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Salluce G, Folgar-Cameán Y, Barba-Bon A, Nikšić-Franjić I, El Anwar S, Grüner B, Lostalé-Seijo I, Nau WM, Montenegro J. Size and Polarizability of Boron Cluster Carriers Modulate Chaotropic Membrane Transport. Angew Chem Int Ed Engl 2024; 63:e202404286. [PMID: 38712936 DOI: 10.1002/anie.202404286] [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: 03/01/2024] [Revised: 04/24/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
Perhalogenated closo-borates represent a new class of membrane carriers. They owe this activity to their chaotropicity, which enables the transport of hydrophilic molecules across model membranes and into living cells. The transport efficiency of this new class of cluster carriers depends on a careful balance between their affinity to membranes and cargo, which varies with chaotropicity. However, the structure-activity parameters that define chaotropic transport remain to be elucidated. Here, we have studied the modulation of chaotropic transport by decoupling the halogen composition from the boron core size. The binding affinity between perhalogenated decaborate and dodecaborate clusters carriers was quantified with different hydrophilic model cargos, namely a neutral and a cationic peptide, phalloidin and (KLAKLAK)2. The transport efficiency, membrane-lytic properties, and cellular toxicity, as obtained from different vesicle and cell assays, increased with the size and polarizability of the clusters. These results validate the chaotropic effect as the driving force behind the membrane transport propensity of boron clusters. This work advances our understanding of the structural features of boron cluster carriers and establishes the first set of rational design principles for chaotropic membrane transporters.
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Affiliation(s)
- Giulia Salluce
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Yeray Folgar-Cameán
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Andrea Barba-Bon
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Ivana Nikšić-Franjić
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Suzan El Anwar
- Institute of Inorganic Chemistry, Czech Academy of Sciences, v.v.i. Hlavní 1001, CZ-250 68, Řež, Czech Republic
| | - Bohumír Grüner
- Institute of Inorganic Chemistry, Czech Academy of Sciences, v.v.i. Hlavní 1001, CZ-250 68, Řež, Czech Republic
| | - Irene Lostalé-Seijo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
| | - Werner M Nau
- School of Science, Constructor University, Campus Ring 1, 28759, Bremen, Germany
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15705, Santiago de Compostela, Spain
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2
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Modak A, Kilic Z, Chattrakun K, Terry DS, Kalathur RC, Blanchard SC. Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function. Annu Rev Biophys 2024; 53:427-453. [PMID: 39013028 DOI: 10.1146/annurev-biophys-070323-024308] [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: 07/18/2024]
Abstract
Integral membrane proteins (IMPs) play central roles in cellular physiology and represent the majority of known drug targets. Single-molecule fluorescence and fluorescence resonance energy transfer (FRET) methods have recently emerged as valuable tools for investigating structure-function relationships in IMPs. This review focuses on the practical foundations required for examining polytopic IMP function using single-molecule FRET (smFRET) and provides an overview of the technical and conceptual frameworks emerging from this area of investigation. In this context, we highlight the utility of smFRET methods to reveal transient conformational states critical to IMP function and the use of smFRET data to guide structural and drug mechanism-of-action investigations. We also identify frontiers where progress is likely to be paramount to advancing the field.
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Affiliation(s)
- Arnab Modak
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Zeliha Kilic
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Kanokporn Chattrakun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Daniel S Terry
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Ravi C Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
| | - Scott C Blanchard
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; , , , , ,
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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3
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Rose K, Jepson T, Shukla S, Maya-Romero A, Kampmann M, Xu K, Hurley JH. Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes. Proc Natl Acad Sci U S A 2024; 121:e2315690121. [PMID: 38781206 PMCID: PMC11145263 DOI: 10.1073/pnas.2315690121] [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: 09/09/2023] [Accepted: 04/08/2024] [Indexed: 05/25/2024] Open
Abstract
The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes and neurons, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification, and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Live cell imaging and STORM superresolution microscopy further show that the nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.
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Affiliation(s)
- Kevin Rose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Tyler Jepson
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
| | - Sankalp Shukla
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Alex Maya-Romero
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA94158
| | - Ke Xu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Department of Chemistry, University of California, Berkeley, CA94720
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
- Graduate Group in Biophysics, University of California, Berkeley, CA94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA94720
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4
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Kozma E, Kele P. Bioorthogonal Reactions in Bioimaging. Top Curr Chem (Cham) 2024; 382:7. [PMID: 38400853 PMCID: PMC10894152 DOI: 10.1007/s41061-024-00452-1] [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: 10/27/2023] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
Visualization of biomolecules in their native environment or imaging-aided understanding of more complex biomolecular processes are one of the focus areas of chemical biology research, which requires selective, often site-specific labeling of targets. This challenging task is effectively addressed by bioorthogonal chemistry tools in combination with advanced synthetic biology methods. Today, the smart combination of the elements of the bioorthogonal toolbox allows selective installation of multiple markers to selected targets, enabling multicolor or multimodal imaging of biomolecules. Furthermore, recent developments in bioorthogonally applicable probe design that meet the growing demands of superresolution microscopy enable more complex questions to be addressed. These novel, advanced probes enable highly sensitive, low-background, single- or multiphoton imaging of biological species and events in live organisms at resolutions comparable to the size of the biomolecule of interest. Herein, the latest developments in bioorthogonal fluorescent probe design and labeling schemes will be discussed in the context of in cellulo/in vivo (multicolor and/or superresolved) imaging schemes. The second part focuses on the importance of genetically engineered minimal bioorthogonal tags, with a particular interest in site-specific protein tagging applications to answer biological questions.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Krt. 2, Budapest, 1117, Hungary.
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Krishnaiah P, Atchudan R, Perumal S, Gangadaran P, Manoj D, Ahn BC, Kumar RS, Almansour AI, Lee YR, Jeon BH. Multifunctional carbon dots originated from waste garlic peel for rapid sensing of heavy metals and fluorescent imaging of 2D and 3D spheroids cultured fibroblast cells. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123422. [PMID: 37734247 DOI: 10.1016/j.saa.2023.123422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/23/2023]
Abstract
Here, we prepared sulfur and nitrogen self-doped carbon dots derived from garlic peel extract (GPSNCDs) using a hydrothermal method. The as-synthesized GPSNCDs were confirmed using Fourier-transform infrared spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and transmission electron microscopy. The analytical techniques indicate that the resulting GPSNCDs exhibit distinct emissive carbon-core with functionalities (owing to various ligands in the GPSNCDs). These functionalities are responsible for excellent hydrophilic and optical properties, including excitation-dependent emission and anti-photobleaching. Fluorescence intensities of GPSNCDs were quenched in the existence of Mn2+ and Fe3+ ions. This indicates that the GPSNCDs were sensitive to Fe3+ and Mn2+ ions with a limited range from 5 to 50 µM and showed lower recognition at ∼0.75 and 0.95 µM, respectively. In addition, the sensing results were generated in a short time (20 s). The cytotoxicity of GPSNCDs was tested to demonstrate that they are sufficiently safe to use for cellular imaging. The novel fluorescent GPSNCDs-based sensor can be used as a high-performance sensor for environmental monitoring. Further, GPSNCDs showed greater biocompatibility with normal fibroblast cells, and In Vitro fluorescent imaging of GPSNCDs revealed strong fluorescence signals in the two-dimensional (2D) and three-dimensional (3D) spheroids cultured fibroblast cells. The properties mentioned above demonstrate that the GPSNCDs can be applied to imaging normal cells without further modifications.
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Affiliation(s)
- Prakash Krishnaiah
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, South Korea
| | - Raji Atchudan
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea; Department of Chemistry, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai 602105, Tamil Nadu, India.
| | - Suguna Perumal
- Department of Chemistry, Sejong University, Seoul 143‑747, Republic of Korea
| | - Prakash Gangadaran
- BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, Republic of Korea
| | - Devaraj Manoj
- Department of Chemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India; Centre for Material Chemistry, Karpagam Academy of Higher Education, Coimbatore 641021, Tamil Nadu, India
| | - Byeong-Cheol Ahn
- BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea; Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu 41944, Republic of Korea
| | - Raju Suresh Kumar
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulrahman I Almansour
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Yong Rok Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul 04763, South Korea.
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6
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Rose K, Jepson T, Shukla S, Maya-Romero A, Kampmann M, Xu K, Hurley JH. Tau fibrils induce nanoscale membrane damage and nucleate cytosolic tau at lysosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.555157. [PMID: 37693477 PMCID: PMC10491128 DOI: 10.1101/2023.08.28.555157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The prion-like spread of protein aggregates is a leading hypothesis for the propagation of neurofibrillary lesions in the brain, including the spread of tau inclusions associated with Alzheimer's disease. The mechanisms of cellular uptake of tau seeds and subsequent nucleated polymerization of cytosolic tau are major questions in the field, and the potential for coupling between the entry and nucleation mechanisms has been little explored. We found that in primary astrocytes, endocytosis of tau seeds leads to their accumulation in lysosomes. This in turn leads to lysosomal swelling, deacidification and recruitment of ESCRT proteins, but not Galectin-3, to the lysosomal membrane. These observations are consistent with nanoscale damage of the lysosomal membrane. Using live cell and STORM, imaging, nucleation of cytosolic tau occurs primarily at the lysosome membrane under these conditions. These data suggest that tau seeds escape from lysosomes via nanoscale damage rather than wholesale rupture, and that nucleation of cytosolic tau commences as soon as tau fibril ends emerge from the lysosomal membrane.
