1
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Chen H, Chen TY. From Monomers to Hexamers: A Theoretical Probability of the Neighbor Density Approach to Dissect Protein Oligomerization in Cells. Anal Chem 2024; 96:895-903. [PMID: 38156958 PMCID: PMC10842889 DOI: 10.1021/acs.analchem.3c04728] [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: 01/03/2024]
Abstract
Deciphering the oligomeric state of proteins within cells is pivotal to understanding their role in intricate cellular processes. With the recent advances in single-molecule localization microscopy, previous efforts have harnessed protein location density approaches, coupled with simulations, to extract membrane protein oligomeric states in cells, highlighting the value of such techniques. However, a comprehensive theoretical approach that can be universally applied across different proteins (e.g., membrane and cytosolic proteins) remains elusive. Here, we introduce the theoretical probability of neighbor density (PND) as a robust tool to discern protein oligomeric states in cellular environments. Utilizing our approach, the theoretical PND was validated against simulated data for both membrane and cytosolic proteins, consistently aligning with experimental baselines for membrane proteins. This congruence was maintained even when adjusting for protein concentrations or exploring proteins of various oligomeric states. The strength of our method lies not only in its precision but also in its adaptability, accommodating diverse cellular protein scenarios without compromising the accuracy. The development and validation of the theoretical PND facilitate accurate protein oligomeric state determination and bolster our understanding of protein-mediated cellular functions.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204
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2
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Huang W, Cheng Y, Zhai J, Qin Y, Zhang W, Xie X. Expanded single-color barcoding in microspheres with fluorescence anisotropy for multiplexed biochemical detection. Analyst 2023; 148:4406-4413. [PMID: 37552039 DOI: 10.1039/d3an00938f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Single-color barcoding strategies could break the limits of spectral crosstalk in conventional intensity-based fluorescence barcodes. Fluorescence anisotropy (FA), a self-referencing quantity able to differentiate spectrally similar fluorophores, is highly attractive in designing fluorescent barcodes within a limited emission window. In this study, FA-based encoding of polystyrene (PS) microspheres was realized for the first time. The FA signals of fluorophores were stabilized inside PS microspheres owing to hampered rotational motion. Fluorescent labels were incorporated with similar emission but different structures, symmetries, and lifetimes. On the one hand, Förster Resonance Energy Transfer (FRET) including homo-FRET and hetero-FRET resulted in a decrease of steady-state FA with increasing dye loading, converting conventional intensity-based codes into FA-based codes. On the other hand, mixing dyes with different intrinsic FA values generated different FA values at the same fluorescence intensity level. Single color 5-plex FA-encoded microspheres were demonstrated and decoded on a homemade microscopic FA imaging platform in real time. The FA-encoded microspheres were successfully applied to detect the oligonucleotide of the foodborne bacterium, Bacillus cereus, without spectral crosstalk between the encoding and reporting dyes. Overall, FA-based encoding with an expanded coding capacity in the FA dimension holds great potential in multiplexed high-throughput chemical and biological analyses.
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Affiliation(s)
- Wenyu Huang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Yu Cheng
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Jingying Zhai
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuemin Qin
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Weian Zhang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Xiaojiang Xie
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.
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3
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Lu YH, Jenkins MC, Richardson KG, Palui S, Islam MS, Tripathy J, Finn MG, Dickson RM. Sequential Two-Photon Delayed Fluorescence Anisotropy for Macromolecular Size Determination. J Phys Chem B 2023; 127:3861-3869. [PMID: 37096986 PMCID: PMC10165651 DOI: 10.1021/acs.jpcb.3c01236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Time-resolved fluorescence anisotropy (FA) uses the fluorophore depolarization rate to report on rotational diffusion, conformation changes, and intermolecular interactions in solution. Although FA is a rapid, sensitive, and nondestructive tool for biomolecular interaction studies, the short (∼ns) fluorescence lifetime of typical dyes largely prevents the application of FA on larger macromolecular species and complexes. By using triplet shelving and recovery of optical excitation, we introduce optically activated delayed fluorescence anisotropy (OADFA) measurements using sequential two-photon excitation, effectively stretching fluorescence anisotropy measurement times from the nanosecond scale to hundreds of microseconds. We demonstrate this scheme for measuring slow depolarization processes of large macromolecular complexes, derive a quantitative rate model, and perform Monte Carlo simulations to describe the depolarization process of OADFA at the molecular level. This setup has great potential to enable future biomacromolecular and colloidal studies.
