1
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Akhtar J, Imran M, Wang G. Protocol for live-cell Förster resonance energy transfer imaging to reveal the bistable insulin response of single C2C12-derived myotubes. STAR Protoc 2024; 5:103109. [PMID: 38829736 PMCID: PMC11179099 DOI: 10.1016/j.xpro.2024.103109] [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: 03/02/2023] [Revised: 04/26/2024] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
Based on our hypothesis that myotubes exhibit a bistable response to insulin, here we present a protocol for finely measuring Akt phosphorylation in single myotubes under insulin stimulation. We describe steps to stably express a Förster resonance energy transfer (FRET)-based Akt biosensor in C2C12-derived myotubes and perform single-cell FRET imaging. This protocol highlights its potential for precision medicine in analyzing protein phosphorylation dynamics at the single-cell level. For complete details on the use and execution of this protocol, please refer to Akhtar et al.1.
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Affiliation(s)
- Javed Akhtar
- Futian Biomedical Innovation R&D Center, The Chinese University of Hong Kong, Shenzhen 518172, China; Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Muhammad Imran
- Department of Computer Science & IT, Institute of Southern Punjab, Multan, Pakistan
| | - Guanyu Wang
- Futian Biomedical Innovation R&D Center, The Chinese University of Hong Kong, Shenzhen 518172, China; Biomedical Science and Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; Center for Endocrinology and Metabolic Diseases, Second Affiliated Hospital, The Chinese University of Hong Kong, Shenzhen 518172, China.
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2
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Hsieh HC, Huang IH, Chang SW, Chen PL, Su YC, Wang S, Tsai WJ, Chen PH, Aroian RV, Chen CS. PRMT-7/PRMT7 activates HLH-30/TFEB to guard plasma membrane integrity compromised by bacterial pore-forming toxins. Autophagy 2024; 20:1335-1358. [PMID: 38261662 PMCID: PMC11210913 DOI: 10.1080/15548627.2024.2306655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/13/2024] [Indexed: 01/25/2024] Open
Abstract
Bacterial pore-forming toxins (PFTs) that disrupt host plasma membrane integrity (PMI) significantly contribute to the virulence of various pathogens. However, how host cells protect PMI in response to PFT perforation in vivo remains obscure. Previously, we demonstrated that the HLH-30/TFEB-dependent intrinsic cellular defense (INCED) is elicited by PFT to maintain PMI in Caenorhabditis elegans intestinal epithelium. Yet, the molecular mechanism for the full activation of HLH-30/TFEB by PFT remains elusive. Here, we reveal that PRMT-7 (protein arginine methyltransferase-7) is indispensable to the nuclear transactivation of HLH-30 elicited by PFTs. We demonstrate that PRMT-7 participates in the methylation of HLH-30 on its RAG complex binding domain to facilitate its nuclear localization and activation. Moreover, we showed that PRMT7 is evolutionarily conserved to regulate TFEB cellular localization and repair plasma damage caused by PFTs in human intestinal cells. Together, our observations not only unveil a novel PRMT-7/PRMT7-dependent post-translational regulation of HLH-30/TFEB but also shed insight on the evolutionarily conserved mechanism of the INCED against PFT in metazoans.
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Affiliation(s)
- Hui-Chen Hsieh
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - I-Hsiang Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shao-Wen Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Lin Chen
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Cheng Su
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shuying Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Jiun Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Hung Chen
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Raffi V. Aroian
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chang-Shi Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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3
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Frost D, Cook K, Sanabria H. Time-heterogeneity of the Förster Radius from Dipole Orientational Dynamics Explains Observed Dynamic Shift. ARXIV 2024:arXiv:2404.09883v1. [PMID: 38699162 PMCID: PMC11065046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Förster resonance energy transfer (FRET) is a quantum mechanical phenomenon involving the non-radiative transfer of energy between coupled electric dipoles. Due to the strong dependence of FRET on the distance between the dipoles, it is frequently used as a "molecular ruler" in biology, chemistry, and physics. This is done by placing dipolar molecules called dyes on molecules of interest. In time-resolved confocal single-molecule FRET (smFRET) experiments, the joint distribution of the FRET efficiency and the donor fluorescence lifetime can reveal underlying molecular conformational dynamics via deviation from their theoretical Förster relationship. This deviation is referred to as a dynamic shift. Quantifying the dynamic shift caused by the motion of the fluorescent dyes is essential to decoupling the dynamics of the studied molecules and the dyes. We develop novel Langevin models for the dye linker dynamics, including rotational dynamics, based on first physics principles and proper dye linker chemistry to match accessible volumes predicted by molecular dynamics simulations. By simulating the dyes' stochastic translational and rotational dynamics, we show that the observed dynamic shift can largely be attributed to the mutual orientational dynamics of the electric dipole moments associated with the dyes, not their accessible volume.
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Affiliation(s)
- David Frost
- School of Mathematical and Statistical Sciences, Clemson University
| | - Keisha Cook
- School of Mathematical and Statistical Sciences, Clemson University
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University
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4
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Yang Y, Wang S, Liu X, Zhang W, Tong W, Luo H, Zhao L. Interactions of ferulic acid and ferulic acid methyl ester with endogenous proteins: Determination using the multi-methods. Heliyon 2024; 10:e24605. [PMID: 38312678 PMCID: PMC10835327 DOI: 10.1016/j.heliyon.2024.e24605] [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: 07/20/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/06/2024] Open
Abstract
Ferulic acid (FA) and ferulic acid methyl ester (FAM) are important phenolic compounds in Baijiu. In this study, the interaction of FA and FAM with human serum albumin (HSA) and lysozyme (LZM) was investigated using multispectral methods and molecular dynamics simulation. FA and FAM could interact with HSA and LZM, changing the conformation and hydrophilicity of the protein. The quenching mechanisms of FA-HSA, FA-LZM, FAM-HSA, and FAM-LZM were all static-quenching. In the FA-HSA, FAM-HSA, and FA-LZM systems, the interaction forces were mainly hydrophobic interactions and hydrogen bonding. In the FAM-LZM system, the interaction forces were mainly hydrophobic interactions, hydrogen bonding, and van der Waals force. Common metal ions such as K+, Ca2+, Cu2+, Mg2+, and Mn2+ could affect the binding ability of FA and FAM to HSA and LZM. Moreover, FA and FAM could increase the stability of HSA and LZM, and the protein bound to FA/FAM was more stable than the free protein. FA and FAM had varying degrees of impact on the physiological activities of HSA and LZM. This study provides relevant information on the interactions and metabolic mechanisms of FA and its derivatives with endogenous proteins.
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Affiliation(s)
- Ying Yang
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin, 644000, China
| | - Shuqin Wang
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin, 644000, China
| | - Xingyan Liu
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin, 644000, China
| | - Wenbin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, 510000, China
| | - Wenhua Tong
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin, 644000, China
- Key Laboratory of Brewing Biotechnology and Application, Yibin, 644000, China
| | - Huibo Luo
- School of Biological Engineering, Sichuan University of Science and Engineering, Yibin, 644000, China
- Key Laboratory of Brewing Biotechnology and Application, Yibin, 644000, China
| | - Liming Zhao
- East China University of Science and Technology, Shanghai, 200000, China
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5
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Hoshino N, Kanadome T, Takasugi T, Itoh M, Kaneko R, Inoue YU, Inoue T, Hirabayashi T, Watanabe M, Matsuda T, Nagai T, Tarusawa E, Yagi T. Visualization of trans homophilic interaction of clustered protocadherin in neurons. Proc Natl Acad Sci U S A 2023; 120:e2301003120. [PMID: 37695902 PMCID: PMC10515168 DOI: 10.1073/pnas.2301003120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/20/2023] [Indexed: 09/13/2023] Open
Abstract
Clustered protocadherin (Pcdh) functions as a cell recognition molecule through the homophilic interaction in the central nervous system. However, its interactions have not yet been visualized in neurons. We previously reported PcdhγB2-Förster resonance energy transfer (FRET) probes to be applicable only to cell lines. Herein, we designed γB2-FRET probes by fusing FRET donor and acceptor fluorescent proteins to a single γB2 molecule and succeeded in visualizing γB2 homophilic interaction in cultured hippocampal neurons. The γB2-FRET probe localized in the soma and neurites, and FRET signals, which were observed at contact sites between neurites, eliminated by ethylene glycol tetraacetic acid (EGTA) addition. Live imaging revealed that the FRET-negative γB2 signals rapidly moved along neurites and soma, whereas the FRET-positive signals remained in place. We observed that the γB2 proteins at synapses rarely interact homophilically. The γB2-FRET probe might allow us to elucidate the function of the homophilic interaction and the cell recognition mechanism.
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Affiliation(s)
- Natsumi Hoshino
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Takashi Kanadome
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Ibaraki, Osaka567-0047, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi, Saitama332-0012, Japan
| | - Tomomi Takasugi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Mizuho Itoh
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Ryosuke Kaneko
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Yukiko U. Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo187-8501, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo187-8501, Japan
| | - Takahiro Hirabayashi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
- Clinical Medicine Research Laboratory, Shonan University of Medical Sciences, Yokohama244-0806, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido060-8638, Japan
| | - Tomoki Matsuda
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Ibaraki, Osaka567-0047, Japan
| | - Takeharu Nagai
- Department of Biomolecular Science and Engineering, SANKEN, Osaka University, Ibaraki, Osaka567-0047, Japan
| | - Etsuko Tarusawa
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka565-0871, Japan
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6
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Benner D, Yadav P, Bhatia D. Red emitting carbon dots: surface modifications and bioapplications. NANOSCALE ADVANCES 2023; 5:4337-4353. [PMID: 37638168 PMCID: PMC10448348 DOI: 10.1039/d3na00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023]
Abstract
Quantum dots (QDs), and carbon quantum dots (CDs) in particular, have received significant attention for their special characteristics. These particles, on the scale of several nanometers, are often produced using simple and green methods, with naturally occurring organic precursors. In addition to facile production methods, CDs present advantageous applications in the field of medicine, primarily for bioimaging, antibacterial and therapeutics. Also, CDs present great potential for surface modification through methods like doping or material mixing during synthesis. However, the bulk of current literature focuses on CDs emitting in the blue wavelengths which are not very suitable for biological applications. Red emitting CDs are therefore of additional interest due to their brightness, photostability, novelty and deeper tissue penetration. In this review article, red CDs, their methods of production, and their biological applications for translational research are explored in depth, with emphasis on the effects of surface modifications and doping.