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Affiliation(s)
- Kevin Rose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Tyler Jepson
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
| | - Sankalp Shukla
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Alex Maya-Romero
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, California 94158
- Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158
| | - Ke Xu
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - James H. Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
- Graduate Group in Biophysics, University of California, Berkeley, CA 94720
- Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720
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7
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Koroleva PI, Gilep AA, Kraevsky SV, Tsybruk TV, Shumyantseva VV. Improving the Efficiency of Electrocatalysis of Cytochrome P450 3A4 by Modifying the Electrode with Membrane Protein Streptolysin O for Studying the Metabolic Transformations of Drugs. BIOSENSORS 2023; 13:bios13040457. [PMID: 37185532 PMCID: PMC10136652 DOI: 10.3390/bios13040457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/30/2023] [Accepted: 04/02/2023] [Indexed: 05/17/2023]
Abstract
In the present work, screen-printed electrodes (SPE) modified with a synthetic surfactant, didodecyldimethylammonium bromide (DDAB) and streptolysin O (SLO) were prepared for cytochrome P450 3A4 (CYP3A4) immobilization, direct non-catalytic and catalytic electrochemistry. The immobilized CYP3A4 demonstrated a pair of redox peaks with a formal potential of -0.325 ± 0.024 V (vs. the Ag/AgCl reference electrode). The electron transfer process showed a surface-controlled mechanism ("protein film voltammetry") with an electron transfer rate constant (ks) of 0.203 ± 0.038 s-1. Electrochemical CYP3A4-mediated reaction of N-demethylation of erythromycin was explored with the following parameters: an applied potential of -0.5 V and a duration time of 20 min. The system with DDAB/SLO as the electrode modifier showed conversion of erythromycin with an efficiency higher than the electrode modified with DDAB only. Confining CYP3A4 inside the protein frame of SLO accelerated the enzymatic reaction. The increases in product formation in the reaction of the electrochemical N-demethylation of erythromycin for SPE/DDAB/CYP3A4 and SPE/DDAB/SLO/CYP3A4 were equal to 100 ± 22% and 297 ± 7%, respectively. As revealed by AFM images, the SPE/DDAB/SLO possessed a more developed surface with protein cavities in comparison with SPE/DDAB for the effective immobilization of the CYP3A4 enzyme.
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Affiliation(s)
- Polina I Koroleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
| | - Andrei A Gilep
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Sergey V Kraevsky
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
| | - Tatiana V Tsybruk
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, 220141 Minsk, Belarus
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10, Build 8, 119121 Moscow, Russia
- Faculty of Biomedicine, Pirogov Russian National Research Medical University, Ostrovitianov Street, 1, 117997 Moscow, Russia
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8
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Kunishige R, Murata M, Kano F. Targeted protein degradation by Trim-Away using cell resealing coupled with microscopic image-based quantitative analysis. Front Cell Dev Biol 2022; 10:1027043. [PMID: 36601537 PMCID: PMC9806799 DOI: 10.3389/fcell.2022.1027043] [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: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
"Trim-Away" technology enables rapid degradation of endogenous proteins without prior modification of protein-coding genes or mRNAs through delivery of antibodies that target proteins of interest. Although this approach can be readily applied to almost any cytosolic protein, strategies for cytosolic antibody delivery have been limited to microinjection or electroporation, which require skill-dependent operation or specialized equipment. Thus, the development of antibody delivery methods that are convenient, scalable, and preferably do not require detachment of adherent cells is required to extend the versatility of the Trim-Away method. Here, we developed a cell resealing technique optimized for Trim-Away degradation, which uses the pore-forming toxin streptolysin O (SLO) to permeabilize the cell membrane and delivered the antibodies of interest into HEK293T, HeLa, and HK-2 cell lines. We demonstrated the ability of Trim-Away protein degradation using IKKα and mTOR as targets, and we showed the availability of the developed system in antibody screening for the Trim-Away method. Furthermore, we effectively coupled Trim-Away with cyclic immunofluorescence and microscopic image-based analysis, which enables single-cell multiplexed imaging analysis. Taking advantage of this new analysis strategy, we were able to compensate for low signal-to-noise due to cell-to-cell variation, which occurs in the Trim-Away method because of the heterogenous contents of the introduced antibody, target protein, and TRIM21 in individual cells. Therefore, the reported cell resealing technique coupled with microscopic image analysis enables Trim-Away users to elucidate target protein function and the effects of target protein degradation on various cellular functions in a more quantitative and precise manner.
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Affiliation(s)
- Rina Kunishige
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan,Multimodal Cell Analysis Collaborative Research Cluster, Tokyo Institute of Technology, Yokohama, Japan
| | - Masayuki Murata
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan,Multimodal Cell Analysis Collaborative Research Cluster, Tokyo Institute of Technology, Yokohama, Japan,International Research Center for Neurointelligence, Institutes for Advanced Study, The University of Tokyo, Tokyo, Japan
| | - Fumi Kano
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan,Multimodal Cell Analysis Collaborative Research Cluster, Tokyo Institute of Technology, Yokohama, Japan,*Correspondence: Fumi Kano,
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9
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Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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10
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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11
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Abstract
The membrane translocation of hydrophilic substances constitutes a challenge for their application as therapeutic compounds and labelling probes1–4. To remedy this, charged amphiphilic molecules have been classically used as carriers3,5. However, such amphiphilic carriers may cause aggregation and non-specific membrane lysis6,7. Here we show that globular dodecaborate clusters, and prominently B12Br122−, can function as anionic inorganic membrane carriers for a broad range of hydrophilic cargo molecules (with molecular mass of 146–4,500 Da). We show that cationic and neutral peptides, amino acids, neurotransmitters, vitamins, antibiotics and drugs can be carried across liposomal membranes. Mechanistic transport studies reveal that the carrier activity is related to the superchaotropic nature of these cluster anions8–12. We demonstrate that B12Br122− affects cytosolic uptake of different small bioactive molecules, including the antineoplastic monomethyl auristatin F, the proteolysis targeting chimera dBET1 and the phalloidin toxin, which has been successfully delivered in living cells for cytoskeleton labelling. We anticipate the broad and distinct delivery spectrum of our superchaotropic carriers to be the starting point of conceptually distinct cell-biological, neurobiological, physiological and pharmaceutical studies. The superchaotropic nature of globular boron cluster anions enables direct passage of a wide range of molecules across lipid membranes.
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12
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McFarlane M, Hall NJ, McConnell G. Enhanced fluorescence from semiconductor quantum dot-labelled cells excited at 280 nm. Methods Appl Fluoresc 2022; 10. [PMID: 35203075 DOI: 10.1088/2050-6120/ac5878] [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: 11/08/2021] [Accepted: 02/24/2022] [Indexed: 11/12/2022]
Abstract
Semiconductor quantum dots (QDs) have significant advantages over more traditional fluorophores used in fluorescence microscopy including reduced photobleaching, long-term photostability and high quantum yields, but due to limitations in light sources and optics, are often excited far from their optimum excitation wavelengths in the deep-UV. Here, we present a quantitative comparison of the excitation of semiconductor QDs at a wavelength of 280 nm, compared to the longer wavelength of 365 nm, within a cellular environment. We report increased fluorescence intensity and enhanced image quality when using 280 nm excitation compared to 365 nm excitation for cell imaging across multiple datasets, with a highest average fluorescence intensity increase of 3.59-fold. We also find no significant photobleaching of QDs associated with 280 nm excitation and find that on average, ~80% of cells can tolerate exposure to high-intensity 280 nm irradiation over a 6-hour period.
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Affiliation(s)
- Mollie McFarlane
- Department of Physics , University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, G4 0NG, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Nicholas James Hall
- Department of Physics, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, G4 0NG, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Gail McConnell
- Department of Physics & Applied Physics, Strathclyde University, John Anderson Building, 107 Rottenrow, Glasgow, G4 0NG, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
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13
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Priya S, Mandal A, Dantham VR. Indium nanoparticle-based surface enhanced fluorescence from deep ultraviolet to near-infrared: A theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120603. [PMID: 34844854 DOI: 10.1016/j.saa.2021.120603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/14/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Herein, for the first time, we report a theoretical investigation on Indium nanoparticle-based surface enhanced fluorescence (SEF) from deep ultraviolet (UV) to near-infrared (NIR). In the beginning, the far- and near-field plasmonic properties of the Indium nanospheres of different sizes are studied to extract the wavelengths of lower and higher-order localized surface plasmon modes and the corresponding local electric field enhancement (EFE) values. Later, the dependence of the SEF enhancement with the separation between the fluorophore and nanoparticle (d), fluorescence, and excitation wavelengths is studied systematically. The role of the surrounding medium on plasmon mode wavelength and the SEF enhancement is also shown. Moreover, the effect of d and fluorescence wavelength on the average SEF enhancement is investigated. Finally, the variation in the plasmonic properties after thin dielectric coating on the surface of single Indium nanospheres is studied.