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Affiliation(s)
- Yi-Han Lu
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Matthew C Jenkins
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Katherine G Richardson
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Sayan Palui
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Md Shariful Islam
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Jagnyaseni Tripathy
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- Department of Physics, School of Applied Sciences, KIIT University, Bhubaneswar 751024, India
| | - M G Finn
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Robert M Dickson
- School of Chemistry and Biochemistry and Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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4
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Chen H, Chen TY. Probing Oxidant Effects on Superoxide Dismutase 1 Oligomeric States in Live Cells Using Single-Molecule Fluorescence Anisotropy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:49-57. [PMID: 37122833 PMCID: PMC10131266 DOI: 10.1021/cbmi.3c00002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 05/02/2023]
Abstract
The protein Cu/Zn superoxide dismutase (SOD1) is known to function as a dimer, but its concentration in cells (∼50 μM) and the dimerization constant (K d of 500 μM) results suggest that it exists in a monomer-dimer equilibrium. It is unclear how the oligomeric state of SOD1 changes when cells are initially exposed to high levels of extracellular oxidative stress. To address this problem, we introduced the single-molecule fluorescence anisotropy (smFA) assay to explore SOD1 oligomeric states in live COS7 cells. smFA specifically probes the fluorescence polarization changes caused by molecular rotations where the fast-rotating molecules (either due to smaller hydrodynamic volume or less viscous environments) deteriorate the emission polarization and thus lower the anisotropy. After validating that smFA is effective in distinguishing monomeric and dimeric fluorescence proteins, we overexpressed SOD1 in live COS7 cells and investigated how its oligomeric state changes under basal, 2 h, and 24 h 100 μM H2O2 treatments. We found that treating cells with H2O2 promotes SOD1 dimerization and decreases cellular viscosity in 2 h. Interestingly, prolonged H2O2 treatments show similar results as the basal conditions, indicating that cells return to a steady state similar to the basal state after 24 h, despite the presence of H2O2. Our results demonstrate that SOD1 changes its oligomeric state equilibrium in response to extracellular oxidative stresses. smFA will open new opportunities to explore the relationship between the SOD1 oligomer state and its H2O2-based signaling and transcription regulation roles.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University
of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University
of Houston, Houston, Texas 77204, United States
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5
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Volpato A, Ollech D, Alvelid J, Damenti M, Müller B, York AG, Ingaramo M, Testa I. Extending fluorescence anisotropy to large complexes using reversibly switchable proteins. Nat Biotechnol 2023; 41:552-559. [PMID: 36217028 PMCID: PMC10110461 DOI: 10.1038/s41587-022-01489-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/26/2022] [Indexed: 11/08/2022]
Abstract
The formation of macromolecular complexes can be measured by detection of changes in rotational mobility using time-resolved fluorescence anisotropy. However, this method is limited to relatively small molecules (~0.1-30 kDa), excluding the majority of the human proteome and its complexes. We describe selective time-resolved anisotropy with reversibly switchable states (STARSS), which overcomes this limitation and extends the observable mass range by more than three orders of magnitude. STARSS is based on long-lived reversible molecular transitions of switchable fluorescent proteins to resolve the relatively slow rotational diffusivity of large complexes. We used STARSS to probe the rotational mobility of several molecular complexes in cells, including chromatin, the retroviral Gag lattice and activity-regulated cytoskeleton-associated protein oligomers. Because STARSS can probe arbitrarily large structures, it is generally applicable to the entire human proteome.