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Affiliation(s)
- Dawson Benner
- Department of Engineering, Texas A&M University College Station 77843 Texas USA
| | - Pankaj Yadav
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar Palaj 382355 Gujarat India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar Palaj 382355 Gujarat India
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7
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Smith JT, Sinsuebphon N, Rudkouskaya A, Michalet X, Intes X, Barroso M. In vivo quantitative FRET small animal imaging: Intensity versus lifetime-based FRET. BIOPHYSICAL REPORTS 2023; 3:100110. [PMID: 37251213 PMCID: PMC10209493 DOI: 10.1016/j.bpr.2023.100110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/27/2023] [Indexed: 05/31/2023]
Abstract
Förster resonance energy transfer (FRET) microscopy is used in numerous biophysical and biomedical applications to monitor inter- and intramolecular interactions and conformational changes in the 2-10 nm range. FRET is currently being extended to in vivo optical imaging, its main application being in quantifying drug-target engagement or drug release in animal models of cancer using organic dye or nanoparticle-labeled probes. Herein, we compared FRET quantification using intensity-based FRET (sensitized emission FRET analysis with the three-cube approach using an IVIS imager) and macroscopic fluorescence lifetime (MFLI) FRET using a custom system using a time-gated-intensified charge-coupled device, for small animal optical in vivo imaging. The analytical expressions and experimental protocols required to quantify the product f D E of the FRET efficiency E and the fraction of donor molecules involved in FRET, f D , are described in detail for both methodologies. Dynamic in vivo FRET quantification of transferrin receptor-transferrin binding was acquired in live intact nude mice upon intravenous injection of a near-infrared-labeled transferrin FRET pair and benchmarked against in vitro FRET using hybridized oligonucleotides. Even though both in vivo imaging techniques provided similar dynamic trends for receptor-ligand engagement, we demonstrate that MFLI-FRET has significant advantages. Whereas the sensitized emission FRET approach using the IVIS imager required nine measurements (six of which are used for calibration) acquired from three mice, MFLI-FRET needed only one measurement collected from a single mouse, although a control mouse might be needed in a more general situation. Based on our study, MFLI therefore represents the method of choice for longitudinal preclinical FRET studies such as that of targeted drug delivery in intact, live mice.
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Affiliation(s)
- Jason T. Smith
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, New York
| | - Nattawut Sinsuebphon
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, New York
| | - Alena Rudkouskaya
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
| | - Xavier Michalet
- Department of Chemistry & Biochemistry, University of California at Los Angeles, Los Angeles, California
| | - Xavier Intes
- Center for Modeling, Simulation and Imaging in Medicine (CeMSIM), Rensselaer Polytechnic Institute, Troy, New York
| | - Margarida Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York
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8
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Wang Z, Zhao T, Cai Y, Zhang J, Hao H, Liang Y, Wang S, Sun Y, Chen T, Bianco PR, Oh K, Lei M. Rapid, artifact-reduced, image reconstruction for super-resolution structured illumination microscopy. Innovation (N Y) 2023; 4:100425. [PMID: 37181226 PMCID: PMC10173768 DOI: 10.1016/j.xinn.2023.100425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Super-resolution structured illumination microscopy (SR-SIM) is finding increasing application in biomedical research due to its superior ability to visualize subcellular dynamics in living cells. However, during image reconstruction artifacts can be introduced and when coupled with time-consuming postprocessing procedures, limits this technique from becoming a routine imaging tool for biologists. To address these issues, an accelerated, artifact-reduced reconstruction algorithm termed joint space frequency reconstruction-based artifact reduction algorithm (JSFR-AR-SIM) was developed by integrating a high-speed reconstruction framework with a high-fidelity optimization approach designed to suppress the sidelobe artifact. Consequently, JSFR-AR-SIM produces high-quality, super-resolution images with minimal artifacts, and the reconstruction speed is increased. We anticipate this algorithm to facilitate SR-SIM becoming a routine tool in biomedical laboratories.
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Affiliation(s)
- Zhaojun Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Tianyu Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yanan Cai
- College of Science, Northwest A&F University, Yangling 712100, China
| | - Jingxiang Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Huiwen Hao
- State Key Laboratory of Membrane Biology & Biomedical Pioneer Innovation Center (BIOPIC) & School of Life Sciences, Peking University, Beijing 100871, China
| | - Yansheng Liang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Shaowei Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology & Biomedical Pioneer Innovation Center (BIOPIC) & School of Life Sciences, Peking University, Beijing 100871, China
| | - Tongsheng Chen
- MOE Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
| | - Piero R. Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Kwangsung Oh
- Department of Computer Science, College of Information Science & Technology, University of Nebraska Omaha, Omaha, NE 68182, USA
| | - Ming Lei
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China
- Corresponding author
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9
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Kamino K, Kadakia N, Avgidis F, Liu ZX, Aoki K, Shimizu T, Emonet T. Optimal inference of molecular interaction dynamics in FRET microscopy. Proc Natl Acad Sci U S A 2023; 120:e2211807120. [PMID: 37014867 PMCID: PMC10104582 DOI: 10.1073/pnas.2211807120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/10/2023] [Indexed: 04/05/2023] Open
Abstract
Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However, inferring the molecular interaction dynamics from the observables remains a challenging inverse problem, particularly when measurement noise and photobleaching are nonnegligible-a common situation in single-cell analysis. The conventional approach is to process the time-series data algebraically, but such methods inevitably accumulate the measurement noise and reduce the signal-to-noise ratio (SNR), limiting the scope of FRET microscopy. Here, we introduce an alternative probabilistic approach, B-FRET, generally applicable to standard 3-cube FRET-imaging data. Based on Bayesian filtering theory, B-FRET implements a statistically optimal way to infer molecular interactions and thus drastically improves the SNR. We validate B-FRET using simulated data and then apply it to real data, including the notoriously noisy in vivo FRET time series from individual bacterial cells to reveal signaling dynamics otherwise hidden in the noise.
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Affiliation(s)
- Keita Kamino
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Institute of Molecular Biology, Academia Sinica, Taipei115, Taiwan
- PRESTO, Japan Science and Technology Agency, Kawaguchi-shi, Saitama332-0012, Japan
| | - Nirag Kadakia
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Swartz Foundation for Theoretical Neuroscience, Yale University, New Haven, CT06511
| | | | - Zhe-Xuan Liu
- Institute of Physics, National Yang Ming Chiao Tung University, Hsinchu30010, Taiwan
| | - Kazuhiro Aoki
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi444-8787, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi240-0193, Japan
| | | | - Thierry Emonet
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT06511
- Quantitative Biology Institute, Yale University, New Haven, CT06511
- Department of Physics, Yale University, New Haven, CT06511
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10
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Kobayashi A, Azuma K, Takeiwa T, Kitami T, Horie K, Ikeda K, Inoue S. A FRET-based respirasome assembly screen identifies spleen tyrosine kinase as a target to improve muscle mitochondrial respiration and exercise performance in mice. Nat Commun 2023; 14:312. [PMID: 36697396 PMCID: PMC9877034 DOI: 10.1038/s41467-023-35865-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023] Open
Abstract
Aerobic muscle activities predominantly depend on fuel energy supply by mitochondrial respiration, thus, mitochondrial activity enhancement may become a therapeutic intervention for muscle disturbances. The assembly of mitochondrial respiratory complexes into higher-order "supercomplex" structures has been proposed to be an efficient biological process for energy synthesis, although there is controversy in its physiological relevance. We here established Förster resonance energy transfer (FRET) phenomenon-based live imaging of mitochondrial respiratory complexes I and IV interactions using murine myoblastic cells, whose signals represent in vivo supercomplex assembly of complexes I, III, and IV, or respirasomes. The live FRET signals were well correlated with supercomplex assembly observed by blue native polyacrylamide gel electrophoresis (BN-PAGE) and oxygen consumption rates. FRET-based live cell screen defined that the inhibition of spleen tyrosine kinase (SYK), a non-receptor protein tyrosine kinase that belongs to the SYK/ zeta-chain-associated protein kinase 70 (ZAP-70) family, leads to an increase in supercomplex assembly in murine myoblastic cells. In parallel, SYK inhibition enhanced mitochondrial respiration in the cells. Notably, SYK inhibitor administration enhances exercise performance in mice. Overall, this study proves the feasibility of FRET-based respirasome assembly assay, which recapitulates in vivo mitochondrial respiration activities.
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Affiliation(s)
- Ami Kobayashi
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan.,Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kotaro Azuma
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Toshihiko Takeiwa
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Toshimori Kitami
- Laboratory for Metabolic Networks, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Kuniko Horie
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan
| | - Kazuhiro Ikeda
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan. .,Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka-shi, Saitama, 350-1241, Japan.
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11
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Mahato J, Ray S, Maji SK, Chowdhury A. Spectrally Resolved FRET Microscopy of α-Synuclein Phase-Separated Liquid Droplets. Methods Mol Biol 2023; 2551:425-447. [PMID: 36310218 DOI: 10.1007/978-1-0716-2597-2_27] [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: 06/16/2023]
Abstract
Liquid-liquid phase separation (LLPS) has emerged as an important phenomenon associated with formation of membraneless organelles. Recently, LLPS has been shown to act as nucleation centers for disease-associated protein aggregation and amyloid fibril formation. Phase-separated α-synuclein droplets gradually rigidify during the course of protein aggregation, and it is very challenging to understand the biomolecular interactions that lead to liquid-like to solid-like transition using conventional ensemble measurements. Here, we describe a spectrally-resolved fluorescence microscopy based Förster resonance energy transfer (FRET) imaging to probe interactions of α-synuclein in individual droplets during LLPS-mediated aggregation. By acquiring entire emission spectral profiles of individual droplets upon sequential excitation of acceptors and donors therein, this technique allows for the quantification of sensitized emission proportional to the extent of FRET, which enables interrogation of the evolution of local interactions of donor-/acceptor-labeled α-synuclein molecules within each droplet. The present study on single droplets is not only an important development for studying LLPS but can also be used to investigate self-assembly or aggregation in biomolecular systems and soft materials.
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Affiliation(s)
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India.
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12
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Saurabh A, Fazel M, Safar M, Sgouralis I, Pressé S. Single-photon smFRET. I: Theory and conceptual basis. BIOPHYSICAL REPORTS 2022; 3:100089. [PMID: 36582655 PMCID: PMC9793182 DOI: 10.1016/j.bpr.2022.100089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
We present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of a single-photon smFRET experiment, including: 1) fluorophore photophysics; 2) continuous time kinetics of the labeled system with large timescale separations between photophysical phenomena such as excited photophysical state lifetimes and events such as transition between system states; 3) unavoidable detector artefacts; 4) background emissions; 5) unknown number of system states; and 6) both continuous and pulsed illumination. These physical features necessarily demand a novel framework that extends beyond existing tools. In particular, the theory naturally brings us to a hidden Markov model with a second-order structure and Bayesian nonparametrics on account of items 1, 2, and 5 on the list. In the second and third companion articles, we discuss the direct effects of these key complexities on the inference of parameters for continuous and pulsed illumination, respectively.