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Affiliation(s)
- Sugandh Priya
- Department of Physics, Indian Institute of Technology Patna, Bihar 801103, India
| | - Amartya Mandal
- Department of Physics, Indian Institute of Technology Patna, Bihar 801103, India
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14
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Lee J, Hestrin R, Nuccio EE, Morrison KD, Ramon CE, Samo TJ, Pett-Ridge J, Ly SS, Laurence TA, Weber PK. Label-Free Multiphoton Imaging of Microbes in Root, Mineral, and Soil Matrices with Time-Gated Coherent Raman and Fluorescence Lifetime Imaging. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1994-2008. [PMID: 35029104 DOI: 10.1021/acs.est.1c05818] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Imaging biogeochemical interactions in complex microbial systems─such as those at the soil-root interface─is crucial to studies of climate, agriculture, and environmental health but complicated by the three-dimensional (3D) juxtaposition of materials with a wide range of optical properties. We developed a label-free multiphoton nonlinear imaging approach to provide contrast and chemical information for soil microorganisms in roots and minerals with epi-illumination by simultaneously imaging two-photon excitation fluorescence (TPEF), coherent anti-Stokes Raman scattering (CARS), second-harmonic generation (SHG), and sum-frequency mixing (SFM). We used fluorescence lifetime imaging (FLIM) and time gating to correct CARS for the autofluorescence background native to soil particles and fungal hyphae (TG-CARS) using time-correlated single-photon counting (TCSPC). We combined TPEF, TG-CARS, and FLIM to maximize image contrast for live fungi and bacteria in roots and soil matrices without fluorescence labeling. Using this instrument, we imaged symbiotic arbuscular mycorrhizal fungi (AMF) structures within unstained plant roots in 3D to 60 μm depth. High-quality imaging was possible at up to 30 μm depth in a clay particle matrix and at 15 μm in complex soil preparation. TG-CARS allowed us to identify previously unknown lipid droplets in the symbiotic fungus, Serendipita bescii. We also visualized unstained putative bacteria associated with the roots of Brachypodium distachyon in a soil microcosm. Our results show that this multimodal approach holds significant promise for rhizosphere and soil science research.
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Affiliation(s)
- Janghyuk Lee
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Rachel Hestrin
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Erin E Nuccio
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Keith D Morrison
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Christina E Ramon
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ty J Samo
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- Life and Environmental Sciences Department, University of California Merced, Merced, California 95343, United States
| | - Sonny S Ly
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Ted A Laurence
- Materials Science Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Physical & Life Sciences, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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15
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Chen KE, Guo Q, Hill TA, Cui Y, Kendall AK, Yang Z, Hall RJ, Healy MD, Sacharz J, Norwood SJ, Fonseka S, Xie B, Reid RC, Leneva N, Parton RG, Ghai R, Stroud DA, Fairlie DP, Suga H, Jackson LP, Teasdale RD, Passioura T, Collins BM. De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. SCIENCE ADVANCES 2021; 7:eabg4007. [PMID: 34851660 PMCID: PMC8635440 DOI: 10.1126/sciadv.abg4007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/14/2021] [Indexed: 05/27/2023]
Abstract
The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function.
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Affiliation(s)
- Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Qian Guo
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Timothy A. Hill
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yi Cui
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Zhe Yang
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ryan J. Hall
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael D. Healy
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Joanna Sacharz
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Suzanne J. Norwood
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Sachini Fonseka
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Boyang Xie
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Robert C. Reid
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Natalya Leneva
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- Centre for Microscopy and Microanalysis, The University of Queensland, Queensland, Australia
| | - Rajesh Ghai
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - David A. Stroud
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Rohan D. Teasdale
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Toby Passioura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
- Sydney Analytical, School of Life and Environmental Sciences and School of Chemistry, The University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
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16
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Xiang L, Chen K, Xu K. Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. ACS NANO 2021; 15:12483-12496. [PMID: 34304562 PMCID: PMC8789943 DOI: 10.1021/acsnano.1c04708] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.
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17
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Mao S, Ying Y, Wu R, Chen AK. Recent Advances in the Molecular Beacon Technology for Live-Cell Single-Molecule Imaging. iScience 2020; 23:101801. [PMID: 33299972 PMCID: PMC7702005 DOI: 10.1016/j.isci.2020.101801] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids, aside from being best known as the carrier of genetic information, are versatile biomaterials for constructing nanoscopic devices for biointerfacing, owing to their unique properties such as specific base pairing and predictable structure. For live-cell analysis of native RNA transcripts, the most widely used nucleic acid-based nanodevice has been the molecular beacon (MB), a class of stem-loop-forming probes that is activated to fluoresce upon hybridization with target RNA. Here, we overview efforts that have been made in developing MB-based bioassays for sensitive intracellular analysis, particularly at the single-molecule level. We also describe challenges that are currently limiting the widespread use of MBs and provide possible solutions. With continued refinement of MBs in terms of labeling specificity and detection accuracy, accompanied by new development in imaging platforms with unprecedented sensitivity, the application of MBs is envisioned to expand in various biological research fields.
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Affiliation(s)
- Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Ruonan Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Antony K. Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
- Corresponding author
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18
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Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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19
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de Beer MA, Giepmans BNG. Nanobody-Based Probes for Subcellular Protein Identification and Visualization. Front Cell Neurosci 2020; 14:573278. [PMID: 33240044 PMCID: PMC7667270 DOI: 10.3389/fncel.2020.573278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/05/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding how building blocks of life contribute to physiology is greatly aided by protein identification and cellular localization. The two main labeling approaches developed over the past decades are labeling with antibodies such as immunoglobulin G (IgGs) or use of genetically encoded tags such as fluorescent proteins. However, IgGs are large proteins (150 kDa), which limits penetration depth and uncertainty of target position caused by up to ∼25 nm distance of the label created by the chosen targeting approach. Additionally, IgGs cannot be easily recombinantly modulated and engineered as part of fusion proteins because they consist of multiple independent translated chains. In the last decade single domain antigen binding proteins are being explored in bioscience as a tool in revealing molecular identity and localization to overcome limitations by IgGs. These nanobodies have several potential benefits over routine applications. Because of their small size (15 kDa), nanobodies better penetrate during labeling procedures and improve resolution. Moreover, nanobodies cDNA can easily be fused with other cDNA. Multidomain proteins can thus be easily engineered consisting of domains for targeting (nanobodies) and visualization by fluorescence microscopy (fluorescent proteins) or electron microscopy (based on certain enzymes). Additional modules for e.g., purification are also easily added. These nanobody-based probes can be applied in cells for live-cell endogenous protein detection or may be purified prior to use on molecules, cells or tissues. Here, we present the current state of nanobody-based probes and their implementation in microscopy, including pitfalls and potential future opportunities.
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Affiliation(s)
- Marit A de Beer
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Ben N G Giepmans
- Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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20
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Li B, Xie S, Xia A, Suo T, Huang H, Zhang X, Chen Y, Zhou X. Recent advance in the sensing of biomarker transcription factors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116039] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Amodeo R, Convertino D, Calvello M, Ceccarelli L, Bonsignore F, Ravelli C, Cattaneo A, Martini C, Luin S, Mitola S, Signore G, Marchetti L. Fluorolabeling of the PPTase-Related Chemical Tags: Comparative Study of Different Membrane Receptors and Different Fluorophores in the Labeling Reactions. Front Mol Biosci 2020; 7:195. [PMID: 32850976 PMCID: PMC7426934 DOI: 10.3389/fmolb.2020.00195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
The set-up of an advanced imaging experiment requires a careful selection of suitable labeling strategies and fluorophores for the tagging of the molecules of interest. Here we provide an experimental workflow to allow evaluation of fluorolabeling performance of the chemical tags target of phosphopantetheinyl transferase enzymes (PPTases), once inserted in the sequence of different proteins of interest. First, S6 peptide tag was fused to three different single-pass transmembrane proteins (the tyrosine receptor kinases TrkA and VEGFR2 and the tumor necrosis factor receptor p75NTR), providing evidence that all of them can be conveniently albeit differently labeled. Moreover, we chose the S6-tagged TrkA construct to test eight different organic fluorophores for the PPTase labeling of membrane receptors in living cells. We systematically compared their non-specific internalization when added to a S6-tag negative cell culture, the percentage of S6-TrkA expressing cells effectively labeled and the relative mean fluorescence intensity, their photostability upon conjugation, and ratio of specific (cellular) versus background (glass-adhered) signal. This allowed to identify which fluorophores are actually recommended for these labeling reactions. Finally, we compared the PPTase labeling of a purified, YBBR-tagged Nerve Growth Factor with two differently charged organic dyes. We detected some batch-to-batch variability in the labeling yield, regardless of the fluorophore used. However, upon purification of the fluorescent species and incubation with living primary DRG neurons, no significant difference could be appreciated in both internalization and axonal transport of the labeled neurotrophins.