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Affiliation(s)
- Andrea Volpato
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dirk Ollech
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jonatan Alvelid
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Martina Damenti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Barbara Müller
- Department of Infectious Diseases, Virology, Centre for Integrative Infectious Disease Research, University Hospital Heidelberg, Heidelberg, Germany
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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Yan L, Yang H, Liu N, Meng F, Zhang S. A photochromic salicylaldehyde hydrazone derivative based on CN isomerization and ESIPT mechanisms and its detection of Al 3+ in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 275:121116. [PMID: 35316626 DOI: 10.1016/j.saa.2022.121116] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/01/2022] [Accepted: 03/05/2022] [Indexed: 06/14/2023]
Abstract
A simple photochromic Schiff base was successfully prepared by the condensation of salicylaldehyde and benzoyl hydrazine. This compound has reversible photochromic properties based on isomerization and ESIPT mechanisms. In organic solvents, after irradiation with 365 nm UV light for 2 min, the absorption peak at 367 nm of the compound showed a significant decrease, while a double absorption peak appeared at 418 nm and 438 nm, accompanied by a significant change of the solution color from colorless to yellow. The compound can also complex with Al3+ at the molar ratio of 2:1 in the water solution (acetonitrile/water, v/v, 1:99), resulting in significantly enhanced fluorescence of the compound, so as to achieve fluorescence detection of Al3+ in living cells and water samples.
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Affiliation(s)
- Liqiang Yan
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, Guangxi 541006, PR China.
| | - Hong Yang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, Guangxi 541006, PR China
| | - Nan Liu
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, Guangxi 541006, PR China
| | - Fengjuan Meng
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, Guangxi 541006, PR China
| | - Shiqing Zhang
- College of Chemistry and Bioengineering, Guilin University of Technology, Guilin, Guangxi 541006, PR China
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7
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Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification. Nat Commun 2022; 13:1850. [PMID: 35387971 PMCID: PMC8986857 DOI: 10.1038/s41467-022-29508-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/18/2022] [Indexed: 11/20/2022] Open
Abstract
Genetically-encoded biosensors based on a single fluorescent protein are widely used to visualize analyte levels or enzymatic activities in cells, though usually to monitor relative changes rather than absolute values. We report photochromism-enabled absolute quantification (PEAQ) biosensing, a method that leverages the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity. We develop proof-of-concept photochromic variants of the popular GCaMP family of Ca2+ biosensors, and show that these can be used to resolve dynamic changes in the absolute Ca2+ concentration in live cells. We also develop intermittent quantification, a technique that combines absolute aquisitions with fast fluorescence acquisitions to deliver fast but fully quantitative measurements. We also show how the photochromism-based measurements can be expanded to situations where the absolute illumination intensities are unknown. In principle, PEAQ biosensing can be applied to other biosensors with photochromic properties, thereby expanding the possibilities for fully quantitative measurements in complex and dynamic systems. Biosensors often report relative rather than absolute values. Here the authors report a method that utilises the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity: photochromism-enabled absolute quantification (PEAQ) biosensing.