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Affiliation(s)
- Ayush Saurabh
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona
| | - Matthew Safar
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Mathematics and Statistical Science, Arizona State University, Tempe, Arizona
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee Knoxville, Knoxville, Tennesse
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona,Department of Physics, Arizona State University, Tempe, Arizona,School of Molecular Sciences, Arizona State University, Tempe, Arizona,Corresponding author
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13
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Thurairajah B, Hudson AJ, Doveston RG. Contemporary biophysical approaches for studying 14-3-3 protein-protein interactions. Front Mol Biosci 2022; 9:1043673. [PMID: 36425654 PMCID: PMC9679655 DOI: 10.3389/fmolb.2022.1043673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 06/28/2024] Open
Abstract
14-3-3 proteins are a family of regulatory hubs that function through a vast network of protein-protein interactions. Their dysfunction or dysregulation is implicated in a wide range of diseases, and thus they are attractive drug targets, especially for molecular glues that promote protein-protein interactions for therapeutic intervention. However, an incomplete understanding of the molecular mechanisms that underpin 14-3-3 function hampers progress in drug design and development. Biophysical methodologies are an essential element of the 14-3-3 analytical toolbox, but in many cases have not been fully exploited. Here, we present a contemporary review of the predominant biophysical techniques used to study 14-3-3 protein-protein interactions, with a focus on examples that address key questions and challenges in the 14-3-3 field.
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Affiliation(s)
| | | | - Richard G. Doveston
- Leicester Institute for Structural and Chemical Biology and School of Chemistry, University of Leicester, Leicester, United Kingdom
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14
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Xia Y, Chen C, Chen J, Hu C, Yang W, Wang L, Liu L, Gao LP, Wu YZ, Chen DD, Shi Q, Chen ZB, Dong XP. Enhanced M-CSF/CSF1R Signaling Closely Associates with PrP Sc Accumulation in the Scrapie-Infected Cell Line and the Brains of Scrapie-Infected Experimental Rodents. Mol Neurobiol 2022; 59:6534-6551. [PMID: 35970974 DOI: 10.1007/s12035-022-02989-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/06/2022] [Indexed: 12/17/2022]
Abstract
Activation and proliferation of microglia are one of the hallmarks of prion disease and is usually accompanied by increased levels of various cytokines and chemokines. Our previous study demonstrated that the level of brain macrophage colony-stimulating factor (M-CSF) was abnormally elevated during prion infection, but its association with PrPSc is not completely clear. In this study, colocalization of the increased M-CSF with accumulated PrPSc was observed by IHC with serial brain sections. Reliable molecular interaction between total PrP and M-CSF was observed in the brain of 263 K-infected hamsters and in cultured prion-infected cell line. Immunofluorescent assays showed that morphological colocalization of M-CSF with neurons and microglia, but not with astrocytes in brains of scrapie-infected animals. The transcriptional and expressing levels of CSF1R were also significantly increased in prion-infected cell line and mice, and colocalization of CSF1R with neurons and microglia was observed in the brains of prion-infected mouse models. Removal of PrPSc replication by resveratrol in SMB-S15 cells induced limited reductions of cellular levels of M-CSF and CSF1R. In addition, we found that the level of IL-34, another ligand of CSF1R, did not change significantly after prion infection, but its distribution on the cell types in the brains shifted from neurons in healthy mice to the proliferated astrocytes and microglia in scrapie-infected mice. Our data demonstrate activation of M-CSF/IL-34/CSF1R signaling in the microenvironment of prion infection, strongly indicating its vital role in the pathophysiology of prions. It provides solid scientific evidence for the therapeutic potential of inhibiting M-CSF/CSF1R signaling in prion diseases.
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Affiliation(s)
- Ying Xia
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Cao Chen
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China.
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
| | - Jia Chen
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Chao Hu
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Wei Yang
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Lin Wang
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lian Liu
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Li-Ping Gao
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Yue-Zhang Wu
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Dong-Dong Chen
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
| | - Qi Shi
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
- China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhi-Bao Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China.
| | - Xiao-Ping Dong
- State Key Laboratory for Infectious Disease Prevention and Control, NHC Key Laboratory of Medical Virology and Viral Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases (Zhejiang University), Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China.
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China.
- Shanghai Institute of Infectious Disease and Biosafety, Shanghai, China.
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15
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Ruggiero FM, Martínez-Koteski N, Fidelio GD, Vilcaes AA, Daniotti JL. Golgi Phosphoprotein 3 Regulates the Physical Association of Glycolipid Glycosyltransferases. Int J Mol Sci 2022; 23:10354. [PMID: 36142273 PMCID: PMC9499508 DOI: 10.3390/ijms231810354] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/20/2022] Open
Abstract
Glycolipid glycosylation is an intricate process that mainly takes place in the Golgi by the complex interplay between glycosyltransferases. Several features such as the organization, stoichiometry and composition of these complexes may modify their sorting properties, sub-Golgi localization, enzymatic activity and in consequence, the pattern of glycosylation at the plasma membrane. In spite of the advance in our comprehension about physiological and pathological cellular states of glycosylation, the molecular basis underlying the metabolism of glycolipids and the players involved in this process remain not fully understood. In the present work, using biochemical and fluorescence microscopy approaches, we demonstrate the existence of a physical association between two ganglioside glycosyltransferases, namely, ST3Gal-II (GD1a synthase) and β3GalT-IV (GM1 synthase) with Golgi phosphoprotein 3 (GOLPH3) in mammalian cultured cells. After GOLPH3 knockdown, the localization of both enzymes was not affected, but the fomation of ST3Gal-II/β3GalT-IV complex was compromised and glycolipid expression pattern changed. Our results suggest a novel control mechanism of glycolipid expression through the regulation of the physical association between glycolipid glycosyltransferases mediated by GOLPH3.
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Affiliation(s)
- Fernando M. Ruggiero
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Natalia Martínez-Koteski
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Gerardo D. Fidelio
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Aldo A. Vilcaes
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
| | - Jose L. Daniotti
- CIQUIBIC (UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
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16
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Fan T, Liang B, Nie L, Wang J, Zhang H, Ciechanover A, Xu Y, An J, Huang Z. A synthetic bivalent peptide ligand of EphB4 with potent agonistic activity. Eur J Med Chem 2022; 244:114804. [DOI: 10.1016/j.ejmech.2022.114804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 12/01/2022]
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17
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Rahman M, Islam KR, Islam MR, Islam MJ, Kaysir MR, Akter M, Rahman MA, Alam SMM. A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices. MICROMACHINES 2022; 13:968. [PMID: 35744582 PMCID: PMC9229244 DOI: 10.3390/mi13060968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023]
Abstract
Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.
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Affiliation(s)
- Mahmudur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Kazi Rafiqul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Rashedul Islam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Jahirul Islam
- Department of Electrical and Electronic Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh;
| | - Md. Rejvi Kaysir
- Department of Electrical and Computer Engineering, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada;
- Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Ave. W, Waterloo, ON N2L 3G1, Canada
| | - Masuma Akter
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - Md. Arifur Rahman
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
| | - S. M. Mahfuz Alam
- Department of Electrical and Electronic Engineering, Dhaka University of Engineering & Technology, Gazipur 1707, Bangladesh; (M.R.); (K.R.I.); (M.R.I.); (M.A.); (M.A.R.)
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18
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Leavesley SJ, Annamdevula N, Johnson S, Pleshinger DJ, Rich TC. Automated Image Analysis of FRET Signals for Subcellular cAMP Quantification. Methods Mol Biol 2022; 2483:167-180. [PMID: 35286675 DOI: 10.1007/978-1-0716-2245-2_10] [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: 06/14/2023]
Abstract
A variety of FRET probes have been developed to examine cAMP localization and dynamics in single cells. These probes offer a readily accessible approach to measure localized cAMP signals. However, given the low signal-to-noise ratio of most FRET probes and the dynamic nature of the intracellular environment, there have been marked limitations in the ability to use FRET probes to study localized signaling events within the same cell. Here, we outline a methodology to dissect kinetics of cAMP-mediated FRET signals in single cells using automated image analysis approaches. We additionally extend these approaches to the analysis of subcellular regions. These approaches offer a unique opportunity to assess localized cAMP kinetics in an unbiased, quantitative fashion.
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Affiliation(s)
- Silas J Leavesley
- Department of Chemical and Biomolecular Engineering, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA.
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA.
| | - Naga Annamdevula
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
- Department of Physiology, University of South Alabama, Mobile, AL, USA
| | - Santina Johnson
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
| | - D J Pleshinger
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
| | - Thomas C Rich
- Department of Pharmacology, University of South Alabama, Mobile, AL, USA
- Center for Lung Biology, University of South Alabama, Mobile, AL, USA
- Department of Physiology, University of South Alabama, Mobile, AL, USA
- College of Engineering, University of South Alabama, Mobile, AL, USA
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19
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Sandhu N, Pandey SK, Tittal RK, Kumar K, Singh AP, Yadav RK, Shrivastava R, Singh AP. Fluorescein dye derivative: Synthesis, characterization, quantum chemical and promising antimicrobial activity studies. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Navjot Sandhu
- Department of Chemistry Chandigarh University Mohali India
| | - Satish Kumar Pandey
- Department of Biotechnology School of Life Sciences, Mizoram University (Central University) Aizawl India
| | - Ram Kumar Tittal
- Department of Chemistry National Institute of Technology Kurukshetra India
| | - Kamlesh Kumar
- Materials Science and Sensors Applications CSIR‐Central Scientific Instruments Organization Chandigarh India
| | | | - Rajesh K. Yadav
- Department of Applied Science (Chemistry) Madan Mohan Malaviya University of Technology Gorakhpur India
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20
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Liu Y, Zhang F, Jiang L, Perry JJP, Zhao Z, Liao J. Product inhibition kinetics determinations - Substrate interaction affinity and enzymatic kinetics using one quantitative FRET assay. Int J Biol Macromol 2021; 193:1481-1487. [PMID: 34780893 DOI: 10.1016/j.ijbiomac.2021.10.211] [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: 09/08/2021] [Accepted: 10/27/2021] [Indexed: 02/05/2023]
Abstract
Product inhibition is a common phenomenon during enzyme-catalyzed reactions. Almost all product molecules of an enzyme reaction should have some structural similarities to the substrate, and can thus still have affinities to the active site of the enzyme as product inhibitor. Currently, the characterizations of product inhibition are generally carried out by different methods to determine product binding affinity to the enzyme and the enzyme kinetics parameters, and then these parameters are combined to determine product inhibition. However, due to different sensitivity and variations, kinetics parameters determined from different methods are often not compatible, resulting in not accurate measurement. Here, we report a novel method that determines the two different classes of kinetics parameters, IC50 and Ki(or KD), Kcat and KM, using one single assay method-quantitative FRET(qFRET) assay for characterizing the product inhibition of pre-SUMO1's maturation by its protease SENP1. One method to determine all kinetics parameters provides, for the first time, not only a convenient method to determine all kinetics parameters, but more importantly, a novel approach to combine different measurements with mutually compatible results and errors.