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Affiliation(s)
- Rosy Amodeo
- NEST, Scuola Normale Superiore, Pisa, Italy.,Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy
| | - Domenica Convertino
- NEST, Scuola Normale Superiore, Pisa, Italy.,Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy
| | | | - Lorenzo Ceccarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy.,Dipartimento di Farmacia, Università di Pisa, Pisa, Italy
| | | | - Cosetta Ravelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | | | | | - Stefano Luin
- NEST, Scuola Normale Superiore, Pisa, Italy.,CNR-NANO, Pisa, Italy
| | - Stefania Mitola
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Giovanni Signore
- NEST, Scuola Normale Superiore, Pisa, Italy.,Fondazione Pisana per la Scienza Onlus, Pisa, Italy
| | - Laura Marchetti
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, Pisa, Italy.,Dipartimento di Farmacia, Università di Pisa, Pisa, Italy
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22
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Guo J, Sesena Rubfiaro A, Lai Y, Moscoso J, Chen F, Liu Y, Wang X, He J. Dynamic single-cell intracellular pH sensing using a SERS-active nanopipette. Analyst 2020; 145:4852-4859. [PMID: 32542257 PMCID: PMC7425357 DOI: 10.1039/d0an00838a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glass nanopipettes have shown promise for applications in single-cell manipulation, analysis, and imaging. In recent years, plasmonic nanopipettes have been developed to enable surface-enhanced Raman spectroscopy (SERS) measurements for single-cell analysis. In this work, we developed a SERS-active nanopipette that can be used to perform long-term and reliable intracellular analysis of single living cells with minimal damage, which is achieved by optimizing the nanopipette geometry and the surface density of the gold nanoparticle (AuNP) layer at the nanopipette tip. To demonstrate its ability in single-cell analysis, we used the nanopipette for intracellular pH sensing. Intracellular pH (pHi) is vital to cells as it influences cell function and behavior and pathological conditions. The pH sensitivity was realized by simply modifying the AuNP layer with the pH reporter molecule 4-mercaptobenzoic acid. With a response time of less than 5 seconds, the pH sensing range is from 6.0 to 8.0 and the maximum sensitivity is 0.2 pH units. We monitored the pHi change of individual HeLa and fibroblast cells, triggered by the extracellular pH (pHe) change. The HeLa cancer cells can better resist pHe change and adapt to the weak acidic environment. Plasmonic nanopipettes can be further developed to monitor other intracellular biomarkers.
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Affiliation(s)
- Jing Guo
- Department of Physics, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA.
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23
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Liu J, Fraire JC, De Smedt SC, Xiong R, Braeckmans K. Intracellular Labeling with Extrinsic Probes: Delivery Strategies and Applications. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000146. [PMID: 32351015 DOI: 10.1002/smll.202000146] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/29/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
Extrinsic probes have outstanding properties for intracellular labeling to visualize dynamic processes in and of living cells, both in vitro and in vivo. Since extrinsic probes are in many cases cell-impermeable, different biochemical, and physical approaches have been used to break the cell membrane barrier for direct delivery into the cytoplasm. In this Review, these intracellular delivery strategies are discussed, briefly explaining the mechanisms and how they are used for live-cell labeling applications. Methods that are discussed include three biochemical agents that are used for this purpose-purpose-different nanocarriers, cell penetrating peptides and the pore-foraming bacterial toxin streptolysin O. Most successful intracellular label delivery methods are, however, based on physical principles to permeabilize the membrane and include electroporation, laser-induced photoporation, micro- and nanoinjection, nanoneedles or nanostraws, microfluidics, and nanomachines. The strengths and weaknesses of each strategy are discussed with a systematic comparison provided. Finally, the extrinsic probes that are reported for intracellular labeling so-far are summarized, together with the delivery strategies that are used and their performance. This combined information should provide for a useful guide for choosing the most suitable delivery method for the desired probes.
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Affiliation(s)
- Jing Liu
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000, Belgium
| | - Juan C Fraire
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent, B-9000, Belgium
- Joint Laboratory of Advanced Biomedical Technology (NFU-UGent), College of Chemical Engineering, Nanjing Forestry University (NFU), Nanjing, 210037, P. R. China
| | - Ranhua Xiong
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent, B-9000, Belgium
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24
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Moon S, Li W, Hauser M, Xu K. Graphene-Enabled, Spatially Controlled Electroporation of Adherent Cells for Live-Cell Super-resolution Microscopy. ACS NANO 2020; 14:5609-5617. [PMID: 32282180 PMCID: PMC7448575 DOI: 10.1021/acsnano.9b10081] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The incorporation of exogenous molecules into live cells is essential for both biological research and therapeutic applications. In particular, for the emerging field of super-resolution microscopy of live mammalian cells, it remains a challenge to deliver tailored, often cell-impermeable, fluorescent probes into live cells for target labeling. Here, utilizing the outstanding mechanical, electrical, and optical properties of graphene, we report a facile approach that enables both high-throughput delivery of fluorescent probes into adherent mammalian cells and in situ super-resolution microscopy on the same device. Approximately 90% delivery efficiencies are achieved for free dyes and dye-tagged affinity probes, short peptides, and whole antibodies, thus enabling high-quality super-resolution microscopy. Moreover, we demonstrate good spatiotemporal controls, which, in combination with the ready patternability of graphene, allow for the spatially selective delivery of two different probes for cells at different locations on the same substrate.
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Affiliation(s)
- Seonah Moon
- Department of Chemistry, University of California, Berkeley, CA 94720
- These authors contributed equally
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, CA 94720
- These authors contributed equally
| | - Meghan Hauser
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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25
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Temporary Membrane Permeabilization via the Pore-Forming Toxin Lysenin. Toxins (Basel) 2020; 12:toxins12050343. [PMID: 32456013 PMCID: PMC7290483 DOI: 10.3390/toxins12050343] [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: 04/29/2020] [Revised: 05/17/2020] [Accepted: 05/20/2020] [Indexed: 12/19/2022] Open
Abstract
Pore-forming toxins are alluring tools for delivering biologically-active, impermeable cargoes to intracellular environments by introducing large conductance pathways into cell membranes. However, the lack of regulation often leads to the dissipation of electrical and chemical gradients, which might significantly affect the viability of cells under scrutiny. To mitigate these problems, we explored the use of lysenin channels to reversibly control the barrier function of natural and artificial lipid membrane systems by controlling the lysenin's transport properties. We employed artificial membranes and electrophysiology measurements in order to identify the influence of labels and media on the lysenin channel's conductance. Two cell culture models: Jurkat cells in suspension and adherent ATDC5 cells were utilized to demonstrate that lysenin channels may provide temporary cytosol access to membrane non-permeant propidium iodide and phalloidin. Permeability and cell viability were assessed by fluorescence spectroscopy and microscopy. Membrane resealing by chitosan or specific media addition proved to be an effective way of maintaining cellular viability. In addition, we loaded non-permeant dyes into liposomes via lysenin channels by controlling their conducting state with multivalent metal cations. The improved control over membrane permeability might prove fruitful for a large variety of biological or biomedical applications that require only temporary, non-destructive access to the inner environment enclosed by natural and artificial membranes.
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26
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Heller JP, Odii T, Zheng K, Rusakov DA. Imaging tripartite synapses using super-resolution microscopy. Methods 2020; 174:81-90. [PMID: 31153907 PMCID: PMC7144327 DOI: 10.1016/j.ymeth.2019.05.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 01/02/2023] Open
Abstract
Astroglia are vital facilitators of brain development, homeostasis, and metabolic support. In addition, they are also essential to the formation and regulation of synaptic circuits. Due to the extraordinary complex, nanoscopic morphology of astrocytes, the underlying cellular mechanisms have been poorly understood. In particular, fine astrocytic processes that can be found in the vicinity of synapses have been difficult to study using traditional imaging techniques. Here, we describe a 3D three-colour super-resolution microscopy approach to unravel the nanostructure of tripartite synapses. The method is based on the SMLM technique direct stochastic optical reconstruction microscopy (dSTORM) which uses conventional fluorophore-labelled antibodies. This approach enables reconstructing the nanoscale localisation of individual astrocytic glutamate transporter (GLT-1) molecules surrounding presynaptic (bassoon) and postsynaptic (Homer1) protein localisations in fixed mouse brain sections. However, the technique is readily adaptable to other types of targets and tissues.
