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Tantirimudalige SN, Raghuvamsi PV, Sharma KK, Wei Bao JC, Anand GS, Wohland T. The ganglioside GM1a functions as a coreceptor/attachment factor for dengue virus during infection. J Biol Chem 2022; 298:102570. [PMID: 36209827 PMCID: PMC9650044 DOI: 10.1016/j.jbc.2022.102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/29/2022] [Accepted: 10/01/2022] [Indexed: 11/09/2022] Open
Abstract
Dengue virus (DENV) is a flavivirus causing an estimated 390 million infections per year around the world. Despite the immense global health and economic impact of this virus, its true receptor(s) for internalization into live cells has not yet been identified, and no successful antivirals or treatments have been isolated to this date. This study aims to improve our understanding of virus entry routes by exploring the sialic acid-based cell surface molecule GM1a and its role in DENV infection. We studied the interaction of the virus with GM1a using fluorescence correlation spectroscopy, fluorescence crosscorrelation spectroscopy, imaging fluorescence correlation spectroscopy, amide hydrogen/deuterium exchange mass spectrometry, and isothermal titration calorimetry. Additionally, we explored the effect of this interaction on infectivity and movement of the virus during infection was explored using plaque assay and fluorescence-based imaging and single particle tracking. GM1a was deemed to interact with DENV at domain I (DI) and domain II (DII) of the E protein of the protein coat at quaternary contacts of a fully assembled virus, leading to a 10-fold and 7-fold increase in infectivity for DENV1 and DENV2 in mammalian cell systems, respectively. We determined that the interaction of the virus with GM1a triggers a speeding up of virus movement on live cell surfaces, possibly resulting from a reduction in rigidity of cellular rafts during infection. Collectively, our results suggest that GM1a functions as a coreceptor/attachment factor for DENV during infection in mammalian systems.
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Affiliation(s)
- Sarala Neomi Tantirimudalige
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Palur Venkata Raghuvamsi
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Bioinformatics Institute (A∗STAR), Singapore, Singapore
| | - Kamal Kant Sharma
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Jonathan Chua Wei Bao
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ganesh S Anand
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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2
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Kari S, Subramanian K, Altomonte IA, Murugesan A, Yli-Harja O, Kandhavelu M. Programmed cell death detection methods: a systematic review and a categorical comparison. Apoptosis 2022; 27:482-508. [PMID: 35713779 PMCID: PMC9308588 DOI: 10.1007/s10495-022-01735-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2022] [Indexed: 01/15/2023]
Abstract
Programmed cell death is considered a key player in a variety of cellular processes that helps to regulate tissue growth, embryogenesis, cell turnover, immune response, and other biological processes. Among different types of cell death, apoptosis has been studied widely, especially in the field of cancer research to understand and analyse cellular mechanisms, and signaling pathways that control cell cycle arrest. Hallmarks of different types of cell death have been identified by following the patterns and events through microscopy. Identified biomarkers have also supported drug development to induce cell death in cancerous cells. There are various serological and microscopic techniques with advantages and limitations, that are available and are being utilized to detect and study the mechanism of cell death. The complexity of the mechanism and difficulties in distinguishing among different types of programmed cell death make it challenging to carry out the interventions and delay its progression. In this review, mechanisms of different forms of programmed cell death along with their conventional and unconventional methods of detection of have been critically reviewed systematically and categorized on the basis of morphological hallmarks and biomarkers to understand the principle, mechanism, application, advantages and disadvantages of each method. Furthermore, a very comprehensive comparative analysis has been drawn to highlight the most efficient and effective methods of detection of programmed cell death, helping researchers to make a reliable and prudent selection among the available methods of cell death assay. Conclusively, how programmed cell death detection methods can be improved and can provide information about distinctive stages of cell death detection have been discussed.
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Affiliation(s)
- Sana Kari
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Kumar Subramanian
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Ilenia Agata Altomonte
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland.,Department of Biotechnology, Lady Doak College, Thallakulam, Madurai, 625002, India
| | - Olli Yli-Harja
- Institute for Systems Biology, 1441N 34th Street, Seattle, WA, USA.,Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101, Tampere, Finland. .,Department of Biotechnology, Lady Doak College, Thallakulam, Madurai, 625002, India.