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Affiliation(s)
- Yan Liu
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Fan Zhang
- State Key Laboratory of Oral Diseases, Department of Periodontology, National Clinical Research Center for Oral Diseases, West China, Hospital of Stomatology, Sichuan University, Chengdu, China; Physical Examination Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Jiang
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - J Jefferson P Perry
- City of Hope Biomedical Research Center, 1218 S. Fifth Avenue, Office 2268 Monrovia, CA 91016, USA
| | - Zhihe Zhao
- State Key Laboratory of Oral Diseases, Department of Periodontology, National Clinical Research Center for Oral Diseases, West China, Hospital of Stomatology, Sichuan University, Chengdu, China.
| | - Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; Biomedical Science, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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21
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Quantitative FRET Microscopy Reveals a Crucial Role of Cytoskeleton in Promoting PI(4,5)P 2 Confinement. Int J Mol Sci 2021; 22:ijms222111727. [PMID: 34769158 PMCID: PMC8583820 DOI: 10.3390/ijms222111727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 01/30/2023] Open
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is an essential plasma membrane component involved in several cellular functions, including membrane trafficking and cytoskeleton organization. This function multiplicity is partially achieved through a dynamic spatiotemporal organization of PI(4,5)P2 within the membrane. Here, we use a Förster resonance energy transfer (FRET) approach to quantitatively assess the extent of PI(4,5)P2 confinement within the plasma membrane. This methodology relies on the rigorous evaluation of the dependence of absolute FRET efficiencies between pleckstrin homology domains (PHPLCδ) fused with fluorescent proteins and their average fluorescence intensity at the membrane. PI(4,5)P2 is found to be significantly compartmentalized at the plasma membrane of HeLa cells, and these clusters are not cholesterol-dependent, suggesting that membrane rafts are not involved in the formation of these nanodomains. On the other hand, upon inhibition of actin polymerization, compartmentalization of PI(4,5)P2 is almost entirely eliminated, showing that the cytoskeleton network is the critical component responsible for the formation of nanoscale PI(4,5)P2 domains in HeLa cells.
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22
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A pair of transporters controls mitochondrial Zn 2+ levels to maintain mitochondrial homeostasis. Protein Cell 2021; 13:180-202. [PMID: 34687432 PMCID: PMC8901913 DOI: 10.1007/s13238-021-00881-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/02/2021] [Indexed: 12/15/2022] Open
Abstract
Zn2+ is required for the activity of many mitochondrial proteins, which regulate mitochondrial dynamics, apoptosis and mitophagy. However, it is not understood how the proper mitochondrial Zn2+ level is achieved to maintain mitochondrial homeostasis. Using Caenorhabditis elegans, we reveal here that a pair of mitochondrion-localized transporters controls the mitochondrial level of Zn2+. We demonstrate that SLC-30A9/ZnT9 is a mitochondrial Zn2+ exporter. Loss of SLC-30A9 leads to mitochondrial Zn2+ accumulation, which damages mitochondria, impairs animal development and shortens the life span. We further identify SLC-25A25/SCaMC-2 as an important regulator of mitochondrial Zn2+ import. Loss of SLC-25A25 suppresses the abnormal mitochondrial Zn2+ accumulation and defective mitochondrial structure and functions caused by loss of SLC-30A9. Moreover, we reveal that the endoplasmic reticulum contains the Zn2+ pool from which mitochondrial Zn2+ is imported. These findings establish the molecular basis for controlling the correct mitochondrial Zn2+ levels for normal mitochondrial structure and functions.
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23
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Liao J, Madahar V, Dang R, Jiang L. Quantitative FRET (qFRET) Technology for the Determination of Protein-Protein Interaction Affinity in Solution. Molecules 2021; 26:molecules26216339. [PMID: 34770748 PMCID: PMC8588070 DOI: 10.3390/molecules26216339] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions play pivotal roles in life, and the protein interaction affinity confers specific protein interaction events in physiology or pathology. Förster resonance energy transfer (FRET) has been widely used in biological and biomedical research to detect molecular interactions in vitro and in vivo. The FRET assay provides very high sensitivity and efficiency. Several attempts have been made to develop the FRET assay into a quantitative measurement for protein-protein interaction affinity in the past. However, the progress has been slow due to complicated procedures or because of challenges in differentiating the FRET signal from other direct emission signals from donor and receptor. This review focuses on recent developments of the quantitative FRET analysis and its application in the determination of protein-protein interaction affinity (KD), either through FRET acceptor emission or donor quenching methods. This paper mainly reviews novel theatrical developments and experimental procedures rather than specific experimental results. The FRET-based approach for protein interaction affinity determination provides several advantages, including high sensitivity, high accuracy, low cost, and high-throughput assay. The FRET-based methodology holds excellent potential for those difficult-to-be expressed proteins and for protein interactions in living cells.
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Affiliation(s)
- Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
- Biomedical Science, School of Medicine, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: ; Tel.: +1-951-827-6240; Fax: +1-951-827-6416
| | - Vipul Madahar
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Runrui Dang
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (V.M.); (R.D.)
| | - Ling Jiang
- Department of Biochemistry and Molecular Biology, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin 150040, China;
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24
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Yuan Y, Solin N. Mechanochemical Preparation and Self-Assembly of Protein:Dye Hybrids for White Luminescence. ACS APPLIED POLYMER MATERIALS 2021; 3:4825-4836. [PMID: 34661113 PMCID: PMC8506585 DOI: 10.1021/acsapm.1c00382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Protein nanofibrils (PNFs) functionalized with multiple dyes are prepared by a combination of mechanochemistry and liquid-phase self-assembly. The three employed dyes are Fluorescent Brightener 378 (F378), 2-butyl-6-(butylamino)-1H-benzo[de]isoquinoline-1,3(2H)-dione (Fluorol 555), and Nile red (NR). F378 acts as the donor with Fluorol 555 as the acceptor. F555 in turn acts as the donor and NR as the acceptor. This enables a FRET cascade that enables conversion of UV light to white light. The efficiency of FRET can be influenced by the details of the self-assembly process. If proteins milled with different dyes are mixed prior to self-assembly, nanofibrils are formed containing all three dyes, thus favoring FRET processes. By tuning the ratio of the three luminescent dyes, PNF dispersions are obtained that display bright white light emission. Moreover, the PNF dispersions can be converted into white luminescent films and gels where the PNFs may help to organize dye molecules. Additionally, the PNF materials can be employed as coatings on commercial LEDs, enabling emission of white light.
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25
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Kaup R, Ten Hove JB, Bunschoten A, van Leeuwen FWB, Velders AH. Multicompartment dendrimicelles with binary, ternary and quaternary core composition. NANOSCALE 2021; 13:15422-15430. [PMID: 34505610 DOI: 10.1039/d1nr04556c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hierarchically built-up multicompartment nanoaggregate systems are of interest for, e.g., novel materials and medicine. Here we present a versatile strategy to generate and unambiguously characterize complex coacervate-core micelles by exploiting four different dendrimeric subcomponents as core-units. The resulting mesoscale structures have a hydrodynamic diameter of 50 nm and a core size of 33 nm, and host about thirty 6th generation polyamidoamine (PAMAM) dendrimers. We have used FRET (efficiency of ∼0.2) between fluorescein and rhodamine moieties immobilized on separate PAMAM dendrimers (G6-F and G6-R, respectively) to prove synchronous encapsulation in the micelle core. Tuning the proximity of the FRET pair molecules either by varying the G6-F : G6-R ratio, or by co-assembling non-functionalized dendrimer (G6-E) in the core, reveals the optimal FRET efficiency to occur at a minimum of 70% loading with G6-F and G6-R. Additional co-encapsulation of 6th generation gold dendrimer-encapsulated nanoparticles (G6-Au) in the micelle core shows a dramatic reduction of the FRET efficiency, which can be restored by chemical etching of the gold nanoparticles from within the micellar core with thiols, leaving the micelle itself intact. This study reveals the controlled co-assembly of up to four different types of subcomponents in one single micellar core and concomitantly shows the wide variety of structures that can be made with a well-defined basic set of subcomponents. It is straightforward to design related strategies, to incorporate inside one micellar core, e.g., even more than 4 different dendrimers, or other classes of (macro)molecules, with different functional groups, other FRET pairs or different encapsulated metal nanoparticles.
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Affiliation(s)
- Rebecca Kaup
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
| | - Jan Bart Ten Hove
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anton Bunschoten
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
| | - Fijs W B van Leeuwen
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aldrik H Velders
- Laboratory of BioNanoTechnology, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Instituto Regional de Investigacion Cientifica Aplicada (IRICA), Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
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26
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Yu-Hao D, Chun C, Xiong F, Rui-Hai L. Study on the pharmacokinetics of mulberry fruit polysaccharides through fluorescence labeling. Int J Biol Macromol 2021; 186:462-471. [PMID: 34271042 DOI: 10.1016/j.ijbiomac.2021.07.075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/11/2021] [Indexed: 01/25/2023]
Abstract
A sensitive and efficient fluorescence labeling method was developed and validated for the microanalysis and detection of polysaccharides. Fluorescein isothiocyanate (FITC) was successfully labeled on mulberry fruit polysaccharides (MFP) through a reductive amination reaction with the assistant of tyramine. The fluorescent labeled polysaccharides (FMFP) was identified by fluorescence, UV-visible, flourier transform infrared (FT-IR) and 1H NMR spectrum. Results demonstrated that the labeling efficiency of FMFP was 0.32%, and the FMFP was stable in simulated digestion fluid without cytotoxicity. The pharmacokinetics and biodistribution after administration were analyzed in rats, which indicated that the FMFP obtained could be absorbed in a short time (tmax 0.50 h) but eliminated slowly (t1/2 8.77 ± 1.38 h). At 24 h after administration, the polysaccharide could be tested mainly in intestine, stomach, liver and kidney. The FITC labeling method lays a foundation for investigating the absorption and metabolism of MFP, and provides references for the microanalysis research of bioactive polysaccharides.
