioluminescence activity. This is specifically relevant in designing assays that require bioluminescence for extended periods, such as in the case of biosensors designed for monitoring slow enzymatic or cellular signaling reactions, without necessitating multiple rounds of luciferase substrate addition or any specialized reagents that result in increased assay costs. In the current manuscript, we report a mutant NLuc that possesses a stable and prolonged bioluminescence activity, albeit lower than the wild-type NLuc, and envisage a wider application of the mutant NLuc in designing biosensors for monitoring slower biological and biomedical events.
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Affiliation(s)
- Wesam S Ahmed
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Anupriya M Geethakumari
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asfia Sultana
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Asma Fatima
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Angelin M Philip
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - S M Nasir Uddin
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar
| | - Kabir H Biswas
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha 34110, Qatar.
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Dombrowsky CS, Happel D, Habermann J, Hofmann S, Otmi S, Cohen B, Kolmar H. A Conditionally Activated Cytosol-Penetrating Antibody for TME-Dependent Intracellular Cargo Delivery. Antibodies (Basel) 2024; 13:37. [PMID: 38804305 PMCID: PMC11130931 DOI: 10.3390/antib13020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/29/2024] Open
Abstract
Currently, therapeutic and diagnostic applications of antibodies are primarily limited to cell surface-exposed and extracellular proteins. However, research has been conducted on cell-penetrating peptides (CPP), as well as cytosol-penetrating antibodies, to overcome these limitations. In this context, a heparin sulfate proteoglycan (HSPG)-binding antibody was serendipitously discovered, which eventually localizes to the cytosol of target cells. Functional characterization revealed that the tested antibody has beneficial cytosol-penetrating capabilities and can deliver cargo proteins (up to 70 kDa) to the cytosol. To achieve tumor-specific cell targeting and cargo delivery through conditional activation of the cell-penetrating antibody in the tumor microenvironment, a single-chain Fc fragment (scFv) and a VL domain were isolated as masking units. Several in vitro assays demonstrated that fusing the masking protein with a cleavable linker to the cell penetration antibody results in the inactivation of antibody cell binding and internalization. Removal of the mask via MMP-9 protease cleavage, a protease that is frequently overexpressed in the tumor microenvironment (TME), led to complete regeneration of binding and cytosol-penetrating capabilities. Masked and conditionally activated cytosol-penetrating antibodies have the potential to serve as a modular platform for delivering protein cargoes addressing intracellular targets in tumor cells.
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Affiliation(s)
- Carolin Sophie Dombrowsky
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Dominic Happel
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Jan Habermann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Sarah Hofmann
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
| | - Sasi Otmi
- Inter-Lab, a Subsidiary of Merck KGaA, South Industrial Area, Yavne 8122004, Israel
| | - Benny Cohen
- Inter-Lab, a Subsidiary of Merck KGaA, South Industrial Area, Yavne 8122004, Israel
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Peter-Grünberg-Strasse 4, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
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Eguchi M, Yoshimura H, Ueda Y, Ozawa T. Split Luciferase-Fragment Reconstitution for Unveiling RNA Localization and Dynamics in Live Cells. ACS Sens 2023; 8:4055-4063. [PMID: 37889477 DOI: 10.1021/acssensors.3c01080] [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] [Indexed: 10/28/2023]
Abstract
The intracellular distribution and dynamics of RNAs play pivotal roles in various physiological phenomena. The ability to monitor the amount and localization of endogenous RNAs in living cells allows for elucidating the mechanisms of various intracellular events. Protein-based fluorescent RNA probes are now widely used to visualize and analyze RNAs in living cells. However, continuously monitoring the temporal changes in RNA localization and dynamics in living cells is challenging. In this study, we developed a bioluminescent probe for spatiotemporal monitoring of RNAs in living cells by using a split-luciferase reconstitution technique. The probe consists of split fragments of a bioluminescent protein, NanoLuc, connected with RNA-binding protein domains generated from a custom-made mutation of a PUM-HD. The probe showed rapid luminescence intensity changes in response to an increase or decrease in the amount of a target RNA in vitro. In live-cell imaging, temporal alteration of the intracellular distribution of endogenous β-actin mRNA was visualized in response to extracellular stimulation. Furthermore, the application of the probe to the visualization of the specific localization of β-actin mRNA in primary hippocampal neurons was conducted. These results demonstrate the capability of the bioluminescent RNA probe to monitor the changes in localization, dynamics, and the amount of target RNA in living cells.
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Affiliation(s)
- Masatoshi Eguchi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshibumi Ueda
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Wu Y, Jiang T. Developments in FRET- and BRET-Based Biosensors. MICROMACHINES 2022; 13:mi13101789. [PMID: 36296141 PMCID: PMC9610962 DOI: 10.3390/mi13101789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 05/25/2023]
Abstract
Resonance energy transfer technologies have achieved great success in the field of analysis. Particularly, fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) provide strategies to design tools for sensing molecules and monitoring biological processes, which promote the development of biosensors. Here, we provide an overview of recent progress on FRET- and BRET-based biosensors and their roles in biomedicine, environmental applications, and synthetic biology. This review highlights FRET- and BRET-based biosensors and gives examples of their applications with their design strategies. The limitations of their applications and the future directions of their development are also discussed.