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8
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Yahav G, Weber Y, Duadi H, Pawar S, Fixler D. Classification of fluorescent anisotropy decay based on the distance approach in the frequency domain. OPTICS EXPRESS 2022; 30:6176-6192. [PMID: 35209559 DOI: 10.1364/oe.453108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Frequency-domain (FD) fluorometry is a widely utilized tool to probe unique features of complex biological structures, which may serve medical diagnostic purposes. The conventional data analysis approaches used today to extract the fluorescence intensity or fluorescence anisotropy (FA) decay data suffer from several drawbacks and are inherently limited by the characteristics and complexity of the decay models. This paper presents the squared distance (D2) technique, which categorized samples based on the direct frequency response data (FRD) of the FA decay. As such, it improves the classification ability of the FD measurements of the FA decay as it avoids any distortion that results from the challenged translation into time domain data. This paper discusses the potential use of the D2 approach to classify biological systems. Mathematical formulation of D2 technique adjusted to the FRD of the FA decay is described. In addition, it validates the D2 approach using 2 simulated data sets of 6 groups with similar widely and closely spaced FA decay data as well as in experimental data of 4 samples of a fluorophore-solvent (fluorescein-glycerol) system. In the simulations, the classification accuracy was above 95% for all 6 groups. In the experimental data, the classification accuracy was 100%. The D2 approach can help classify samples whose FA decay data are difficult to extract making FA in the FD a realistic diagnostic tool. The D2 approach offers an advanced method for sorting biological samples with differences beyond the practical temporal resolution limit in a reliable and efficient manner based on the FRD of their time-resolved fluorescence measurements thereby achieving better diagnostic quality in a shorter time.
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9
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POLArIS, a versatile probe for molecular orientation, revealed actin filaments associated with microtubule asters in early embryos. Proc Natl Acad Sci U S A 2021; 118:2019071118. [PMID: 33674463 DOI: 10.1073/pnas.2019071118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Biomolecular assemblies govern the physiology of cells. Their function often depends on the changes in molecular arrangements of constituents, both in the positions and orientations. While recent advancements of fluorescence microscopy including super-resolution microscopy have enabled us to determine the positions of fluorophores with unprecedented accuracy, monitoring the orientation of fluorescently labeled molecules within living cells in real time is challenging. Fluorescence polarization microscopy (FPM) reports the orientation of emission dipoles and is therefore a promising solution. For imaging with FPM, target proteins need labeling with fluorescent probes in a sterically constrained manner, but because of difficulties in the rational three-dimensional design of protein connection, a universal method for constrained tagging with fluorophore was not available. Here, we report POLArIS, a genetically encoded and versatile probe for molecular orientation imaging. Instead of using a direct tagging approach, we used a recombinant binder connected to a fluorescent protein in a sterically constrained manner that can target specific biomolecules of interest by combining with phage display screening. As an initial test case, we developed POLArISact, which specifically binds to F-actin in living cells. We confirmed that the orientation of F-actin can be monitored by observing cells expressing POLArISact with FPM. In living starfish early embryos expressing POLArISact, we found actin filaments radially extending from centrosomes in association with microtubule asters during mitosis. By taking advantage of the genetically encoded nature, POLArIS can be used in a variety of living specimens, including whole bodies of developing embryos and animals, and also be expressed in a cell type/tissue specific manner.
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10
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Jain P, Aida T, Motosuke M. Fluorescence Anisotropy as a Temperature-Sensing Molecular Probe Using Fluorescein. MICROMACHINES 2021; 12:1109. [PMID: 34577751 PMCID: PMC8469510 DOI: 10.3390/mi12091109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/08/2021] [Accepted: 09/12/2021] [Indexed: 01/28/2023]
Abstract
Fluorescence anisotropy, a technique to study the folding state of proteins or affinity of ligands, is used in this present work as a temperature sensor, to measure the microfluidic temperature field, by adding fluorophore in the liquid. Fluorescein was used as a temperature-sensing probe, while glycerol-aq. ammonia solution was used as a working fluid. Fluorescence anisotropy of fluorescein was measured by varying various parameters. Apart from this, a comparison of fluorescence anisotropy and fluorescence intensity is also performed to demonstrate the validity of anisotropy to be applied in a microfluidic field with non-uniform liquid thickness. Viscosity dependence and temperature dependence on the anisotropy are also clarified; the results indicate an appropriate selection of relation between molecule size and viscosity is important to obtain a large temperature coefficient in anisotropy. Furthermore, a practical calibration procedure of the apparatus constant is proposed. In addition, the potential of temperature imaging is confirmed by the measurement of temperature distribution under focused laser heating.