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Affiliation(s)
- Janosch Peter Heller
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Tuamoru Odii
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Physiology, Faculty of Basic Medical Sciences, Alex Ekwueme Federal University Ndufu-Alike Ikwo, PMB 1010 Abakaliki, Nigeria
| | - Kaiyu Zheng
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Dmitri A Rusakov
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
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27
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Liu J, Hebbrecht T, Brans T, Parthoens E, Lippens S, Li C, De Keersmaecker H, De Vos WH, De Smedt SC, Boukherroub R, Gettemans J, Xiong R, Braeckmans K. Long-term live-cell microscopy with labeled nanobodies delivered by laser-induced photoporation. NANO RESEARCH 2020; 13:485-495. [PMID: 33154805 PMCID: PMC7116313 DOI: 10.1007/s12274-020-2633-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Fluorescence microscopy is the method of choice for studying intracellular dynamics. However, its success depends on the availability of specific and stable markers. A prominent example of markers that are rapidly gaining interest are nanobodies (Nbs, ~ 15 kDa), which can be functionalized with bright and photostable organic fluorophores. Due to their relatively small size and high specificity, Nbs offer great potential for high-quality long-term subcellular imaging, but suffer from the fact that they cannot spontaneously cross the plasma membrane of live cells. We have recently discovered that laser-induced photoporation is well suited to deliver extrinsic labels to living cells without compromising their viability. Being a laser-based technology, it is readily compatible with light microscopy and the typical cell recipients used for that. Spurred by these promising initial results, we demonstrate here for the first time successful long-term imaging of specific subcellular structures with labeled nanobodies in living cells. We illustrate this using Nbs that target GFP/YFP-protein constructs accessible in the cytoplasm, actin-bundling protein Fascin, and the histone H2A/H2B heterodimers. With an efficiency of more than 80% labeled cells and minimal toxicity (~ 2%), photoporation proved to be an excellent intracellular delivery method for Nbs. Time-lapse microscopy revealed that cell division rate and migration remained unaffected, confirming excellent cell viability and functionality. We conclude that laser-induced photoporation labeled Nbs can be easily delivered into living cells, laying the foundation for further development of a broad range of Nbs with intracellular targets as a toolbox for long-term live-cell microscopy.
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Affiliation(s)
- Jing Liu
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
| | - Tim Hebbrecht
- Department of Biomolecular medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Toon Brans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
| | - Eef Parthoens
- VIB-UGent Center for Inflammation Research, VIB, Ghent B-9000, Belgium
- VIB Bioimaging Core Ghent, VIB, Ghent B-9000, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent B-9000, Belgium
| | - Saskia Lippens
- VIB-UGent Center for Inflammation Research, VIB, Ghent B-9000, Belgium
- VIB Bioimaging Core Ghent, VIB, Ghent B-9000, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent B-9000, Belgium
| | - Chengnan Li
- Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520-IEMN, Lille F-59000, France
| | - Herlinde De Keersmaecker
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
| | - Winnok H De Vos
- Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, 2020 Antwerp, Belgium
| | - Stefaan C De Smedt
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
| | - Rabah Boukherroub
- Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520-IEMN, Lille F-59000, France
| | - Jan Gettemans
- Department of Biomolecular medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent B-9000, Belgium
| | - Ranhua Xiong
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent B-9000, Belgium
- Centre for Advanced Light Microscopy, Ghent University, Ghent B-9000, Belgium
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28
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Alex A, Voss B, Musacchio A, Maffini S. Electroporation of Recombinant Proteins for in vivo Functional Studies in Cultured Mammalian Cells. Bio Protoc 2020. [DOI: 10.21769/bioprotoc.5003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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29
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Choi J, Grosely R, Puglisi EV, Puglisi JD. Expanding single-molecule fluorescence spectroscopy to capture complexity in biology. Curr Opin Struct Biol 2019; 58:233-240. [PMID: 31213390 PMCID: PMC6778503 DOI: 10.1016/j.sbi.2019.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 05/03/2019] [Accepted: 05/08/2019] [Indexed: 11/16/2022]
Abstract
Fundamental biological processes are driven by diverse molecular machineries. In recent years, single-molecule fluorescence spectroscopy has matured as a unique tool in biology to study how structural dynamics of molecular complexes drive various biochemical reactions. In this review, we highlight underlying developments in single-molecule fluorescence methods that enable deep biological investigations. Recent progress in these methods points toward increasing complexity of measurements to capture biological processes in a living cell, where multiple processes often occur simultaneously and are mechanistically coupled.
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Affiliation(s)
- Junhong Choi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305-4090, USA
| | - Rosslyn Grosely
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
| | - Elisabetta V Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.
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30
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Visualization of Endogenous Transcription Factors in Single Cells Using an Antibody Electroporation-Based Imaging Approach. Methods Mol Biol 2019; 2038:209-221. [PMID: 31407287 DOI: 10.1007/978-1-4939-9674-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
In this chapter, we describe an antibody electroporation-based imaging approach that allows for precise imaging and quantification of endogenous transcription factor (i.e., RNA Polymerase II) distributions in single cells using 3D structured illumination microscopy (3D-SIM). The labeling is achieved by the efficient and harmless delivery of fluorescent dye-conjugated antibodies into living cells and the specific binding of these antibodies to the targeted factors. Our step-by-step protocol describes the procedure of the labeling of the specific antibodies, their electroporation into living cells, the sample preparation and 3D-SIM imaging as well as the postimaging analyses of the labeled endogenous transcription factors to obtain information about their nuclear distribution as well as their function. This protocol can be applied to a plethora of endogenous nuclear factors by using target specific noninhibiting antibodies.
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31
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Jiang N, Li H, Sun H. Recognition of Proteins by Metal Chelation-Based Fluorescent Probes in Cells. Front Chem 2019; 7:560. [PMID: 31448265 PMCID: PMC6695521 DOI: 10.3389/fchem.2019.00560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/23/2019] [Indexed: 01/23/2023] Open
Abstract
Fluorescent probes such as thiol-reactive and Ni2+-nitrilotriacetate (NTA) based probes provide a powerful toolbox for real-time visualization of a protein and a proteome in living cells. Herein, we first went through basic principles and applications of thiol-reactive based probes in protein imaging and recognition. We then summarize a family of metal-NTA based fluorescence probes in the visualization of His6-tagged protein and identification of metalloproteins at proteome-wide scale. The pros and cons of the probes, as well as ways to optimize them, are discussed.
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Affiliation(s)
| | | | - Hongzhe Sun
- Department of Chemistry, The University of Hong Kong, Hong Kong, China
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32
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Alex A, Piano V, Polley S, Stuiver M, Voss S, Ciossani G, Overlack K, Voss B, Wohlgemuth S, Petrovic A, Wu Y, Selenko P, Musacchio A, Maffini S. Electroporated recombinant proteins as tools for in vivo functional complementation, imaging and chemical biology. eLife 2019; 8:48287. [PMID: 31310234 PMCID: PMC6656429 DOI: 10.7554/elife.48287] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
Delivery of native or chemically modified recombinant proteins into mammalian cells shows promise for functional investigations and various technological applications, but concerns that sub-cellular localization and functional integrity of delivered proteins may be affected remain high. Here, we surveyed batch electroporation as a delivery tool for single polypeptides and multi-subunit protein assemblies of the kinetochore, a spatially confined and well-studied subcellular structure. After electroporation into human cells, recombinant fluorescent Ndc80 and Mis12 multi-subunit complexes exhibited native localization, physically interacted with endogenous binding partners, and functionally complemented depleted endogenous counterparts to promote mitotic checkpoint signaling and chromosome segregation. Farnesylation is required for kinetochore localization of the Dynein adaptor Spindly. In cells with chronically inhibited farnesyl transferase activity, in vitro farnesylation and electroporation of recombinant Spindly faithfully resulted in robust kinetochore localization. Our data show that electroporation is well-suited to deliver synthetic and chemically modified versions of functional proteins, and, therefore, constitutes a promising tool for applications in chemical and synthetic biology.
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Affiliation(s)
- Amal Alex
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Valentina Piano
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soumitra Polley
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Marchel Stuiver
- In-Cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany
| | - Stephanie Voss
- Chemical Genomics Centre, Max Planck Society, Dortmund, Germany
| | - Giuseppe Ciossani
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Katharina Overlack
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Beate Voss
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sabine Wohlgemuth
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Arsen Petrovic
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Yaowen Wu
- Chemical Genomics Centre, Max Planck Society, Dortmund, Germany.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Philipp Selenko
- In-Cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Berlin, Germany.,Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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33
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Croop B, Zhang C, Lim Y, Gelfand RM, Han KY. Recent advancement of light-based single-molecule approaches for studying biomolecules. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 11:e1445. [PMID: 30724484 DOI: 10.1002/wsbm.1445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/01/2018] [Accepted: 01/08/2019] [Indexed: 12/27/2022]
Abstract
Recent advances in single-molecule techniques have led to new discoveries in analytical chemistry, biophysics, and medicine. Understanding the structure and behavior of single biomolecules provides a wealth of information compared to studying large ensembles. However, developing single-molecule techniques is challenging and requires advances in optics, engineering, biology, and chemistry. In this paper, we will review the state of the art in single-molecule applications with a focus over the last few years of development. The advancements covered will mainly include light-based in vitro methods, and we will discuss the fundamentals of each with a focus on the platforms themselves. We will also summarize their limitations and current and future applications to the wider biological and chemical fields. This article is categorized under: Laboratory Methods and Technologies > Imaging Laboratory Methods and Technologies > Macromolecular Interactions, Methods Analytical and Computational Methods > Analytical Methods.