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Affiliation(s)
- Dong Yu-Hao
- SCUT-Zhuhai Institute of Modern Industrial Innovation, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chen Chun
- SCUT-Zhuhai Institute of Modern Industrial Innovation, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangzhou Institute of Modern Industrial Technology, Nansha, 511458, China; School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou 510640, China.
| | - Fu Xiong
- SCUT-Zhuhai Institute of Modern Industrial Innovation, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; Guangzhou Institute of Modern Industrial Technology, Nansha, 511458, China; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou 510640, China.
| | - Liu Rui-Hai
- Department of Food Science, Stocking Hall, Cornell University, Ithaca, NY 14853, USA
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27
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Cevheroğlu O, Murat M, Mingu-Akmete S, Son ÇD. Ste2p Under the Microscope: the Investigation of Oligomeric States of a Yeast G Protein-Coupled Receptor. J Phys Chem B 2021; 125:9526-9536. [PMID: 34433281 DOI: 10.1021/acs.jpcb.1c05872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligomerization of G protein-coupled receptors (GPCRs) may play important roles in maturation, internalization, signaling, and pharmacology of these receptors. However, the nature and extent of their oligomerization is still under debate. In our study, Ste2p, a yeast mating pheromone GPCR, was tagged with enhanced green fluorescent protein (EGFP), mCherry, and with split florescent protein fragments at the receptor C-terminus. The Förster resonance energy transfer (FRET) technique was used to detect receptors' oligomerization by calculating the energy transfer from EGFP to mCherry. Stimulation of Ste2p oligomers with the receptor ligand did not result in any significant change on observed FRET values. The bimolecular fluorescence complementation (BiFC) assay was combined with FRET to further investigate the tetrameric complexes of Ste2p. Our results suggest that in its quiescent (nonligand-activated) state, Ste2p is found at least as a tetrameric complex on the plasma membrane. Intriguingly, receptor tetramers in their active form showed a significant increase in FRET. This study provides a direct in vivo visualization of Ste2p tetramers and the pheromone effect on the extent of the receptor oligomerization.
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Affiliation(s)
- Orkun Cevheroğlu
- Stem Cell Institute, Ankara University, Cankaya, 06520 Ankara, Turkey
| | - Merve Murat
- Stem Cell Institute, Ankara University, Cankaya, 06520 Ankara, Turkey.,Department of Biological Sciences, Middle East Technical University, Cankaya, 06800 Ankara, Turkey
| | - Sara Mingu-Akmete
- Stem Cell Institute, Ankara University, Cankaya, 06520 Ankara, Turkey.,Department of Biological Sciences, Middle East Technical University, Cankaya, 06800 Ankara, Turkey
| | - Çağdaş D Son
- Department of Biological Sciences, Middle East Technical University, Cankaya, 06800 Ankara, Turkey
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28
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Li M. Optimization of N-hydroxysuccinimide ester coupling with aminoallyl-modified RNA for fluorescent labeling. Bioengineered 2021; 11:599-606. [PMID: 32449472 PMCID: PMC8291868 DOI: 10.1080/21655979.2020.1765487] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Site-specific fluorescent labeling of RNA is crucial for obtaining the structural and dynamic information of RNAs by fluorescence techniques. Post-synthetic modification of RNA based on N-hydroxysuccinimide (NHS) coupling reaction is an economic, efficient and simple strategy to introduce fluorophore to samples. However, this strategy are not that frequently used in RNA molecules, and the reported reaction conditions and yields varied among different systems. This study results mainly focused on screening the reaction conditions (reactants concentrations, dimethylsulfoxide concentration, solution conditions, pH and reaction time) between NHS-linked fluorophore and aminoallyl-RNA (aa-RNA) to optimize the yield of fluorescent RNA up to 55%, doubled the initial yield. What's more, as low as one tenth of fluorescent reagent was used in our protocol compared with the reported protocols, greatly reducing the experimental cost. The protocol can be applied as a general guide potentially for RNA labeling by NHS-ester coupling reaction.
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Affiliation(s)
- Mengyang Li
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University , Shanghai, P. R. China
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29
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Liu Y, Shen Y, Song Y, Xu L, P. Perry JJ, Liao J. Isopeptidase Kinetics Determination by a Real Time and Sensitive qFRET Approach. Biomolecules 2021; 11:biom11050673. [PMID: 33946350 PMCID: PMC8145275 DOI: 10.3390/biom11050673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 02/05/2023] Open
Abstract
Isopeptidase activity of proteases plays critical roles in physiological and pathological processes in living organisms, such as protein stability in cancers and protein activity in infectious diseases. However, the kinetics of protease isopeptidase activity has not been explored before due to a lack of methodology. Here, we report the development of novel qFRET-based protease assay for characterizing the isopeptidase kinetics of SENP1. The reversible process of SUMOylation in vivo requires an enzymatic cascade that includes E1, E2, and E3 enzymes and Sentrin/SUMO-specific proteases (SENPs), which can act either as endopeptidases that process the pre-SUMO before its conjugation, or as isopeptidases to deconjugate SUMO from its target substrate. We first produced the isopeptidase substrate of CyPet-SUMO1/YPet-RanGAP1c by SUMOylation reaction in the presence of SUMO E1 and E2 enzymes. Then a qFRET analyses of real-time FRET signal reduction of the conjugated substrate of CyPet-SUMO1/YPet-RanGAP1c to free CyPet-SUMO1 and YPet-RanGAP1c by the SENP1 were able to obtain the kinetic parameters, Kcat, KM, and catalytic efficiency (Kcat/KM) of SENP1. This represents a pioneer effort in isopeptidase kinetics determination. Importantly, the general methodology of qFRET-based protease isopeptidase kinetic determination can also be applied to other proteases.
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Affiliation(s)
- Yan Liu
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (Y.L.); (Y.S.)
| | - Yali Shen
- Department of Abdominal Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China;
| | - Yang Song
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (Y.L.); (Y.S.)
| | - Lei Xu
- Department of Geography & the Environment, California State University, Fullerton, 800 N State College Blvd, Fullerton, CA 92831, USA;
| | - J. Jefferson P. Perry
- Department of Biochemistry, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: (J.J.P.P.); (J.L.)
| | - Jiayu Liao
- Department of Bioengineering, Bourns College of Engineering, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA; (Y.L.); (Y.S.)
- Department of Abdominal Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China;
- Department of Biochemistry, University of California at Riverside, 900 University Avenue, Riverside, CA 92521, USA
- Correspondence: (J.J.P.P.); (J.L.)
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30
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Simões M, Urstöger G, Schennach R, Hirn U. Quantification and Imaging of Nanoscale Contact with Förster Resonance Energy Transfer. ACS APPLIED MATERIALS & INTERFACES 2021; 13:19521-19529. [PMID: 33856765 PMCID: PMC8153545 DOI: 10.1021/acsami.1c04226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Adhesion is caused by molecular interactions that only take place if the surfaces are in nanoscale contact (NSC); i.e., the distance between the surfaces is in the range of 0.1-0.4 nm. However, there are several difficulties measuring the NSC between surfaces, mainly because regions that appear to be in full contact at low magnification may show no NSC when observed at higher magnifications. Thus, the measurement area of NSC is very small with imaging techniques, and an experimental technique to evaluate NSC for large contact areas has not been available thus far. Here, we are proposing Förster resonance energy transfer (FRET) spectroscopy/microscopy for this purpose. We demonstrate that NSC in a distance range of 1-10 nm can be evaluated. Our experiments reveal that, for thin films pressed under different loads, NSC increases with the applied pressure, resulting in a higher FRET signal and a corresponding increase in adhesion force/energy when separating the films. Furthermore, we show that local variations in molecular contact can be visualized with FRET microscopy. Thus, we are introducing a spectroscopic technique for quantification (FRET spectroscopy) and imaging (FRET microscopy) of NSC between surfaces, demonstrated here for the application of surface adhesion. This could be of interest for all fields where adhesion or nanoscale surface contact are playing a role, for example, soft matter, biological materials, and polymers, but also engineering applications, like tribology, adhesives, and sealants.
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Affiliation(s)
- Mónica
G. Simões
- Institute
of Bioproducts and Paper Technology, Inffeldgasse 23, 8010 Graz, Austria
- CD
Laboratory for Fiber Swelling and Paper Performance, Inffeldgasse 23, 8010 Graz, Austria
| | - Georg Urstöger
- Institute
of Bioproducts and Paper Technology, Inffeldgasse 23, 8010 Graz, Austria
- CD
Laboratory for Fiber Swelling and Paper Performance, Inffeldgasse 23, 8010 Graz, Austria
| | - Robert Schennach
- CD
Laboratory for Fiber Swelling and Paper Performance, Inffeldgasse 23, 8010 Graz, Austria
- Institute
of Solid-State Physics, Graz University
of Technology, Petersgasse 16, 8010 Graz, Austria
| | - Ulrich Hirn
- Institute
of Bioproducts and Paper Technology, Inffeldgasse 23, 8010 Graz, Austria
- CD
Laboratory for Fiber Swelling and Paper Performance, Inffeldgasse 23, 8010 Graz, Austria
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31
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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: 10] [Impact Index Per Article: 3.3] [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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32
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Delgadillo RF, Carnes KA, Zaleta-Rivera K, Olmos O, Parkhurst LJ. A FLIM Microscopy Based on Acceptor-Detected Förster Resonance Energy Transfer. Anal Chem 2021; 93:4841-4849. [PMID: 33691398 PMCID: PMC7992049 DOI: 10.1021/acs.analchem.0c04492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Time-resolved donor-detected
Förster resonance energy transfer
(trDDFRET) allows the observation of molecular interactions of dye-labeled
biomolecules in the ∼10–100 Å region. However,
we can observe longer-range interactions when using time-resolved
acceptor-detected FRET (trADFRET), since the signal/noise ratio can
be improved when observing the acceptor emission. Therefore, we propose
a new methodology based on trADFRET to construct a new fluorescence
lifetime microscopy (FLIM-trADFRET) technique to observe biological
machinery in the range of 100–300 Å in vivo, the last
frontier in biomolecular medicine. The integrated trADFRET signal
is extracted in such a way that noise is canceled, and more photons
are collected, even though trADFRET and trDDFRET have the same rate
of transfer. To assess our new methodology, proof of concept was demonstrated
with a set of well-defined DNA scaffolds.
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Affiliation(s)
- Roberto F Delgadillo
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States.,Tecnologico de Monterrey, School of Engineering and Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico.,BASF Enzymes LLC, 3550 John Hopkins Ct, San Diego, California 92121, United States
| | - Katie A Carnes
- GlaxoSmithKline, Medicinal Science and Technology, CMC Analytical - Drug Substance and Product Analysis, King of Prussia, Pennsylvania, 19406, United States
| | - Kathia Zaleta-Rivera
- Department of Bioengineering, University of California San Diego, San Diego, California, 92093-0412, United States
| | - Omar Olmos
- Tecnologico de Monterrey, School of Engineering and Sciences, Av. Eugenio Garza Sada 2501 Sur, Monterrey, Nuevo Leon 64849, Monterrey, Mexico
| | - Lawrence J Parkhurst
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, Nebraska 68588-0304, United States
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33
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Zhang W, Bertinetti L, Blank KG, Dimova R, Gao C, Schneck E, Fratzl P. Spatiotemporal Measurement of Osmotic Pressures by FRET Imaging. Angew Chem Int Ed Engl 2021; 60:6488-6495. [PMID: 33188706 PMCID: PMC7986915 DOI: 10.1002/anie.202011983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/06/2020] [Indexed: 12/21/2022]
Abstract
Osmotic pressures (OPs) play essential roles in biological processes and numerous technological applications. However, the measurement of OP in situ with spatiotemporal resolution has not been achieved so far. Herein, we introduce a novel kind of OP sensor based on liposomes loaded with water-soluble fluorescent dyes exhibiting resonance energy transfer (FRET). The liposomes experience volume changes in response to OP due to water outflux. The FRET efficiency depends on the average distance between the entrapped dyes and thus provides a direct measure of the OP surrounding each liposome. The sensors exhibit high sensitivity to OP in the biologically relevant range of 0-0.3 MPa in aqueous solutions of salt, small organic molecules, and macromolecules. With the help of FRET microscopy, we demonstrate the feasibility of spatiotemporal OP imaging, which can be a promising new tool to investigate phenomena involving OPs and their dynamics in biology and technology.