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Affiliation(s)
- Puneet Jain
- Department of Mechanical Engineering, Faculty of Engineering, Tokyo University of Science, 6-3-1, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (T.A.); (M.M.)
| | - Takuya Aida
- Department of Mechanical Engineering, Faculty of Engineering, Tokyo University of Science, 6-3-1, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (T.A.); (M.M.)
| | - Masahiro Motosuke
- Department of Mechanical Engineering, Faculty of Engineering, Tokyo University of Science, 6-3-1, Niijuku, Katsushika-ku, Tokyo 125-8585, Japan; (T.A.); (M.M.)
- Water Frontier Research Center, Research Institute for Science and Technology, Tokyo University of Science, 1-3, Kagurazaka, Shinjuku-ku, Tokyo 125-8585, Japan
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11
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Recent advances in FRET-Based biosensors for biomedical applications. Anal Biochem 2021; 630:114323. [PMID: 34339665 DOI: 10.1016/j.ab.2021.114323] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 01/12/2023]
Abstract
Fluorescence resonance energy transfer (FRET)-based biosensors are effective analytical tools extensively used in fields of biomedicine, pharmacology, toxicology, and food sciences. Ratiometric imaging of substantial cellular processes, molecular components, and biological interactions is widely performed by these biosensors. A variety of FRET-based biosensors have provided comprehensive insights into underlying mechanisms of pathological conditions in live cells, tissues, and organisms. Moreover, integration of FRET-based biosensors with the current bioanalytical techniques allows for accurate, rapid, and sensitive diagnosis and proposes the advanced strategies for treatment. Precise analysis of ligand-receptor interactions by FRET-based biosensors has presented a basis for determination of novel therapeutic agents. Therefore, this study was designed to review the recent developments in FRET-based biosensors and their biomedical applications. In addition, characteristics, challenges, and outlooks of these biosensors were discussed.
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12
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Huang Q, Chen B, Shen J, Liu L, Li J, Shi J, Li Q, Zuo X, Wang L, Fan C, Li J. Encoding Fluorescence Anisotropic Barcodes with DNA Fameworks. J Am Chem Soc 2021; 143:10735-10742. [PMID: 34242004 DOI: 10.1021/jacs.1c04942] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescence anisotropy (FA) holds great potential for multiplexed analysis and imaging of biomolecules since it can effectively discriminate fluorophores with overlapping emission spectra. Nevertheless, its susceptibility to environmental variation hampers its widespread applications in biology and biotechnology. In this study, we design FA DNA frameworks (FAFs) by scaffolding fluorophores in a fluorescent protein-like microenvironment. We find that the FA stability of the fluorophores is remarkably improved due to the sequestration effects of FAFs. The FA level of the fluorophores can be finely tuned when placed at different locations on an FAF, analogous to spectral shifts of protein-bound fluorophores. The high programmability of FAFs further enables the design of a spectrum of encoded FA barcodes for multiplexed sensing of nucleic acids and multiplexed labeling of live cells. This FAF system thus establishes a new paradigm for designing multiplexing FA probes for cellular imaging and other biological applications.
