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Prentice JA, Kasivisweswaran S, van de Weerd R, Bridges AA. Biofilm dispersal patterns revealed using far-red fluorogenic probes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.15.603607. [PMID: 39071379 PMCID: PMC11275749 DOI: 10.1101/2024.07.15.603607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Bacteria frequently colonize niches by forming multicellular communities called biofilms. To explore new territories, cells exit biofilms through an active process called dispersal. Biofilm dispersal is essential for bacteria to spread between infection sites, yet how the process is executed at the single-cell level remains mysterious. Here, we characterize dispersal at unprecedented resolution for the global pathogen Vibrio cholerae . To do so, we first developed a far-red cell-labeling strategy that overcomes pitfalls of fluorescent protein-based approaches. We reveal that dispersal initiates at the biofilm periphery and ∼25% of cells never disperse. We define novel micro-scale patterns that occur during dispersal, including biofilm compression and the formation of dynamic channels. These patterns are attenuated in mutants that reduce overall dispersal or that increase dispersal at the cost of homogenizing local mechanical properties. Collectively, our findings provide fundamental insights into the mechanisms of biofilm dispersal, advancing our understanding of how pathogens disseminate.
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2
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Oppenheimer KG, Hager NA, McAtee CK, Filiztekin E, Shang C, Warnick JA, Bruchez MP, Brodsky JL, Prosser DC, Kwiatkowski AV, O’Donnell AF. Optimization of the fluorogen-activating protein tag for quantitative protein trafficking and colocalization studies in S. cerevisiae. Mol Biol Cell 2024; 35:mr5. [PMID: 38809589 PMCID: PMC11244157 DOI: 10.1091/mbc.e24-04-0174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/30/2024] Open
Abstract
Spatial and temporal tracking of fluorescent proteins (FPs) in live cells permits visualization of proteome remodeling in response to extracellular cues. Historically, protein dynamics during trafficking have been visualized using constitutively active FPs fused to proteins of interest. While powerful, such FPs label all cellular pools of a protein, potentially masking the dynamics of select subpopulations. To help study protein subpopulations, bioconjugate tags, including the fluorogen activation proteins (FAPs), were developed. FAPs are comprised of two components: a single-chain antibody (SCA) fused to the protein of interest and a malachite-green (MG) derivative, which fluoresces only when bound to the SCA. Importantly, the MG derivatives can be either cell-permeant or -impermeant, thus permitting isolated detection of SCA-tagged proteins at the cell surface and facilitating quantitative endocytic measures. To expand FAP use in yeast, we optimized the SCA for yeast expression, created FAP-tagging plasmids, and generated FAP-tagged organelle markers. To demonstrate FAP efficacy, we coupled the SCA to the yeast G-protein coupled receptor Ste3. We measured Ste3 endocytic dynamics in response to pheromone and characterized cis- and trans-acting regulators of Ste3. Our work significantly expands FAP technology for varied applications in S. cerevisiae.
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Affiliation(s)
| | - Natalie A. Hager
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | - Ceara K. McAtee
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | - Elif Filiztekin
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | - Chaowei Shang
- Department of Biological Sciences, University of Pittsburgh, PA 15260
| | | | - Marcel P. Bruchez
- Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213
| | | | - Derek C. Prosser
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284
| | - Adam V. Kwiatkowski
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261
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3
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Werner M, Thomas F. Brought to Light: A Fluorogenic Probe to Monitor Immunosuppressants. ACS CENTRAL SCIENCE 2024; 10:953-955. [PMID: 38799673 PMCID: PMC11117300 DOI: 10.1021/acscentsci.4c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Affiliation(s)
- Marius Werner
- Heidelberg University, Institute of Organic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Franziska Thomas
- Heidelberg University, Institute of Organic Chemistry, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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4
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Moore WM, Brea RJ, Knittel C, Wrightsman E, Hui B, Lou J, Ancajas CF, Best MD, Devaraj NK, Budin I. Subcellular imaging of lipids and sugars using genetically encoded proximity sensors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592120. [PMID: 38746395 PMCID: PMC11092643 DOI: 10.1101/2024.05.01.592120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Live cell imaging of lipids and other metabolites is a long-standing challenge in cell biology. Bioorthogonal labeling tools allow for the conjugation of fluorophores to several phospholipid classes, but cannot discern their trafficking between adjacent organelles or asymmetry across individual membrane leaflets. Here we present fluorogen-activating coincidence sensing (FACES), a chemogenetic tool capable of quantitatively imaging subcellular lipid pools and reporting their transbilayer orientation in living cells. FACES combines bioorthogonal chemistry with genetically encoded fluorogen-activating proteins (FAPs) for reversible proximity sensing of conjugated molecules. We first validate this approach for quantifying discrete phosphatidylcholine pools in the ER and mitochondria that are trafficked by lipid transfer proteins. We then show that transmembrane domain-containing FAPs can be used to reveal the membrane asymmetry of multiple lipid classes that are generated in the trans-Golgi network. Lastly, we demonstrate that FACES is a generalizable tool for subcellular bioorthogonal imaging by measuring changes in mitochondrial N -acetylhexosamine levels. These results demonstrate the use of fluorogenic tags for spatially-defined molecular imaging.