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Affiliation(s)
- Yuexin Wu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Tianyu Jiang
- Shenzhen Research Institute of Shandong University, Shenzhen 518000, China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China
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Sousa J, Magalhães CM, González-Berdullas P, Esteves da Silva JCG, Pinto da Silva L. Comparative Investigation of the Chemiluminescent Properties of a Dibrominated Coelenterazine Analog. Int J Mol Sci 2022; 23:ijms23158490. [PMID: 35955625 PMCID: PMC9369366 DOI: 10.3390/ijms23158490] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Chemi- and bioluminescence are remarkable light-emitting phenomena, in which thermal energy is converted into excitation energy due to a (bio)chemical reaction. Among a wide variety of chemi-/bioluminescent systems, one of the most well-known and studied systems is that of marine imidazopyrazinones, such as Coelenterazine and Cypridina luciferin. Due to the increasing usefulness of their chemi-/bioluminescent reactions in terms of imaging and sensing applications, among others, significant effort has been made over the years by researchers to develop new derivatives with enhanced properties. Herein, we report the synthesis and chemiluminescent characterization of a novel dibrominated Coelenterazine analog. This novel compound consistently showed superior luminescence, in terms of total light output and emission lifetime, to natural imidazopyrazinones and commercially available analogs in aprotic media, while being capable of yellow light emission. Finally, this new compound showed enhanced chemiluminescence in an aqueous solution when triggered by superoxide anion, showing potential to be used as a basis for optimized probes for reactive oxygen species. In conclusion, bromination of the imidazopyrazinone scaffold appears to be a suitable strategy for obtaining Coelenterazines with enhanced properties.
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Affiliation(s)
- João Sousa
- Centro de Investigação em Química (CIQUP), Instituto de Ciências Moleculares (IMS), Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; (J.S.); (C.M.M.); (P.G.-B.); (J.C.G.E.d.S.)
| | - Carla M. Magalhães
- Centro de Investigação em Química (CIQUP), Instituto de Ciências Moleculares (IMS), Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; (J.S.); (C.M.M.); (P.G.-B.); (J.C.G.E.d.S.)
| | - Patricia González-Berdullas
- Centro de Investigação em Química (CIQUP), Instituto de Ciências Moleculares (IMS), Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; (J.S.); (C.M.M.); (P.G.-B.); (J.C.G.E.d.S.)
| | - Joaquim C. G. Esteves da Silva
- Centro de Investigação em Química (CIQUP), Instituto de Ciências Moleculares (IMS), Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; (J.S.); (C.M.M.); (P.G.-B.); (J.C.G.E.d.S.)
- LACOMEPHI, GreenUPorto, Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Luís Pinto da Silva
- Centro de Investigação em Química (CIQUP), Instituto de Ciências Moleculares (IMS), Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; (J.S.); (C.M.M.); (P.G.-B.); (J.C.G.E.d.S.)
- LACOMEPHI, GreenUPorto, Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- Correspondence:
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Tian X, Zhang Y, Li X, Xiong Y, Wu T, Ai HW. A luciferase prosubstrate and a red bioluminescent calcium indicator for imaging neuronal activity in mice. Nat Commun 2022; 13:3967. [PMID: 35803917 PMCID: PMC9270435 DOI: 10.1038/s41467-022-31673-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023] Open
Abstract
Although fluorescent indicators have been broadly utilized for monitoring bioactivities, fluorescence imaging, when applied to mammals, is limited to superficial targets or requires invasive surgical procedures. Thus, there is emerging interest in developing bioluminescent indicators for noninvasive mammalian imaging. Bioluminescence imaging (BLI) of neuronal activity is highly desired but hindered by insufficient photons needed to digitalize fast brain activities. In this work, we develop a luciferase prosubstrate deliverable at an increased dose and activated in vivo by nonspecific esterase. We further engineer a bright, bioluminescent indicator with robust responsiveness to calcium ions (Ca2+) and appreciable emission above 600 nm. Integration of these advantageous components enables the imaging of the activity of neuronal ensembles in awake mice minimally invasively with excellent signal-to-background and subsecond temporal resolution. This study thus establishes a paradigm for studying brain function in health and disease.
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Affiliation(s)
- Xiaodong Tian
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Yiyu Zhang
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Xinyu Li
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA ,grid.411643.50000 0004 1761 0411Present Address: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Ying Xiong
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Tianchen Wu
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA
| | - Hui-Wang Ai
- grid.27755.320000 0000 9136 933XDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XCenter for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22908 USA ,grid.27755.320000 0000 9136 933XThe UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908 USA
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