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Affiliation(s)
- Benjamin Croop
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Chenyi Zhang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Youngbin Lim
- Department of Bioengineering, Stanford University, Stanford, California
| | - Ryan M Gelfand
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida
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34
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Heller JP, Rusakov DA. A Method to Visualize the Nanoscopic Morphology of Astrocytes In Vitro and In Situ. Methods Mol Biol 2019; 1938:69-84. [PMID: 30617973 DOI: 10.1007/978-1-4939-9068-9_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In recent years it has become apparent that astroglia are not only essential players in brain development, homeostasis, and metabolic support but are also important for the formation and regulation of synaptic circuits. Fine astrocytic processes that can be found in the vicinity of synapses undergo considerable structural plasticity associated with age- and use-dependent changes in neural circuitries. However, due to the extraordinary complex, essentially nanoscopic morphology of astroglia, the underlying cellular mechanisms remain poorly understood.Here we detail a super-resolution microscopy approach, based on the single-molecule localisation microscopy (SMLM) technique direct stochastic optical reconstruction microscopy (dSTORM) to visualize astroglial morphology on the nanoscale. This approach enables visualization of key morphological changes that occur in nanoscopic astrocyte processes, whose characteristic size falls below the diffraction limit of conventional optical microscopy.
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Affiliation(s)
- Janosch P Heller
- UCL Queen Square Institute of Neurology, University College London, Queen Square, London, UK.
| | - Dmitri A Rusakov
- UCL Queen Square Institute of Neurology, University College London, Queen Square, London, UK.
- Laboratory of Brain Microcircuits, Institute of Neuroscience, University of Nizhny Novgorod, Nizhny Novgorod, Russia.
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35
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Samrat SK, Gu H. Temporal Analysis of the Nuclear-to-cytoplasmic Translocation of a Herpes Simplex Virus 1 Protein by Immunofluorescent Confocal Microscopy. J Vis Exp 2018. [PMID: 30451237 DOI: 10.3791/58504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Infected cell protein 0 (ICP0) of herpes simplex virus 1 (HSV-1) is an immediate early protein containing a RING-type E3 ubiquitin ligase. It is responsible for the proteasomal degradation of host restrictive factors and the subsequent viral gene activation. ICP0 contains a canonical nuclear localization sequence (NLS). It enters the nucleus immediately after de novo synthesis and executes its anti-host defense functions mainly in the nucleus. However, later in infection, ICP0 is found solely in the cytoplasm, suggesting the occurrence of a nuclear-to-cytoplasmic translocation during HSV-1 infection. Presumably ICP0 translocation enables ICP0 to modulate its functions according to its subcellular locations at different infection phases. In order to delineate the biological function and regulatory mechanism of ICP0 nuclear-to-cytoplasmic translocation, we modified an immunofluorescent microscopy method to monitor ICP0 trafficking during HSV-1 infection. This protocol involves immunofluorescent staining, confocal microscope imaging, and nuclear vs. cytoplasmic distribution analysis. The goal of this protocol is to adapt the steady state confocal images taken in a time course into a quantitative documentation of ICP0 movement throughout the lytic infection. We propose that this method can be generalized to quantitatively analyze nuclear vs. cytoplasmic localization of other viral or cellular proteins without involving live imaging technology.
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Affiliation(s)
| | - Haidong Gu
- Department of Biological Sciences, Wayne State University;
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36
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Klein A, Hank S, Raulf A, Joest EF, Tissen F, Heilemann M, Wieneke R, Tampé R. Live-cell labeling of endogenous proteins with nanometer precision by transduced nanobodies. Chem Sci 2018; 9:7835-7842. [PMID: 30429993 PMCID: PMC6194584 DOI: 10.1039/c8sc02910e] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 11/21/2022] Open
Abstract
Accurate labeling of endogenous proteins for advanced light microscopy in living cells remains challenging. Nanobodies have been widely used for antigen labeling, visualization of subcellular protein localization and interactions. To facilitate an expanded application, we present a scalable and high-throughput strategy to simultaneously target multiple endogenous proteins in living cells with micro- to nanometer resolution. For intracellular protein labeling, we advanced nanobodies by site-specific and stoichiometric attachment of bright organic fluorophores. Their fast and fine-tuned intracellular transfer by microfluidic cell squeezing enabled high-throughput delivery with less than 10% dead cells. This strategy allowed for the dual-color imaging of distinct endogenous cellular structures, and culminated in super-resolution imaging of native protein networks in genetically non-modified living cells. The simultaneous delivery of multiple engineered nanobodies does not only offer exciting prospects for multiplexed imaging of endogenous protein, but also holds potential for visualizing native cellular structures with unprecedented accuracy.
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Affiliation(s)
- A Klein
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - S Hank
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - A Raulf
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany
| | - E F Joest
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - F Tissen
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - M Heilemann
- Institute of Physical and Theoretical Chemistry , Goethe University Frankfurt , Max-von-Laue-Str. 7 , 60438 Frankfurt/Main , Germany
| | - R Wieneke
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
| | - R Tampé
- Institute of Biochemistry, Biocenter , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany .
- Cluster of Excellence - Macromolecular Complexes , Goethe University Frankfurt , Max-von-Laue-Str. 9 , 60438 Frankfurt/Main , Germany
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37
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Baumdick M, Gelléri M, Uttamapinant C, Beránek V, Chin JW, Bastiaens PIH. A conformational sensor based on genetic code expansion reveals an autocatalytic component in EGFR activation. Nat Commun 2018; 9:3847. [PMID: 30242154 PMCID: PMC6155120 DOI: 10.1038/s41467-018-06299-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/10/2018] [Indexed: 12/26/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) activation by growth factors (GFs) relies on dimerization and allosteric activation of its intrinsic kinase activity, resulting in trans-phosphorylation of tyrosines on its C-terminal tail. While structural and biochemical studies identified this EGF-induced allosteric activation, imaging collective EGFR activation in cells and molecular dynamics simulations pointed at additional catalytic EGFR activation mechanisms. To gain more insight into EGFR activation mechanisms in living cells, we develop a Förster resonance energy transfer (FRET)-based conformational EGFR indicator (CONEGI) using genetic code expansion that reports on conformational transitions in the EGFR activation loop. Comparing conformational transitions, self-association and auto-phosphorylation of CONEGI and its Y845F mutant reveals that Y845 phosphorylation induces a catalytically active conformation in EGFR monomers. This conformational transition depends on EGFR kinase activity and auto-phosphorylation on its C-terminal tail, generating a looped causality that leads to autocatalytic amplification of EGFR phosphorylation at low EGF dose. Upon ligand binding epidermal growth factor receptor (EGFR) dimerizes and activates its intrinsic kinase to auto-phosphorylate EGFR. Here, the authors engineer and image a FRET-based conformational EGFR indicator which reveals that activation loop phosphorylation induces a catalytically active conformation in EGFR monomers.
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Affiliation(s)
- Martin Baumdick
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany
| | - Márton Gelléri
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany.,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany
| | - Chayasith Uttamapinant
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Václav Beránek
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Street 11, 44227, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 6, 44227, Dortmund, Germany.
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38
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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39
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Teng KW, Ren P, Selvin PR. Delivery of Fluorescent Probes Using Streptolysin O for Fluorescence Microscopy of Living Cells. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2018; 93:e60. [PMID: 30058756 PMCID: PMC6097887 DOI: 10.1002/cpps.60] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Methods to efficiently deliver fluorophores across the cell membrane are crucial for imaging the dynamics of intracellular proteins using fluorescence. Here we describe a simple protocol for permeabilizing living cells using streptolysin O, a bacterial toxin, which allows transient uptake of fluorescent probes for labeling specific intracellular proteins. The technique is applicable for delivering different classes of fluorescent probes with a molecular weight of <150 kDa, and it is also applicable to a variety of different cell lines. The technique enables the utilization of a broad range of fluorophores for live cell imaging of intracellular proteins. Extended observation of intracellular fluorescence bound to specific proteins is now possible through super-resolution microscopy by using fluorophores that are photostable in "cell-friendly" deoxygenating and reducing conditions. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Kai Wen Teng
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pin Ren
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Paul R. Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
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40
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A peptide tag-specific nanobody enables high-quality labeling for dSTORM imaging. Nat Commun 2018; 9:930. [PMID: 29500346 PMCID: PMC5834503 DOI: 10.1038/s41467-018-03191-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/26/2018] [Indexed: 11/08/2022] Open
Abstract
Dense fluorophore labeling without compromising the biological target is crucial for genuine super-resolution microscopy. Here we introduce a broadly applicable labeling strategy for fixed and living cells utilizing a short peptide tag-specific nanobody (BC2-tag/bivBC2-Nb). BC2-tagging of ectopically introduced or endogenous proteins does not interfere with the examined structures and bivBC2-Nb staining results in a close-grained fluorophore labeling with minimal linkage errors. This allowed us to perform high-quality dSTORM imaging of various targets in mammalian and yeast cells. We expect that this versatile strategy will render many more demanding cellular targets amenable to dSTORM imaging.