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5
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Mazzarella D, Bortolato T, Pelosi G, Dell'Amico L. Photocatalytic (3 + 2) dipolar cycloadditions of aziridines driven by visible-light. Chem Sci 2023; 15:271-277. [PMID: 38131079 PMCID: PMC10732004 DOI: 10.1039/d3sc05997a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Herein, we document the design and development of a novel (3 + 2) cycloaddition reaction aided by the activity of an organic photocatalyst and visible light. The process is extremely fast, taking place in a few minutes, with virtually complete atom economy. A large variety of structurally diverse aziridines were used as masked ylides in the presence of different types of dipolarophiles (28 examples with up to 94% yield and >95 : 5 dr). Mechanistic insights obtained from photophysical, electrochemical and experimental studies highlight that the chemistry is driven by the in situ generation of the reactive ylide through two consecutive electron-transfer processes. We also report an aerobic cascade process, where an additional oxidation step grants access to a vast array of pyrrole derivatives (19 examples with up to 95% yield). Interestingly, the extended aromatic core exhibits a distinctive absorption and emission profile, which can be easily used to tag the effectiveness of this covalent linkage.
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Affiliation(s)
- Daniele Mazzarella
- Department of Chemical Sciences, University of Padova Via Francesco Marzolo 1 35131 Padova Italy
| | - Tommaso Bortolato
- Department of Chemical Sciences, University of Padova Via Francesco Marzolo 1 35131 Padova Italy
| | - Giorgio Pelosi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma Parco Area delle Scienze 17 43124 Parma Italy
| | - Luca Dell'Amico
- Department of Chemical Sciences, University of Padova Via Francesco Marzolo 1 35131 Padova Italy
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6
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Wang C, Jiang W, Tan D, Huang L, Li J, Qiao Q, Yadav P, Liu X, Xu Z. Monitoring amyloid aggregation via a twisted intramolecular charge transfer (TICT)-based fluorescent sensor array. Chem Sci 2023; 14:4786-4795. [PMID: 37181777 PMCID: PMC10171079 DOI: 10.1039/d2sc06710b] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
Imaging amyloid-beta (Aβ) aggregation is critical for understanding the pathology and aiding the pre-symptomatic intervention of Alzheimer's disease (AD). Amyloid aggregation consists of multiple phases with increasing viscosities and demands probes with broad dynamic ranges and gradient sensitivities for continuous monitoring. Yet, existing probes designed based on the twisted intramolecular charge transfer (TICT) mechanism mainly focused on donor engineering, limiting the sensitivities and/or dynamic ranges of these fluorophores to a narrow window. Herein, using quantum chemical calculations, we investigated multiple factors affecting the TICT process of fluorophores. It includes the conjugation length, the net charge of the fluorophore scaffold, the donor strength, and the geometric pre-twisting. We have established an integrative framework for tuning TICT tendencies. Based on this framework, a platter of hemicyanines with varied sensitivities and dynamic ranges is synthesized, forming a sensor array and enabling the observation of various stages of Aβ aggregations. This approach will significantly facilitate the development of TICT-based fluorescent probes with tailored environmental sensitivities for numerous applications.