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Affiliation(s)
- Wenbo Zhang
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Luca Bertinetti
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Kerstin G. Blank
- Mechano(bio)chemistryMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Rumiana Dimova
- Department of Theory & Bio-SystemsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and FunctionalizationDepartment of Polymer Science and EngineeringZhejiang UniversityHangzhou310027China
| | - Emanuel Schneck
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
- Department of PhysicsTechnische Universität Darmstadt64289DarmstadtGermany
| | - Peter Fratzl
- Department of BiomaterialsMax Planck Institute of Colloids and Interfaces14476PotsdamGermany
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34
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Zhang W, Bertinetti L, Blank KG, Dimova R, Gao C, Schneck E, Fratzl P. Spatiotemporal Measurement of Osmotic Pressures by FRET Imaging. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Wenbo Zhang
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Luca Bertinetti
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Kerstin G. Blank
- Mechano(bio)chemistry Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Rumiana Dimova
- Department of Theory & Bio-Systems Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
| | - Changyou Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization Department of Polymer Science and Engineering Zhejiang University Hangzhou 310027 China
| | - Emanuel Schneck
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
- Department of Physics Technische Universität Darmstadt 64289 Darmstadt Germany
| | - Peter Fratzl
- Department of Biomaterials Max Planck Institute of Colloids and Interfaces 14476 Potsdam Germany
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35
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Impairing activation of phospholipid synthesis by c-Fos interferes with glioblastoma cell proliferation. Biochem J 2021; 477:4675-4688. [PMID: 33211090 DOI: 10.1042/bcj20200465] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022]
Abstract
Glioblastoma multiforme is the most aggressive type of tumor of the CNS with an overall survival rate of approximately one year. Since this rate has not changed significantly over the last 20 years, the development of new therapeutic strategies for the treatment of these tumors is peremptory. The over-expression of the proto-oncogene c-Fos has been observed in several CNS tumors including glioblastoma multiforme and is usually associated with a poor prognosis. Besides its genomic activity as an AP-1 transcription factor, this protein can also activate phospholipid synthesis by a direct interaction with key enzymes of their metabolic pathways. Given that the amino-terminal portion of c-Fos (c-Fos-NA: amino acids 1-138) associates to but does not activate phospholipid synthesizing enzymes, we evaluated if c-Fos-NA or some shorter derivatives are capable of acting as dominant-negative peptides of the activating capacity of c-Fos. The over-expression or the exogenous administration of c-Fos-NA to cultured T98G cells hampers the interaction between c-Fos and PI4K2A, an enzyme activated by c-Fos. Moreover, it was observed a decrease in tumor cell proliferation rates in vitro and a reduction in tumor growth in vivo when a U87-MG-generated xenograft on nude mice is intratumorally treated with recombinant c-Fos-NA. Importantly, a smaller peptide of 92 amino acids derived from c-Fos-NA retains the capacity to interfere with tumor proliferation in vitro and in vivo. Taken together, these results support the use of the N-terminal portion of c-Fos, or shorter derivatives as a novel therapeutic strategy for the treatment of glioblastoma multiforme.
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Mao WT, Hsu WH, Li JY, Yang CH. Distance-based measurement determines the coexistence of B protein hetero- and homodimers in lily tepal and stamen tetrameric complexes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1357-1373. [PMID: 33277739 DOI: 10.1111/tpj.15117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
The floral quartet model proposes that plant MADS box proteins function as higher order tetrameric complexes. However, in planta evidence for MADS box tetramers remains scarce. Here, we applied a strategy using in vivo fluorescence resonance energy transfer (FRET) based on the distance change and distance symmetry of stable tetrameric complexes in tobacco (Nicotiana benthamiana) leaf cells to improve the accuracy of the estimation of heterotetrameric complex formation. This measuring system precisely verified the stable state of Arabidopsis petal (AP3/PI/SEP3/AP1) and stamen (AP3/PI/SEP3/AG) complexes and showed that the lily (Lilium longiflorum) PI co-orthologs LMADS8 and LMADS9 likely formed heterotetrameric petal complexes with Arabidopsis AP3/SEP3/AP1, which rescued petal defects of pi mutants. However, L8/L9 did not form heterotetrameric stamen complexes with Arabidopsis AP3/SEP3/AG to rescue the stamen defects of the pi mutants. Importantly, this system was applied successfully to find complicated tepal and stamen heterotetrameric complexes in lily. We found that heterodimers of B function AP3/PI orthologs (L1/L8) likely coexist with the homodimers of PI orthologs (L8/L8, L9/L9) to form five (two most stable and three stable) tepal- and four (one most stable and three stable) stamen-related heterotetrameric complexes with A/E and C/E function proteins in lily. Among these combinations, L1 preferentially interacted with L8 to form the most stable heterotetrameric complexes, and the importance of the L8/L8 and L9/L9 homodimers in tepal/stamen formation in lily likely decreased to a minor part during evolution. The system provides substantial improvements for successfully estimating the existence of unknown tetrameric complexes in plants.
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Affiliation(s)
- Wan-Ting Mao
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
| | - Wei-Han Hsu
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
| | - Jen-Ying Li
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
| | - Chang-Hsien Yang
- Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan ROC
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan ROC
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Kutashev KO, Franek M, Diamanti K, Komorowski J, Olšinová M, Dvořáčková M. Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1534-1548. [PMID: 33314374 DOI: 10.1111/tpj.15130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/30/2020] [Indexed: 05/15/2023]
Abstract
Arabidopsis thaliana 45S ribosomal genes (rDNA) are located in tandem arrays called nucleolus organizing regions on the termini of chromosomes 2 and 4 (NOR2 and NOR4) and encode rRNA, a crucial structural element of the ribosome. The current model of rDNA organization suggests that inactive rRNA genes accumulate in the condensed chromocenters in the nucleus and at the nucleolar periphery, while the nucleolus delineates active genes. We challenge the perspective that all intranucleolar rDNA is active by showing that a subset of nucleolar rDNA assembles into condensed foci marked by H3.1 and H3.3 histones that also contain the repressive H3K9me2 histone mark. By using plant lines containing a low number of rDNA copies, we further found that the condensed foci relate to the folding of rDNA, which appears to be a common mechanism of rDNA regulation inside the nucleolus. The H3K9me2 histone mark found in condensed foci represents a typical modification of bulk inactive rDNA, as we show by genome-wide approaches, similar to the H2A.W histone variant. The euchromatin histone marks H3K27me3 and H3K4me3, in contrast, do not colocalize with nucleolar foci and their overall levels in the nucleolus are very low. We further demonstrate that the rDNA promoter is an important regulatory region of the rDNA, where the distribution of histone variants and histone modifications are modulated in response to rDNA activity.
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Affiliation(s)
- Konstantin O Kutashev
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, Brno, 61137, Czech Republic
| | - Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
| | - Klev Diamanti
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, 751 08, Sweden
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, 751 24, Sweden
- Institute of Computer Science, Polish Academy of Sciences, Warsaw, 012-48, Poland
| | - Marie Olšinová
- BioCEV Imaging Methods Core Facility, Průmyslová 595, Vestec, 252 50, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, CEITEC, Masaryk University, Kamenice 5, Brno, 62500, Czech Republic
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Yang L, Chen X, Ma P, Jin D, Zhou J, He H, Cheng Z, Lin J. Upconversion nanoparticles coated with molecularly imprinted polymers for specific sensing. Dalton Trans 2020; 49:17200-17206. [PMID: 33200757 DOI: 10.1039/d0dt03555f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of fluorescent sensors based on lanthanide-doped luminescent nanoparticles has increased their application in biomarker detection. Lanthanide-doped upconversion nanoparticles (UCNPs) have been explored as one of the most promising sensors owing to their merits such as excellent photostability, zero background auto-fluorescence, and reduced side effects of near-infrared triggered treatments. However, traditional upconversion luminescence assay based on direct Fluorescence Resonance Energy Transfer (FRET) between the target molecules and surface of UCNPs encounters low detection accuracy due to superficial adsorption interactions. In this work, we use a molecularly imprinting technique to achieve the specific interaction between UCNPs and molecules for accurate sensing. We demonstrate this by synthesizing a nanostructure with a molecularly imprinted polymer at the surface of UCNPs, in which the imprinted cavities can specifically capture the target molecule of rhodamine B. The upconversion signal changes in relation to the molecule concentration due to FRET. Quantitative analysis shows that the fluorescence-quenching rate is consistent with the Stern-Volmer equation, resulting in a limit of detection of 6.27 μg mL-1. Our fluorescence sensing approach integrates the advantages of both nonlinear upconversion and molecular imprinting technologies, showing great potential for the detection of specific molecules.
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Affiliation(s)
- Ling Yang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
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Yeroslavsky G, Umezawa M, Okubo K, Nigoghossian K, Thi Kim Dung D, Miyata K, Kamimura M, Soga K. Stabilization of indocyanine green dye in polymeric micelles for NIR-II fluorescence imaging and cancer treatment. Biomater Sci 2020; 8:2245-2254. [PMID: 32129330 DOI: 10.1039/c9bm02010a] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
One of the most commonly used near infrared (NIR) dyes is indocyanine green (ICG), which has been extensively used for NIR bioimaging, photothermal and photodynamic therapy. However, upon excitation this dye can react with molecular oxygen to form singlet oxygen (SO), which can then cleave ICG to form non-fluorescent debris. In order to reduce the reaction between ICG and oxygen, we used energy transfer (ET) between the former and the NIR dye IR-1061. The two dyes were encapsulated in micelles composed of biocompatible poly(ethylene glycol)-block-poly(ε-caprolactone) (PCL-PEG). Micelles were characterized for their size using dynamic light scattering (DLS) and were found to measure about 35 nm in diameter. Fluorescence emission measurements were conducted to show that the stability of ICG against photodecomposition is increased. Moreover, this increased stability allows the encapsulated dye to generate more heat and for a longer time, compared to its free form. Studies with a SO indicator showed that as more IR-1061 is added to the micelles, less SO is produced. These results show how by changing the amount of added IR-1061 it is possible to tune the heat and SO generated by the system. Cell viability studies demonstrated that while particles were nontoxic under physiological conditions, upon 808 nm irradiation they become potent at eradicating MCF7 cancer cells. Moreover, it was demonstrated that both the increase of temperature and the creation of decomposition debris play a role in the cytotoxic efficacy of the micelles. Dye-loaded micelles that were injected to live mice showed bright fluorescence in the over 1000 nm NIR (OTN-NIR) region, allowing for visualization of blood vessels and internal organs. Most importantly, the encapsulated dyes remained stable for over 30 minutes, gradually accumulating in the liver and spleen. The presence of IR-1061 in addition to the heat-generating dye ICG allowed for simultaneous temperature modification and monitoring. We were able to assess the change in temperature by measuring the change in the fluorescence intensity of IR-1061 in the OTN-NIR region, a range with deep penetration of living tissues. These features illustrate the potential use of ICG/IR-1061 in PCL-PEG micelles as promising candidates for cancer treatment and diagnosis.