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41
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Conic S, Desplancq D, Ferrand A, Fischer V, Heyer V, Reina San Martin B, Pontabry J, Oulad-Abdelghani M, Babu N K, Wright GD, Molina N, Weiss E, Tora L. Imaging of native transcription factors and histone phosphorylation at high resolution in live cells. J Cell Biol 2018; 217:1537-1552. [PMID: 29440513 PMCID: PMC5881509 DOI: 10.1083/jcb.201709153] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/15/2017] [Accepted: 01/18/2018] [Indexed: 01/16/2023] Open
Abstract
Conic et al. introduce a versatile antibody-based imaging approach to track endogenous nuclear factors in living cells. It allows efficient intracellular delivery of any fluorescent dye–conjugated antibody, or Fab fragment, into a variety of cell types. The dynamics of nuclear targets or posttranslational modifications can be monitored with high precision using confocal and super-resolution microscopy. Fluorescent labeling of endogenous proteins for live-cell imaging without exogenous expression of tagged proteins or genetic manipulations has not been routinely possible. We describe a simple versatile antibody-based imaging approach (VANIMA) for the precise localization and tracking of endogenous nuclear factors. Our protocol can be implemented in every laboratory allowing the efficient and nonharmful delivery of organic dye-conjugated antibodies, or antibody fragments, into different metazoan cell types. Live-cell imaging permits following the labeled probes bound to their endogenous targets. By using conventional and super-resolution imaging we show dynamic changes in the distribution of several nuclear transcription factors (i.e., RNA polymerase II or TAF10), and specific phosphorylated histones (γH2AX), upon distinct biological stimuli at the nanometer scale. Hence, considering the large panel of available antibodies and the simplicity of their implementation, VANIMA can be used to uncover novel biological information based on the dynamic behavior of transcription factors or posttranslational modifications in the nucleus of single live cells.
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Affiliation(s)
- Sascha Conic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | | | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Vincent Heyer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bernardo Reina San Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Pontabry
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epigenetics and Stem Cells, München, Germany
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Kishore Babu N
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Etienne Weiss
- Institut de Recherche de l'ESBS, UMR 7242, Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France .,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France.,School of Biological Sciences, Nanyang Technological University, Singapore
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42
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Youn Y, Ishitsuka Y, Jin C, Selvin PR. Thermal nanoimprint lithography for drift correction in super-resolution fluorescence microscopy. OPTICS EXPRESS 2018; 26:1670-1680. [PMID: 29402038 PMCID: PMC5901072 DOI: 10.1364/oe.26.001670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Localization-based super-resolution microscopy enables imaging of biological structures with sub-diffraction-limited accuracy, but generally requires extended acquisition time. Consequently, stage drift often limits the spatial precision. Previously, we reported a simple method to correct for this by creating an array of 1 μm3 fiducial markers, every ~8 μm, on the coverslip, using UV-nanoimprint lithography (UV-NIL). While this allowed reliable and accurate 3D drift correction, it suffered high autofluorescence background with shorter wavelength illumination, unstable adsorption to the substrate glass surface, and suboptimal biocompatibility. Here, we present an improved fiducial micro-pattern prepared by thermal nanoimprint lithography (T-NIL). The new pattern is made of a thermal plastic material with low fluorescence backgrounds across the wide excitation range, particularly in the blue-region; robust structural stability under cell culturing condition; and a high bio-compatibility in terms of cell viability and adhesion. We demonstrate drift precision to 1.5 nm for lateral (x, y) and 6.1 nm axial (z) axes every 0.2 seconds for a total of 1 min long image acquisition. As a proof of principle, we acquired 4-color wide-field fluorescence images of live mammalian cells; we also acquired super-resolution images of fixed hippocampal neurons, and super-resolution images of live glutamate receptors and postsynaptic density proteins.
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Affiliation(s)
- Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- These authors contributed equally to this work
| | - Yuji Ishitsuka
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- These authors contributed equally to this work
| | - Chaoyi Jin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paul R. Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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43
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Lerner E, Cordes T, Ingargiol A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transfer. Science 2018; 359:eaan1133. [PMID: 29348210 PMCID: PMC6200918 DOI: 10.1126/science.aan1133] [Citation(s) in RCA: 323] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Classical structural biology can only provide static snapshots of biomacromolecules. Single-molecule Förster resonance energy transfer (smFRET) paved the way for studying dynamics in macromolecular structures under biologically relevant conditions. Since its first implementation in 1996, smFRET experiments have confirmed previously hypothesized mechanisms and provided new insights into many fundamental biological processes, such as DNA maintenance and repair, transcription, translation, and membrane transport. We review 22 years of contributions of smFRET to our understanding of basic mechanisms in biochemistry, molecular biology, and structural biology. Additionally, building on current state-of-the-art implementations of smFRET, we highlight possible future directions for smFRET in applications such as biosensing, high-throughput screening, and molecular diagnostics.
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Affiliation(s)
- Eitan Lerner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Antonino Ingargiol
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Yazan Alhadid
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - SangYoon Chung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Xavier Michalet
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
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44
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Liu J, Xiong R, Brans T, Lippens S, Parthoens E, Zanacchi FC, Magrassi R, Singh SK, Kurungot S, Szunerits S, Bové H, Ameloot M, Fraire JC, Teirlinck E, Samal SK, Rycke RD, Houthaeve G, De Smedt SC, Boukherroub R, Braeckmans K. Repeated photoporation with graphene quantum dots enables homogeneous labeling of live cells with extrinsic markers for fluorescence microscopy. LIGHT, SCIENCE & APPLICATIONS 2018; 7:47. [PMID: 30839577 PMCID: PMC6106998 DOI: 10.1038/s41377-018-0048-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/08/2018] [Accepted: 06/15/2018] [Indexed: 05/22/2023]
Abstract
In the replacement of genetic probes, there is increasing interest in labeling living cells with high-quality extrinsic labels, which avoid over-expression artifacts and are available in a wide spectral range. This calls for a broadly applicable technology that can deliver such labels unambiguously to the cytosol of living cells. Here, we demonstrate that nanoparticle-sensitized photoporation can be used to this end as an emerging intracellular delivery technique. We replace the traditionally used gold nanoparticles with graphene nanoparticles as photothermal sensitizers to permeabilize the cell membrane upon laser irradiation. We demonstrate that the enhanced thermal stability of graphene quantum dots allows the formation of multiple vapor nanobubbles upon irradiation with short laser pulses, allowing the delivery of a variety of extrinsic cell labels efficiently and homogeneously into live cells. We demonstrate high-quality time-lapse imaging with confocal, total internal reflection fluorescence (TIRF), and Airyscan super-resolution microscopy. As the entire procedure is readily compatible with fluorescence (super resolution) microscopy, photoporation with graphene quantum dots has the potential to become the long-awaited generic platform for controlled intracellular delivery of fluorescent labels for live-cell imaging.