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Affiliation(s)
- Chao Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Wenchao Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Davin Tan
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Lu Huang
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
- Ocean College, Minjiang University Fuzhou 350108 China
| | - Jin Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
| | - Priya Yadav
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design 8 Somapah Road Singapore 487372 Singapore
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences 457 Zhongshan Road Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
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7
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Sokolov AI, Baleeva NS, Baranov MS. Halogen-Containing 4-Hydroxybenzylidene-Rhodanines as Fast Protein Fluorogens. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022050247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Ding Y, Jin Y, Peng T, Gao Y, Zang Y, He H, Li F, Zhang Y, Zhang H, Chen L. Fabrication of multifunctional metal-organic frameworks nanoparticles via layer-by-layer self-assembly to efficiently discover PSD95-nNOS uncouplers for stroke treatment. J Nanobiotechnology 2022; 20:379. [PMID: 35964123 PMCID: PMC9375364 DOI: 10.1186/s12951-022-01583-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/31/2022] [Indexed: 11/24/2022] Open
Abstract
Background Disruption of the postsynaptic density protein-95 (PSD95)—neuronal nitric oxide synthase (nNOS) coupling is an effective way to treat ischemic stroke, however, it still faces some challenges, especially lack of satisfactory PSD95-nNOS uncouplers and the efficient high throughput screening model to discover them. Results Herein, the multifunctional metal–organic framework (MMOF) nanoparticles as a new screening system were innovatively fabricated via layer-by-layer self-assembly in which His-tagged nNOS was selectively immobilized on the surface of magnetic MOF, and then PSD95 with green fluorescent protein (GFP-PSD95) was specifically bound on it. It was found that MMOF nanoparticles not only exhibited the superior performances including the high loading efficiency, reusability, and anti-interference ability, but also possessed the good fluorescent sensitivity to detect the coupled GFP-PSD95. After MMOF nanoparticles interacted with the uncouplers, they would be rapidly separated from uncoupled GFP-PSD95 by magnet, and the fluorescent intensities could be determined to assay the uncoupling efficiency at high throughput level. Conclusions In conclusion, MMOF nanoparticles were successfully fabricated and applied to screen the natural actives as potential PSD95-nNOS uncouplers. Taken together, our newly developed method provided a new material as a platform for efficiently discovering PSD95-nNOS uncouplers for stoke treatment. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-022-01583-7.
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Affiliation(s)
- Yingying Ding
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China
| | - Yang Jin
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China
| | - Tao Peng
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China
| | - Yankun Gao
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China
| | - Yang Zang
- College of Economics and Management, Anhui Agricultural University, Hefei, Anhui, 230036, People's Republic of China
| | - Hongliang He
- Department of Pharmacy, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China
| | - Fei Li
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China
| | - Yu Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China.
| | - Hongjuan Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China.
| | - Lina Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, People's Republic of China.
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9
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Khrulev AA, Baleeva NS, Kamzeeva PN, Baranov MS, Aralov AV. Cyanine Dyes as Fluorogens for FAST and NanoFAST Proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Zhang Y, Zhou W, Xu N, Wang G, Li J, An K, Jiang W, Zhou X, Qiao Q, Jiang X, Xu Z. Aniline as a TICT rotor to derive methine fluorogens for biomolecules: A curcuminoid-BF2 compound for lighting up HSA/BSA. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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He J, Zhou Y, Liu Y, Guo R, Jiang J, Bruchez MP. Fluorogen-Activating-Protein-Loaded Tantalum Oxide Nanoshells for in Vivo On-Demand Fluorescence/Photoacoustic Imaging. ACS APPLIED BIO MATERIALS 2022; 5:1057-1063. [PMID: 35191667 DOI: 10.1021/acsabm.1c01113] [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: 11/29/2022]
Abstract
Optical imaging of targeted compartments within living animals has been widely adopted in many research areas. In particular, various fluorescence-based probes and emerged photoacoustic molecules that enable sensitive and specific imaging through tissue have greatly advanced clinically relevant studies. However, delivery and signal penetration have placed requirements on the performance of conventional optical probes. Here, we use hallow tantalum oxide (TaOx) nanoparticles to enclose fluorogen-activating protein (FAP) for the in vivo fluorescence and photoacoustic imaging of cancer cells. We found that the TaOx shell can provide a natural cover for the enclosed fluorogen/FAP complexes, protecting them from photobleaching and common biodegradation. Moreover, we have developed a near-infrared excitable tetrafluorinated photoacoustic fluorogen for the specific and persistent photoacoustic imaging of tumors. We believe that this enclosing and delivery strategy of optical biomolecules will be an attractive alternative for bioimaging.