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Affiliation(s)
- Gil Yeroslavsky
- Imaging Frontier Center (IFC), Research Institute for Science and Technology (RIST), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan.
| | - Masakazu Umezawa
- Imaging Frontier Center (IFC), Research Institute for Science and Technology (RIST), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. and Department Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Kyohei Okubo
- Imaging Frontier Center (IFC), Research Institute for Science and Technology (RIST), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. and Department Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Karina Nigoghossian
- Department Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Doan Thi Kim Dung
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, 6-5-1, Kashiwanoha, Kashiwashi, Chiba 277-8577, Japan
| | - Keiji Miyata
- Department Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Masao Kamimura
- Imaging Frontier Center (IFC), Research Institute for Science and Technology (RIST), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. and Department Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Kohei Soga
- Imaging Frontier Center (IFC), Research Institute for Science and Technology (RIST), Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan. and Department Materials Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
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Gordon F, Elcoroaristizabal S, Ryder AG. Modelling Förster resonance energy transfer (FRET) using anisotropy resolved multi-dimensional emission spectroscopy (ARMES). Biochim Biophys Acta Gen Subj 2020; 1865:129770. [PMID: 33214128 DOI: 10.1016/j.bbagen.2020.129770] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND Förster Resonance Energy Transfer (FRET) is widely used to study the structure and dynamics of biomolecular systems and also causes the non-linear fluorescence response observed in multi-fluorophore proteins. Accurate FRET analysis, in terms of measuring changes in donor and acceptor spectra and energy transfer efficiency is therefore critical. METHODS We demonstrate a novel quantitative FRET analysis using anisotropy resolved multidimensional emission spectroscopy (ARMES) in a Human Serum Albumin (HSA) and 1,8-anilinonaphathalene sulfonate (ANS) model. ARMES combines 4D measurement of polarized excitation emission matrices (pEEM) with multivariate data analysis to spectrally resolve contributing fluorophores. Multivariate analysis (Parallel Factor, PARAFAC and restricted Tucker3) was used to resolve fluorophore contributions and for modelling the quenching of HSA emission and the HSA-ANS interactions. RESULTS pEEM spectra were modelled using Tucker3 which accommodates non-linearities introduced by FRET and a priori chemical knowledge was used to optimise the solution, thus resolving three components: HSA emission, ANS emission from indirect FRET excitation, and ANS emission from direct excitation. Perpendicular emission measurements were more sensitive to indirectly excited acceptor emission. PARAFAC modelling of HSA, donor emission, separated ANS FRET interacting (Tryptophan) and non-interacting (Tyrosine) components. This enabled a new way of calculating quenching constants using the multi-dimensional emission of individual donor fluorophores. CONCLUSIONS FRET efficiency could be calculated using the multi-dimensional, resolved emission of the interacting donor fluorophores only which yielded higher ET efficiencies compared to conventional methods. GENERAL SIGNIFICANCE Shows the potential of multidimensional fluorescence measurements and data analysis for more accurate FRET modelling in proteins.
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Affiliation(s)
- Fiona Gordon
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, Galway, Galway H91 CF50, Ireland.
| | - Saioa Elcoroaristizabal
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, Galway, Galway H91 CF50, Ireland.
| | - Alan G Ryder
- Nanoscale BioPhotonics Laboratory, School of Chemistry, National University of Ireland, Galway, Galway H91 CF50, Ireland.
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Liu Y, Yang G, Jin S, Zhang R, Chen P, Tengjisi, Wang L, Chen D, Weitz DA, Zhao C. J‐Aggregate‐Based FRET Monitoring of Drug Release from Polymer Nanoparticles with High Drug Loading. Angew Chem Int Ed Engl 2020; 59:20065-20074. [DOI: 10.1002/anie.202008018] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/29/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Yun Liu
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Guangze Yang
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Song Jin
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Peng Chen
- Nanomaterials Centre School of Chemical Engineering Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane QLD 4072 Australia
| | - Tengjisi
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Lianzhou Wang
- Nanomaterials Centre School of Chemical Engineering Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane QLD 4072 Australia
| | - Dong Chen
- Institute of Process Equipment College of Energy Engineering Zhejiang University Hangzhou Zhejiang 310027 China
| | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA
| | - Chun‐Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
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Liu Y, Yang G, Jin S, Zhang R, Chen P, Tengjisi, Wang L, Chen D, Weitz DA, Zhao C. J‐Aggregate‐Based FRET Monitoring of Drug Release from Polymer Nanoparticles with High Drug Loading. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yun Liu
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Guangze Yang
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Song Jin
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Peng Chen
- Nanomaterials Centre School of Chemical Engineering Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane QLD 4072 Australia
| | - Tengjisi
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
| | - Lianzhou Wang
- Nanomaterials Centre School of Chemical Engineering Australian Institute for Bioengineering and Nanotechnology The University of Queensland Brisbane QLD 4072 Australia
| | - Dong Chen
- Institute of Process Equipment College of Energy Engineering Zhejiang University Hangzhou Zhejiang 310027 China
| | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences Harvard University Cambridge MA 02138 USA
| | - Chun‐Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology University of Queensland St. Lucia Queensland 4072 Australia
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Menaesse A, Sumetsky D, Emanuely N, Stein JL, Gates EM, Hoffman BD, Boustany NN. Simplified Instrument Calibration for Wide-Field Fluorescence Resonance Energy Transfer (FRET) Measured by the Sensitized Emission Method. Cytometry A 2020; 99:407-416. [PMID: 32700451 DOI: 10.1002/cyto.a.24194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/30/2020] [Accepted: 07/17/2020] [Indexed: 12/21/2022]
Abstract
Fӧrster (or fluorescence) resonance energy transfer (FRET) is a quantifiable energy transfer in which a donor fluorophore nonradiatively transfers its excitation energy to an acceptor fluorophore. A change in FRET efficiency indicates a change of proximity and environment of these fluorophores, which enables the study of intermolecular interactions. Measurement of FRET efficiency using the sensitized emission method requires a donor-acceptor calibrated system. One of these calibration factors named the G factor, which depends on instrument parameters related to the donor and acceptor measurement channels and on the fluorophores quantum efficiencies, can be determined in several different ways and allows for conversion of the raw donor and acceptor emission signals to FRET efficiency. However, the calculated value of the G factor from experimental data can fluctuate significantly depending on the chosen experimental method and the size of the sample. In this technical note, we extend the results of Gates et al. (Cytometry Part A 95A (2018) 201-213) by refining the calibration method used for calibration of FRET from image pixel data. Instead of using the pixel histograms of two constructs with high and low FRET efficiency to determine the G factor, we use pixel histogram data from one construct of known efficiency. We validate this method by determining the G factor with the same constructs developed and used by Gates et al. and comparing the results from the two approaches. While the two approaches are equivalent theoretically, we demonstrate that the use of a single construct with known efficiency provides a more precise experimental measurement of the G factor that can be attained by collecting a smaller number of images. © 2020 International Society for Advancement of Cytometry.
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Affiliation(s)
- Audrey Menaesse
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA.,School of Life Sciences Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Daniel Sumetsky
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Nicolas Emanuely
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA.,Institut d'Optique Graduate School, Palaiseau, France
| | - Jeremy L Stein
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
| | - Evan M Gates
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Brenton D Hoffman
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA
| | - Nada N Boustany
- Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, USA
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Szabó Á, Nagy P. I Am the Alpha and the …Gamma, and the G. Calibration of Intensity-Based FRET Measurements. Cytometry A 2020; 99:369-371. [PMID: 32790096 DOI: 10.1002/cyto.a.24206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Ágnes Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Szabó Á, Szendi-Szatmári T, Szöllősi J, Nagy P. Quo vadis FRET? Förster's method in the era of superresolution. Methods Appl Fluoresc 2020; 8:032003. [PMID: 32521530 DOI: 10.1088/2050-6120/ab9b72] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although the theoretical foundations of Förster resonance energy transfer (FRET) were laid in the 1940s as part of the quantum physical revolution of the 20th century, it was only in the 1970s that it made its way to biology as a result of the availability of suitable measuring and labeling technologies. Thanks to its ease of application, FRET became widely used for studying molecular associations on the nanometer scale. The development of superresolution techniques at the turn of the millennium promised an unprecedented insight into the structure and function of molecular complexes. Without downplaying the significance of superresolution microscopies this review expresses our view that FRET is still a legitimate tool in the armamentarium of biologists for studying molecular associations since it offers distinct advantages and overcomes certain limitations of superresolution approaches.
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Affiliation(s)
- Ágnes Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary. MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem square 1, 4032 Debrecen, Hungary
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Mizutani S, Murata M, Taniai N, Sukegawa M, Nakata R, Furuki H, Yoshida H. Förster resonance energy transfer (FRET)-Labeled nanoprobe enables real-time diagnosis of pancreatic juice activation due to postoperative pancreatic fistula. Pancreatology 2020; 20:960-967. [PMID: 32622759 DOI: 10.1016/j.pan.2020.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 05/13/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Postoperative pancreatic fistula (POPF) subsequent to pancreatectomy often causes activation of pancreatic juice, resulting in serious complications. In POPF, the types of pancreatic juices found are active and inactive, and the identification of these two types of pancreatic juice greatly contributes to the development of postoperative management after pancreatectomy. This study reports favorable results of the clinical application of the Förster resonance energy transfer (FRET) nanoprobe that was independently developed to distinguish between the active and inactive types of pancreatic juice. METHODS The FRET nanoprobe developed was a nanoprotein capsule. It exuded a red color when the capsule structure was maintained. When activated protease in the pancreatic juice acts on it, the capsules are reduced quantitatively and FRET is abolished, resulting in a change in color from red to green. Pancreatic juice activation can be measured by the FRET signal. A total of 117 drainage fluid samples from 16 postpancreatoduodenectomy cases were obtained and evaluated. RESULTS The diagnosis of pancreatic juice activation was possible using the FRET signal with a cut-off value of 1.6. Pancreatic juice activation was not associated with drainage fluid amylase (AMY) levels. The results demonstrated that pancreatic juice was activated when drainage fluid was infected. CONCLUSION The use of a FRET nanoprobe enabled real-time detection of the presence or absence of pancreatic juice activation in pancreatic fistula after pancreatic surgery. There was an adequate correlation between infection and pancreatic juice activation regardless of drain AMY levels.