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Affiliation(s)
- Jing Liu
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
| | - Ranhua Xiong
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
| | - Toon Brans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
| | - Saskia Lippens
- VIB-UGent Centre for Inflammation Research, VIB, Ghent, B-9000 Belgium
- VIB Bioimaging Core, VIB, Ghent, B-9000 Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9000 Belgium
| | - Eef Parthoens
- VIB-UGent Centre for Inflammation Research, VIB, Ghent, B-9000 Belgium
- VIB Bioimaging Core, VIB, Ghent, B-9000 Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, B-9000 Belgium
| | | | - Raffaella Magrassi
- Nanophysics (NAPH), Istituto Italiano di Tecnologia, Genova, 16163 Italy
- Biophysics Institute (IBF), National Research Council (CNR), Via De Marini, 6-16149–GE Genova, Italy
| | - Santosh K. Singh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008 India
- Academy of Scientific and Innovative Research, Anusandhan Bhawan, 2 RafiMarg, New Delhi, 110 001 India
| | - Sreekumar Kurungot
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008 India
- Academy of Scientific and Innovative Research, Anusandhan Bhawan, 2 RafiMarg, New Delhi, 110 001 India
| | - Sabine Szunerits
- Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520-IEMN, Lille, F-59000 France
| | - Hannelore Bové
- Biomedical Research Institute, Hasselt University, Agoralaan Building C, Diepenbeek, 3590 Belgium
- Centre for Surface Chemistry and Catalysis, KU Leuven, Celestijnenlaan 200F, Leuven, 3001 Belgium
| | - Marcel Ameloot
- Biomedical Research Institute, Hasselt University, Agoralaan Building C, Diepenbeek, 3590 Belgium
| | - Juan C. Fraire
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
| | - Eline Teirlinck
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
| | - Sangram Keshari Samal
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
| | - Riet De Rycke
- Inflammation Research Center, Image Core Facility, VIB, 9052 Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Gaëlle Houthaeve
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
- Univ Lille 1, Univ Lille Nord France, Lab Phys Lasers Atomes & Mol, Villeneuve Dascq, UMR 8523, 59655 France
| | - Stefaan C. De Smedt
- College of Chemical Engineering, Jiangsu Key Lab of Biomass-based Green Fuels and Chemicals, Nanjing Forestry University (NFU), Nanjing, 210037 China
| | - Rabah Boukherroub
- Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520-IEMN, Lille, F-59000 France
| | - Kevin Braeckmans
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmacy, Ghent University, Ghent, B-9000 Belgium
- Centre for Nano- and Biophotonics, Ghent University, Ghent, B-9000 Belgium
- UMR 8523, Laboratoire de Physique des Lasers, Atomes et Molécules, Université de Lille, Villeneuve d’Ascq, France
- IEMN, UMR 8520, Université de Lille, Villeneuve d’Ascq, France
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45
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Sheung JY, Ge P, Lim SJ, Lee SH, Smith AM, Selvin PR. Structural Contributions to Hydrodynamic Diameter for Quantum Dots Optimized for Live-Cell Single-Molecule Tracking. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:17406-17412. [PMID: 31656549 PMCID: PMC6814160 DOI: 10.1021/acs.jpcc.8b02516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Quantum dots are fluorescent nanoparticles with narrow-band, size-tunable, and long-lasting emission. Typical formulations used for imaging proteins in cells are hydrodynamically much larger than the protein targets, so it is critical to assess the impact of steric effects deriving from hydrodynamic size. This report analyzes a new class of quantum dots that have been engineered for minimized size specifically for imaging receptors in narrow synaptic junctions between neurons. We use fluorescence correlation spectroscopy and transmission electron microscopy to calculate the contributions of the crystalline core, organic coating, and targeting proteins (streptavidin) to the total hydrodynamic diameter of the probe, using a wide range of core materials with emission spanning 545-705 nm. We find the contributing thickness of standard commercial amphiphilic polymers to be ~8 to ~14 nm, whereas coatings based on the compact ligand HS-(CH2)11 - (OCH2CH2)4-OH contribute ~6 to ~9 nm, reducing the diameter by ~2 to ~5 nm, depending on core size. When the number of streptavidins for protein targeting is minimized, the total diameter can be further reduced by ~5 to ~11 nm, yielding a diameter of 13.8-18.4 nm. These findings explain why access to the narrow synapse derive primarily from the protein functionalization of commercial variants, rather than the organic coating layers. They also explain why those quantum dots with size around 14 nm with only a few streptavidins can access narrow cellular structures for neuronal labeling, whereas those >27 nm and a large number of streptavidins, cannot.
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Affiliation(s)
- Janet Y. Sheung
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
- Department of Physics and Astronomy, Vassar College, Poughkeepsie, New York 12604, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
| | - Pinghua Ge
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
| | - Sung Jun Lim
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
- Intelligent Devices and Systems Research Group, DGIST, 333 Techno Jungang-Daero, Hyeonpung, Daegu 42988, Republic of Korea
| | - Sang Hak Lee
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
| | - Andrew M. Smith
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
- Department of Materials Science and Engineering and University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
| | - Paul R. Selvin
- Department of Physics, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana–Champaign, Champaign, Illinois 61801, United States
- Corresponding Author, P. R. Selvin.
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46
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Conic S, Desplancq D, Tora L, Weiss E. Electroporation of Labeled Antibodies to Visualize Endogenous Proteins and Posttranslational Modifications in Living Metazoan Cell Types. Bio Protoc 2018; 8:e3069. [PMID: 30467550 DOI: 10.21769/bioprotoc.3069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The spatiotemporal localization of different intracellular factors in real-time and their detection in live cells are important parameters to understand dynamic protein-based processes. Therefore, there is a demand to perform live-cell imaging and to measure endogenous protein dynamics in single cells. However, fluorescent labeling of endogenous protein in living cells without overexpression of fusion proteins or genetic tagging has not been routinely possible. Here we describe a versatile antibody-based imaging approach (VANIMA) to be able to precisely locate and track endogenous proteins in living cells. The labeling is achieved by the efficient and harmless delivery of fluorescent dye-conjugated antibodies or antibody fragments (Fabs) into living cells and the specific binding of these antibodies to the target protein inside of the cell. Our protocol describes step by step the procedure from testing of the suitability of the desired antibody, over the digestion of the antibody to Fabs until the labeling and the delivery by electroporation of the antibody or Fab into the cells. VANIMA can be adapted to any monoclonal antibody, self-produced or commercial, and many different metazoan cell lines. Additionally, our method is simple to implement and can be used not only to visualize and track endogenous factors, but also to specifically label posttranslational modifications, which cannot be achieved by any other labeling technique so far.
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Affiliation(s)
- Sascha Conic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France
| | - Dominique Desplancq
- Université de Strasbourg, 67404, Illkirch, France.,Biotechnology and Cell Signaling, UMR 7242, 67404 Illkirch, France
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France
| | - Etienne Weiss
- Université de Strasbourg, 67404, Illkirch, France.,Biotechnology and Cell Signaling, UMR 7242, 67404 Illkirch, France
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47
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Heller JP, Rusakov DA. The Nanoworld of the Tripartite Synapse: Insights from Super-Resolution Microscopy. Front Cell Neurosci 2017; 11:374. [PMID: 29225567 PMCID: PMC5705901 DOI: 10.3389/fncel.2017.00374] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022] Open
Abstract
Synaptic connections between individual nerve cells are fundamental to the process of information transfer and storage in the brain. Over the past decades a third key partner of the synaptic machinery has been unveiled: ultrathin processes of electrically passive astroglia which often surround pre- and postsynaptic structures. The recent advent of super-resolution (SR) microscopy has begun to uncover the dynamic nanoworld of synapses and their astroglial environment. Here we overview and discuss the current progress in our understanding of the synaptic nanoenvironment, as gleaned from the imaging methods that go beyond the diffraction limit of conventional light microscopy. We argue that such methods are essential to achieve a new level of comprehension pertinent to the principles of signal integration in the brain.
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Affiliation(s)
- Janosch P Heller
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Dmitri A Rusakov
- UCL Institute of Neurology, University College London, London, United Kingdom.,Institute of Neuroscience, University of Nizhny Novgorod, Nizhny Novgorod, Russia
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Molecular Counting with Localization Microscopy: A Bayesian Estimate Based on Fluorophore Statistics. Biophys J 2017; 112:1777-1785. [PMID: 28494949 DOI: 10.1016/j.bpj.2017.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 03/16/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022] Open
Abstract
Superresolved localization microscopy has the potential to serve as an accurate, single-cell technique for counting the abundance of intracellular molecules. However, the stochastic blinking of single fluorophores can introduce large uncertainties into the final count. Here we provide a theoretical foundation for applying superresolved localization microscopy to the problem of molecular counting based on the distribution of blinking events from a single fluorophore. We also show that by redundantly tagging single molecules with multiple, blinking fluorophores, the accuracy of the technique can be enhanced by harnessing the central limit theorem. The coefficient of variation then, for the number of molecules M estimated from a given number of blinks B, scales like ∼1/Nl, where Nl is the mean number of labels on a target. As an example, we apply our theory to the challenging problem of quantifying the cell-to-cell variability of plasmid copy number in bacteria.
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Iino R, Iida T, Nakamura A, Saita EI, You H, Sako Y. Single-molecule imaging and manipulation of biomolecular machines and systems. Biochim Biophys Acta Gen Subj 2017; 1862:241-252. [PMID: 28789884 DOI: 10.1016/j.bbagen.2017.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/23/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. SCOPE OF REVIEW We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. MAJOR CONCLUSIONS Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan.
| | - Tatsuya Iida
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Akihiko Nakamura
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Japan
| | - Ei-Ichiro Saita
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, Japan
| | - Huijuan You
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, China.
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Bruce VJ, McNaughton BR. Inside Job: Methods for Delivering Proteins to the Interior of Mammalian Cells. Cell Chem Biol 2017; 24:924-934. [DOI: 10.1016/j.chembiol.2017.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/19/2017] [Accepted: 06/27/2017] [Indexed: 10/19/2022]
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