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Affiliation(s)
- Jianjun He
- College of Biology, Hunan University, Changsha 410082, China
| | - Yancen Zhou
- College of Biology, Hunan University, Changsha 410082, China
| | - Yinxia Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Rui Guo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Department of Biological Sciences, Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15217, United States
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12
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Visualizing G protein-coupled receptor homomers using photoactivatable dye localization microscopy. Methods Cell Biol 2022; 169:27-41. [DOI: 10.1016/bs.mcb.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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13
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Gao J, Prachyathipsakul T, Thayumanavan S. Multichannel dual protein sensing using amphiphilic supramolecular assemblies. Chem Commun (Camb) 2021; 57:12828-12831. [PMID: 34787137 PMCID: PMC8771897 DOI: 10.1039/d1cc05407d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein sensing strategies have implications in detection of many human pathologies. Here, a supramolecular strategy for sensing two different proteins using a multichannel readout approach is outlined. Protein-ligand binding or enzymatic cleavage can both be programmed to induce supramolecular disassembly, which leads to fluorescence enhancement via aggregation-induced emission (AIE), protein-induced fluorescence enhancement (PIFE), or disassembly-induced fluorescence enhancement (DIFE). The accompanying signal change from two different fluorophores and their patterns are then used for specific protein sensing.
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Affiliation(s)
- Jingjing Gao
- Department of Chemistry, University of Massachusetts Amherst, MA, 01002, USA.
| | | | - S Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, MA, 01002, USA.
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14
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Baleeva NS, Smirnov AY, Myasnyanko IN, Gavrikov AS, Baranov MS. A Thiophene Analog of the GFP Chromophore As Fluorogen for FAST Protein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021050198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Kolesov DV, Sokolinskaya EL, Lukyanov KA, Bogdanov AM. Molecular Tools for Targeted Control of Nerve Cell Electrical Activity. Part II. Acta Naturae 2021; 13:17-32. [PMID: 35127143 PMCID: PMC8807539 DOI: 10.32607/actanaturae.11415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
In modern life sciences, the issue of a specific, exogenously directed manipulation of a cell's biochemistry is a highly topical one. In the case of electrically excitable cells, the aim of the manipulation is to control the cells' electrical activity, with the result being either excitation with subsequent generation of an action potential or inhibition and suppression of the excitatory currents. The techniques of electrical activity stimulation are of particular significance in tackling the most challenging basic problem: figuring out how the nervous system of higher multicellular organisms functions. At this juncture, when neuroscience is gradually abandoning the reductionist approach in favor of the direct investigation of complex neuronal systems, minimally invasive methods for brain tissue stimulation are becoming the basic element in the toolbox of those involved in the field. In this review, we describe three approaches that are based on the delivery of exogenous, genetically encoded molecules sensitive to external stimuli into the nervous tissue. These approaches include optogenetics (overviewed in Part I), as well as chemogenetics and thermogenetics (described here, in Part II), which is significantly different not only in the nature of the stimuli and structure of the appropriate effector proteins, but also in the details of experimental applications. The latter circumstance is an indication that these are rather complementary than competing techniques.
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Affiliation(s)
- D. V. Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - E. L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - K. A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - A. M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
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Lyu Z, Genereux JC. Methodologies for Measuring Protein Trafficking across Cellular Membranes. Chempluschem 2021; 86:1397-1415. [PMID: 34636167 DOI: 10.1002/cplu.202100304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/19/2021] [Indexed: 12/11/2022]
Abstract
Nearly all proteins are synthesized in the cytosol. The majority of this proteome must be trafficked elsewhere, such as to membranes, to subcellular compartments, or outside of the cell. Proper trafficking of nascent protein is necessary for protein folding, maturation, quality control and cellular and organismal health. To better understand cellular biology, molecular and chemical technologies to properly characterize protein trafficking (and mistrafficking) have been developed and applied. Herein, we take a biochemical perspective to review technologies that enable spatial and temporal measurement of protein distribution, focusing on both the most widely adopted methodologies and exciting emerging approaches.