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Affiliation(s)
- Qiuling Huang
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Chen
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianlei Shen
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiajun Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lihua Wang
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.,Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200127, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiang Li
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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13
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Hou Y, Wang Q, Han B, Chen Y, Qiao X, Wang L. CD36 promotes NLRP3 inflammasome activation via the mtROS pathway in renal tubular epithelial cells of diabetic kidneys. Cell Death Dis 2021; 12:523. [PMID: 34021126 PMCID: PMC8140121 DOI: 10.1038/s41419-021-03813-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 02/04/2023]
Abstract
Tubulointerstitial inflammation plays a key role in the pathogenesis of diabetic nephropathy (DN). Interleukin-1β (IL-1β) is the key proinflammatory cytokine associated with tubulointerstitial inflammation. The NLRP3 inflammasome regulates IL-1β activation and secretion. Reactive oxygen species (ROS) represents the main mediator of NLRP3 inflammasome activation. We previously reported that CD36, a class B scavenger receptor, mediates ROS production in DN. Here, we determined whether CD36 is involved in NLRP3 inflammasome activation and explored the underlying mechanisms. We observed that high glucose induced-NLRP3 inflammasome activation mediate IL-1β secretion, caspase-1 activation, and apoptosis in HK-2 cells. In addition, the levels of CD36, NLRP3, and IL-1β expression (protein and mRNA) were all significantly increased under high glucose conditions. CD36 knockdown resulted in decreased NLRP3 activation and IL-1β secretion. CD36 knockdown or the addition of MitoTempo significantly inhibited ROS production in HK-2 cells. CD36 overexpression enhanced NLRP3 activation, which was reduced by MitoTempo. High glucose levels induced a change in the metabolism of HK-2 cells from fatty acid oxidation (FAO) to glycolysis, which promoted mitochondrial ROS (mtROS) production after 72 h. CD36 knockdown increased the level of AMP-activated protein kinase (AMPK) activity and mitochondrial FAO, which was accompanied by the inhibition of NLRP3 and IL-1β. The in vivo experimental results indicate that an inhibition of CD36 could protect diabetic db/db mice from tubulointerstitial inflammation and tubular epithelial cell apoptosis. CD36 mediates mtROS production and NLRP3 inflammasome activation in db/db mice. CD36 inhibition upregulated the level of FAO-related enzymes and AMPK activity in db/db mice. These results suggest that NLRP3 inflammasome activation is mediated by CD36 in renal tubular epithelial cells in DN, which suppresses mitochondrial FAO and stimulates mtROS production.
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Affiliation(s)
- Yanjuan Hou
- grid.263452.40000 0004 1798 4018Department of Nephrology, Second Hospital, Shanxi Medical University, Taiyuan, China
| | - Qian Wang
- grid.263452.40000 0004 1798 4018Department of Nephrology, Second Hospital, Shanxi Medical University, Taiyuan, China
| | - Baosheng Han
- grid.477944.dDepartment of Cardiac Surgery, Shanxi Cardiovascular Hospital, Taiyuan, China
| | - Yiliang Chen
- grid.280427.b0000 0004 0434 015XBlood Research Institute, Blood Center of Wisconsin, Milwaukee, WI USA ,grid.30760.320000 0001 2111 8460Department of Medicine, Medical College of Wisconsin, Milwaukee, WI USA
| | - Xi Qiao
- grid.263452.40000 0004 1798 4018Department of Nephrology, Second Hospital, Shanxi Medical University, Taiyuan, China
| | - Lihua Wang
- grid.263452.40000 0004 1798 4018Department of Nephrology, Second Hospital, Shanxi Medical University, Taiyuan, China
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14
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Simultaneous readout of multiple FRET pairs using photochromism. Nat Commun 2021; 12:2005. [PMID: 33790271 PMCID: PMC8012603 DOI: 10.1038/s41467-021-22043-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/17/2021] [Indexed: 01/11/2023] Open
Abstract
Förster resonant energy transfer (FRET) is a powerful mechanism to probe associations in situ. Simultaneously performing more than one FRET measurement can be challenging due to the spectral bandwidth required for the donor and acceptor fluorophores. We present an approach to distinguish overlapping FRET pairs based on the photochromism of the donor fluorophores, even if the involved fluorophores display essentially identical absorption and emission spectra. We develop the theory underlying this method and validate our approach using numerical simulations. To apply our system, we develop rsAKARev, a photochromic biosensor for cAMP-dependent protein kinase (PKA), and combine it with the spectrally-identical biosensor EKARev, a reporter for extracellular signal-regulated kinase (ERK) activity, to deliver simultaneous readout of both activities in the same cell. We further perform multiplexed PKA, ERK, and calcium measurements by including a third, spectrally-shifted biosensor. Our work demonstrates that exploiting donor photochromism in FRET can be a powerful approach to simultaneously read out multiple associations within living cells. Performing multiple FRET measurements at once can be challenging. Here the authors report a method to discriminate between overlapping FRET pairs, even if the fluorophores display almost identical absorption and emission spectra, based on the photochromism of the donor fluorophores.