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Affiliation(s)
- Satoshi Mizutani
- Digestive Surgery, Nippon Medical School Musashikosugi Hospital, 211-8533, 1-396, Kosugicho, Nakaharaku, Kawasaki, Kanagawa, Japan.
| | - Masaharu Murata
- Center for Advanced Medical Innovation, Kyushu University, Fukuoka, Japan
| | - Nobuhiko Taniai
- Digestive Surgery, Nippon Medical School Musashikosugi Hospital, 211-8533, 1-396, Kosugicho, Nakaharaku, Kawasaki, Kanagawa, Japan
| | - Makoto Sukegawa
- Digestive Surgery, Nippon Medical School Musashikosugi Hospital, 211-8533, 1-396, Kosugicho, Nakaharaku, Kawasaki, Kanagawa, Japan
| | - Ryosuke Nakata
- Digestive Surgery, Nippon Medical School Musashikosugi Hospital, 211-8533, 1-396, Kosugicho, Nakaharaku, Kawasaki, Kanagawa, Japan
| | - Hiroyasu Furuki
- Digestive Surgery, Nippon Medical School Musashikosugi Hospital, 211-8533, 1-396, Kosugicho, Nakaharaku, Kawasaki, Kanagawa, Japan
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Huang AYS, Woo J, Sardar D, Lozzi B, Bosquez Huerta NA, Lin CCJ, Felice D, Jain A, Paulucci-Holthauzen A, Deneen B. Region-Specific Transcriptional Control of Astrocyte Function Oversees Local Circuit Activities. Neuron 2020; 106:992-1008.e9. [PMID: 32320644 PMCID: PMC7879989 DOI: 10.1016/j.neuron.2020.03.025] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/24/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023]
Abstract
Astrocytes play essential roles in brain function by supporting synaptic connectivity and associated circuits. How these roles are regulated by transcription factors is unknown. Moreover, there is emerging evidence that astrocytes exhibit regional heterogeneity, and the mechanisms controlling this diversity remain nascent. Here, we show that conditional deletion of the transcription factor nuclear factor I-A (NFIA) in astrocytes in the adult brain results in region-specific alterations in morphology and physiology that are mediated by selective DNA binding. Disruptions in astrocyte function following loss of NFIA are most pronounced in the hippocampus, manifested by impaired interactions with neurons, coupled with diminution of learning and memory behaviors. These changes in hippocampal astrocytes did not affect basal neuronal properties but specifically inhibited synaptic plasticity, which is regulated by NFIA in astrocytes through calcium-dependent mechanisms. Together, our studies reveal region-specific transcriptional dependencies for astrocytes and identify astrocytic NFIA as a key transcriptional regulator of hippocampal circuits.
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Affiliation(s)
- Anna Yu-Szu Huang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Junsung Woo
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Debosmita Sardar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Navish A Bosquez Huerta
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chia-Ching John Lin
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniela Felice
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA.
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48
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Rodríguez-Berdini L, Ferrero GO, Bustos Plonka F, Cardozo Gizzi AM, Prucca CG, Quiroga S, Caputto BL. The moonlighting protein c-Fos activates lipid synthesis in neurons, an activity that is critical for cellular differentiation and cortical development. J Biol Chem 2020; 295:8808-8818. [PMID: 32385110 DOI: 10.1074/jbc.ra119.010129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 04/28/2020] [Indexed: 01/07/2023] Open
Abstract
Differentiation of neuronal cells is crucial for the development and function of the nervous system. This process involves high rates of membrane expansion, during which the synthesis of membrane lipids must be tightly regulated. In this work, using a variety of molecular and biochemical assays and approaches, including immunofluorescence microscopy and FRET analyses, we demonstrate that the proto-oncogene c-Fos (c-Fos) activates cytoplasmic lipid synthesis in the central nervous system and thereby supports neuronal differentiation. Specifically, in hippocampal primary cultures, blocking c-Fos expression or its activity impairs neuronal differentiation. When examining its subcellular localization, we found that c-Fos co-localizes with endoplasmic reticulum markers and strongly interacts with lipid-synthesizing enzymes, whose activities were markedly increased in vitro in the presence of recombinant c-Fos. Of note, the expression of c-Fos dominant-negative variants capable of blocking its lipid synthesis-activating activity impaired neuronal differentiation. Moreover, using an in utero electroporation model, we observed that neurons with blocked c-Fos expression or lacking its AP-1-independent activity fail to initiate cortical development. These results highlight the importance of c-Fos-mediated activation of lipid synthesis for proper nervous system development.
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Affiliation(s)
- Lucia Rodríguez-Berdini
- Centro de Investigaciones en Química Biológica de Córdoba (Consejo Nacional de Investigaciones Científicas y Técnicas), Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Gabriel Orlando Ferrero
- Centro de Investigaciones en Química Biológica de Córdoba (Consejo Nacional de Investigaciones Científicas y Técnicas), Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Florentyna Bustos Plonka
- Centro de Investigaciones en Química Biológica de Córdoba (Consejo Nacional de Investigaciones Científicas y Técnicas), Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrés Mauricio Cardozo Gizzi
- Centro de Investigaciones en Química Biológica de Córdoba (Consejo Nacional de Investigaciones Científicas y Técnicas), Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - César Germán Prucca
- Centro de Investigaciones en Química Biológica de Córdoba (Consejo Nacional de Investigaciones Científicas y Técnicas), Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Santiago Quiroga
- Centro de Investigaciones en Química Biológica de Córdoba (Consejo Nacional de Investigaciones Científicas y Técnicas), Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Beatriz Leonor Caputto
- Centro de Investigaciones en Química Biológica de Córdoba (Consejo Nacional de Investigaciones Científicas y Técnicas), Departamento de Química Biológica "Ranwel Caputto", Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
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49
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Balatskaya MN, Baglay AI, Rubtsov YP, Sharonov GV. Analysis of GPI-Anchored Receptor Distribution and Dynamics in Live Cells by Tag-mediated Enzymatic Labeling and FRET. Methods Protoc 2020; 3:mps3020033. [PMID: 32349461 PMCID: PMC7359698 DOI: 10.3390/mps3020033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/25/2020] [Accepted: 04/26/2020] [Indexed: 01/17/2023] Open
Abstract
The analysis of glycosylphosphatidylinositol (GPI)-anchored receptor distribution and dynamics in live cells is challenging, because their clusters exhibit subdiffraction-limited sizes and are highly dynamic. However, the cellular response depends on the GPI-anchored receptor clusters' distribution and dynamics. Here, we compare three approaches to GPI-anchored receptor labeling (with antibodies, fluorescent proteins, and enzymatically modified small peptide tags) and use several variants of Förster resonance energy transfer (FRET) detection by confocal microscopy and flow cytometry in order to obtain insight into the distribution and the ligand-induced dynamics of GPI-anchored receptors. We found that the enzyme-mediated site-specific fluorescence labeling of T-cadherin modified with a short peptide tag (12 residues in length) have several advantages over labeling by fluorescent proteins or antibodies, including (i) the minimized distortion of the protein's properties, (ii) the possibility to use a cell-impermeable fluorescent substrate that allows for selective labeling of surface-exposed proteins in live cells, and (iii) superior control of the donor to acceptor molar ratio. We successfully detected the FRET of GPI-anchored receptors, T-cadherin, and ephrin-A1, without ligands, and showed in real time that adiponectin induces stable T-cadherin cluster formation. In this paper (which is complementary to our recent research (Balatskaya et al., 2019)), we present the practical aspects of labeling and the heteroFRET measurements of GPI-anchored receptors to study their dynamics on a plasma membrane in live cells.
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Affiliation(s)
- Maria N. Balatskaya
- Faculty of Medicine, Lomonosov Moscow State University, Lomonosovskiy av. 27-1, 119192 Moscow, Russia; (A.I.B.); (Y.P.R.); (G.V.S.)
- Correspondence:
| | - Alexandra I. Baglay
- Faculty of Medicine, Lomonosov Moscow State University, Lomonosovskiy av. 27-1, 119192 Moscow, Russia; (A.I.B.); (Y.P.R.); (G.V.S.)
| | - Yury P. Rubtsov
- Faculty of Medicine, Lomonosov Moscow State University, Lomonosovskiy av. 27-1, 119192 Moscow, Russia; (A.I.B.); (Y.P.R.); (G.V.S.)
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - George V. Sharonov
- Faculty of Medicine, Lomonosov Moscow State University, Lomonosovskiy av. 27-1, 119192 Moscow, Russia; (A.I.B.); (Y.P.R.); (G.V.S.)
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry RAS, str. Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia
- Laboratory of Genomics of Antitumor Adaptive Immunity, Privolzhsky Research Medical University, 10/1 Minin & Pozharsky sq., 603005 Nizhny Novgorod, Russia
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QuanTI-FRET: a framework for quantitative FRET measurements in living cells. Sci Rep 2020; 10:6504. [PMID: 32300110 PMCID: PMC7162988 DOI: 10.1038/s41598-020-62924-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/17/2020] [Indexed: 12/15/2022] Open
Abstract
Förster Resonance Energy Transfer (FRET) allows for the visualization of nanometer-scale distances and distance changes. This sensitivity is regularly achieved in single-molecule experiments in vitro but is still challenging in biological materials. Despite many efforts, quantitative FRET in living samples is either restricted to specific instruments or limited by the complexity of the required analysis. With the recent development and expanding utilization of FRET-based biosensors, it becomes essential to allow biologists to produce quantitative results that can directly be compared. Here, we present a new calibration and analysis method allowing for quantitative FRET imaging in living cells with a simple fluorescence microscope. Aside from the spectral crosstalk corrections, two additional correction factors were defined from photophysical equations, describing the relative differences in excitation and detection efficiencies. The calibration is achieved in a single step, which renders the Quantitative Three-Image FRET (QuanTI-FRET) method extremely robust. The only requirement is a sample of known stoichiometry donor:acceptor, which is naturally the case for intramolecular FRET constructs. We show that QuanTI-FRET gives absolute FRET values, independent of the instrument or the expression level. Through the calculation of the stoichiometry, we assess the quality of the data thus making QuanTI-FRET usable confidently by non-specialists.
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