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Affiliation(s)
- Ziqi Lyu
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
| | - Joseph C Genereux
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, 92521, Riverside, CA, USA
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17
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The Cutting Edge of Disease Modeling: Synergy of Induced Pluripotent Stem Cell Technology and Genetically Encoded Biosensors. Biomedicines 2021; 9:biomedicines9080960. [PMID: 34440164 PMCID: PMC8392144 DOI: 10.3390/biomedicines9080960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 08/02/2021] [Indexed: 11/17/2022] Open
Abstract
The development of cell models of human diseases based on induced pluripotent stem cells (iPSCs) and a cell therapy approach based on differentiated iPSC derivatives has provided a powerful stimulus in modern biomedical research development. Moreover, it led to the creation of personalized regenerative medicine. Due to this, in the last decade, the pathological mechanisms of many monogenic diseases at the cell level have been revealed, and clinical trials of various cell products derived from iPSCs have begun. However, it is necessary to reach a qualitatively new level of research with cell models of diseases based on iPSCs for more efficient searching and testing of drugs. Biosensor technology has a great application prospect together with iPSCs. Biosensors enable researchers to monitor ions, molecules, enzyme activities, and channel conformation in live cells and use them in live imaging and drug screening. These probes facilitate the measurement of steady-state concentrations or activity levels and the observation and quantification of in vivo flux and kinetics. Real-time monitoring of drug action in a specific cellular compartment, organ, or tissue type; the ability to screen at the single-cell resolution; and the elimination of the false-positive results caused by low drug bioavailability that is not detected by in vitro testing methods are a few of the benefits of using biosensors in drug screening. Here, we discuss the possibilities of using biosensor technology in combination with cell models based on human iPSCs and gene editing systems. Furthermore, we focus on the current achievements and problems of using these methods.
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18
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Wang X, Wang Q, Zhang Q, Han X, Xu S, Yin D, Hu HY. Developing fluoromodule-based probes for in vivo monitoring the bacterial infections and antibiotic responses. Talanta 2021; 233:122610. [PMID: 34215094 DOI: 10.1016/j.talanta.2021.122610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/26/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Recently, antibiotic resistant has become a serious public health concern, which warrants new generations of antibiotics to be developed. Pharmacodynamic evaluation is crucial in drug discovery processes. Despite numerous advanced imaging systems are available nowadays, technologies for the sensitive in vivo diagnosis of bacterial infections and direct visualization of drug efficacy are yet to be developed. In this study, we have developed novel near-infrared (NIR) fluorogenic probes. These probes are dark in solution but highly fluorescent when bound to the cognate reporter, fluorogen-activating protein (FAP). We established the in vivo bacterial infection model using FAP_dH6.2 recombinantly expressed E. coli and applied this NIR fluoromodule-based system for diagnosing bacterial infections and monitoring disease progressions and its responses to a type of antibiotics through classic mechanism of membrane lysis. This NIR fluoromodule-based system will discover new information on bacterial infections and identify newer antibacterial entities.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qinghua Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Qingyang Zhang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Xiaowan Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Shengnan Xu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Dali Yin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China.
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Luther DC, Jeon T, Goswami R, Nagaraj H, Kim D, Lee YW, Rotello VM. Protein Delivery: If Your GFP (or Other Small Protein) Is in the Cytosol, It Will Also Be in the Nucleus. Bioconjug Chem 2021; 32:891-896. [PMID: 33872490 PMCID: PMC8508718 DOI: 10.1021/acs.bioconjchem.1c00103] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Intracellular protein delivery is a transformative tool for biologics research and medicine. Delivery into the cytosol allows proteins to diffuse throughout the cell and access subcellular organelles. Inefficient delivery caused by endosomal entrapment is often misidentified as cytosolic delivery. This inaccuracy muddles what should be a key checkpoint in assessing delivery efficiency. Green fluorescent protein (GFP) is a robust cargo small enough to passively diffuse from the cytosol into the nucleus. Fluorescence of GFP in the nucleus is a direct readout for cytosolic access and effective delivery. Here, we highlight recent examples from the literature for the accurate assessment of cytosolic protein delivery using GFP fluorescence in the cytosol and nucleus.