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Zhang X, Bai Y, Jiang Y, Wang N, Yang F, Zhan L, Huang C. Homo-FRET enhanced ratiometric fluorescence strategy for exonuclease III activity detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1489-1494. [PMID: 33690735 DOI: 10.1039/d0ay02315a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this work, homo-FRET (Förster resonance energy transfer between the same kind of fluorophores) takes place in a hetero-FRET (FRET between two different fluorophores) system and can effectively improve the energy transfer efficiency. Herein, a novel ratiometric fluorescence method was developed for the detection of nuclease activity. Exonuclease III (Exo III), an enzyme which has a high exodeoxyribonuclease activity for double-stranded DNA (dsDNA) in the 3' to 5' direction, was chosen as a proof of concept of this strategy. In a linear dsDNA template, the occurrence of homo-FRET in two Cy3 donors enables the highly efficient transfer of energy to the Cy5 acceptor. The ratio of fluorescence intensity between Cy3 and Cy5 (FD/FA) increases in an Exo III concentration-dependent manner, which built the foundation of Exo III quantification. This method exhibits a linear range from 0.25 to 8 U mL-1 with a detection limit of 0.17 U mL-1. Importantly, this platform also shows the potential for screening Exo III inhibitors and detecting Exo III activity in complex samples.
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Affiliation(s)
- Xu Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China.
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16
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Cai C, Sun H, Hu L, Fan Z. Visualization of integrin molecules by fluorescence imaging and techniques. ACTA ACUST UNITED AC 2021; 45:229-257. [PMID: 34219865 PMCID: PMC8249084 DOI: 10.32604/biocell.2021.014338] [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] [Indexed: 11/15/2022]
Abstract
Integrin molecules are transmembrane αβ heterodimers involved in cell adhesion, trafficking, and signaling. Upon activation, integrins undergo dynamic conformational changes that regulate their affinity to ligands. The physiological functions and activation mechanisms of integrins have been heavily discussed in previous studies and reviews, but the fluorescence imaging techniques -which are powerful tools for biological studies- have not. Here we review the fluorescence labeling methods, imaging techniques, as well as Förster resonance energy transfer assays used to study integrin expression, localization, activation, and functions.
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Affiliation(s)
- Chen Cai
- Department of Immunology, School of Medicine, UConn Health, Farmington, 06030, USA
| | - Hao Sun
- Department of Medicine, University of California, San Diego, La Jolla, 92093, USA
| | - Liang Hu
- Cardiovascular Institute of Zhengzhou University, Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450051, China
| | - Zhichao Fan
- Department of Immunology, School of Medicine, UConn Health, Farmington, 06030, USA
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17
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Chen H, Xie X, Chen TY. Single-molecule microscopy for in-cell quantification of protein oligomeric stoichiometry. Curr Opin Struct Biol 2020; 66:112-118. [PMID: 33242727 DOI: 10.1016/j.sbi.2020.10.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
Abstract
Protein organization modification plays a vital role in initiating signaling pathways, transcriptional regulation, and cell apoptosis regulation. Simultaneous quantification of oligomeric state and cellular parameters in the same cell, even though challenging, is required to understand their correlation at the molecular level. Recent advances of fluorescence protein and single-molecule localization microscopy enables the determination of localizations and oligomeric states of target proteins in cells. We reviewed the fluorescence intensity-based, localization-based, and photophysical property-based approaches for in-cell quantification of protein oligomeric stoichiometry. We discussed their working principles, applications, advantages, and limitations. These results also imply the combination of methodologies targeting different biological parameters at the single-cell level is essential to uncover the structure-function relationship at the molecular level.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, United States
| | - Xihong Xie
- Department of Chemistry, University of Houston, Houston, TX 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, United States.
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