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Affiliation(s)
- David C. Luther
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA
- These authors contributed equally
| | - Taewon Jeon
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, 230 Stockbridge Road, Amherst, MA 01003, USA
- These authors contributed equally
| | - Ritabrita Goswami
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Harini Nagaraj
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Dongkap Kim
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA
- Center for Biomaterials, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
- Department of Chemistry, Hanyang University, Seoul 04763, Republic of Korea
| | - Yi-Wei Lee
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Vincent M. Rotello
- Department of Chemistry, University of Massachusetts, 710 North Pleasant Street, Amherst, MA 01003, USA
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Chen Y. Recent progress in natural product-based inhibitor screening with enzymatic fluorescent probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1778-1787. [PMID: 33885636 DOI: 10.1039/d1ay00245g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Drug discovery is a complex process in which many challenges need to be overcome, from the discovery of a drug candidate to ensuring the efficacy and safety of the candidate in humans. Modern analytical methods allow tens of thousands of drug candidates to be screened for their inhibition of specific enzymes or receptors. In recent years, fluorescent probes have been used for the detection and diagnosis of human pathogens as well as high-throughput screening. This review focuses on recent progress in organic small-molecule based enzyme-activated fluorescent probes for screening of inhibitors from natural products. The contents include the construction of fluorescent probes, working mechanism and the process of inhibitor screening. The progress suggests that fluorescent probes are a vital and rapidly growing technology for inhibitor screening of enzymes, in particular, inhibitor screening in situ.
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Affiliation(s)
- Yi Chen
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, China. and University of Chinese Academy of Sciences, Beijing, 100049, China
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21
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Al Mazid MF, Shkel O, Kharkivska Y, Lee JS. Application of fluorescent turn-on aptamers in RNA studies. Mol Omics 2021; 17:483-491. [PMID: 34137415 DOI: 10.1039/d1mo00085c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an intermediate player between DNA transcription and protein translation. RNAs also interact with other macromolecules and metabolites and regulate their fate. The emerging number of RNA identifications expanded new areas of study to determine their applicability and functional analysis. Recently, extensive research has been focused on visualizing RNA in living biological samples and a method has been developed by the evolution of specific fluorophore-binding aptamers through the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method. Several promising fluorescent turn-on aptamers are currently available, and they can detect RNA-RNA, RNA-protein, ligand binding, small molecule, and metabolite interactions in vitro and under live-cell conditions. Here we review the currently available fluorescent turn-on aptamers and discuss their applicability for analyzing the fate of targeted RNAs in in vitro and in vivo systems.
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Affiliation(s)
| | - Olha Shkel
- Bio-Med Program KIST-School UST, Seoul, 02792, Republic of Korea
| | | | - Jun-Seok Lee
- Department of Pharmacology, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
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22
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Hoelzel CA, Zhang X. Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies. Chembiochem 2020; 21:1935-1946. [PMID: 32180315 PMCID: PMC7367766 DOI: 10.1002/cbic.202000037] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/27/2020] [Indexed: 12/25/2022]
Abstract
Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self-labeling protein tags, focusing mainly on the application of HaloTag and SNAP-tag systems. We describe the latest developments in small-molecule probes that enable fluorogenic (no wash) imaging and super-resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP-tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self-labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.
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Affiliation(s)
- Conner A Hoelzel
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
| | - Xin Zhang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
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23
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Abstract
Most biological molecules are intrinsically non- or weakly-fluorescent, hence requiring labeling with an external fluorophore(s) to be studied via fluorescence-based techniques. However, such labeling could perturb the native property of the system in question. One effective strategy to minimize such undesirable perturbation is to use fluorophores that are simple analogs of natural amino acids. In this chapter, we describe the synthesis and spectroscopic utility of two indole-based fluorophores, 4-cynaotryprophan (4CN-Trp) and 4-cyanoindole-2'-deoxyribonucleoside (4CNI-NS), with a focus on 4CN-Trp. This unnatural amino acid, which is only slightly larger than its natural counterpart, tryptophan (Trp), exhibits unique photophysical properties, making it a versatile fluorophore in biological spectroscopic and imaging applications. Through several specific examples, we highlight its broad utility in the study of various biological problems and processes.
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