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3
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Dawes ML, Soeller C, Scholpp S. Studying molecular interactions in the intact organism: fluorescence correlation spectroscopy in the living zebrafish embryo. Histochem Cell Biol 2020; 154:507-519. [PMID: 33067656 PMCID: PMC7609432 DOI: 10.1007/s00418-020-01930-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Cell behaviour and function is determined through the interactions of a multitude of molecules working in concert. To observe these molecular dynamics, biophysical studies have been developed that track single interactions. Fluorescence correlation spectroscopy (FCS) is an optical biophysical technique that non-invasively resolves single molecules through recording the signal intensity at the femtolitre scale. However, recording the behaviour of these biomolecules using in vitro-based assays often fails to recapitulate the full range of variables in vivo that directly confer dynamics. Therefore, there has been an increasing interest in observing the state of these biomolecules within living organisms such as the zebrafish Danio rerio. In this review, we explore the advancements of FCS within the zebrafish and compare and contrast these findings to those found in vitro.
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Affiliation(s)
- Michael L Dawes
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Christian Soeller
- Living Systems Institute, College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Steffen Scholpp
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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4
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Ghosh A, Enderlein J, Butkevich E. Dimerization of Human Drebrin-like Protein Governs Its Biological Activity. Biochemistry 2020; 59:1553-1558. [PMID: 32282191 DOI: 10.1021/acs.biochem.9b01095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drebrin-like protein (DBNL) is a multidomain F-actin-binding protein, which also interacts with other molecules within different intracellular pathways. Here, we present quantitative measurements on the size and conformation of human DBNL. Using dual-focus fluorescence correlation spectroscopy, we determined the hydrodynamic radius of the DBNL monomer. Native gel electrophoresis and dual-color fluorescence cross-correlation spectroscopy show that both endogenous DBNL and recombinant DBNL exist as dimers under physiological conditions. We demonstrate that C-terminal truncations of DBNL downstream of the coiled-coil domain result in its oligomerization at nanomolar concentrations. In contrast, the ADF-H domain alone is a monomer, which displays a concentration-dependent self-assembly. In vivo FLIM-FRET imaging shows that the presence of only actin-binding domains is not sufficient for DBNL to localize properly at the actin filament inside the cell. In summary, our work provides detailed insight into the structure-function relationship of human drebrin-like protein.
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Affiliation(s)
- Arindam Ghosh
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Jörg Enderlein
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Eugenia Butkevich
- Third Institute of Physics-Biophysics, Georg August University, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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5
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Di Silvio D, Martínez-Moro M, Salvador C, de Los Angeles Ramirez M, Caceres-Velez PR, Ortore MG, Dupin D, Andreozzi P, Moya SE. Self-assembly of poly(allylamine)/siRNA nanoparticles, their intracellular fate and siRNA delivery. J Colloid Interface Sci 2019; 557:757-766. [PMID: 31569055 DOI: 10.1016/j.jcis.2019.09.082] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/17/2019] [Accepted: 09/21/2019] [Indexed: 12/18/2022]
Abstract
Silencing RNA (siRNA) technologies attract significant interest as a therapeutic tool for a large number of diseases. However, the medical translation of this technology is hampered by the lack of effective delivery vehicles for siRNAs in cytosol that prevent their degradation in the bloodstream. The use of molecular complexes based on polyamines have great potential for siRNA delivery as polyamines can protect the siRNA during circulation and at the same time favor siRNA translocation in cytosol. Here, nanoparticles are prepared by complexation of poly(allylamine hydrochloride) (PAH) and siRNA varying the ratio of nitrogen groups from PAH to phosphate groups from siRNA (N/P ratio). Nanoparticles are characterized by transmission electron microscopy and dynamic light scattering. The stability of complexes of green rhodamine labelled PAH (G-PAH) and Cy5 labelled siRNA (R-siRNA) at different pHs and in cell media is studied by fluorescence cross-correlation spectroscopy (FCCS). FCCS studies show that the nanoparticles are stable at physiological pH and in cell media but they disassemble at acidic pH. An optimal N/P ratio of 2 is identified in terms of stability in media, degradation at endosomal pH and toxicity. The intracellular fate of the complexes is studied following uptake in A549 cells. The cross-correlation between G-PAH and R-siRNA decreases substantially 24 h after uptake, while diffusion times of siRNA decrease indicating that the complexes disassemble, liberating the siRNAs. The release of siRNAs into the cytosol is confirmed with parallel confocal laser scanning microscopy. Flow cytometry studies show that PAH/siRNA nanoparticles are effective at silencing green fluorescent protein expression at low N/P ratios at which polyethylenimine/siRNA shows no significant silencing.
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Affiliation(s)
- Desirè Di Silvio
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain
| | - Marta Martínez-Moro
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain
| | - Cristian Salvador
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain; CIDETEC Nanomedicine, Paseo Miramón, 196, 20014 Donostia-San Sebastián, Spain
| | - Maria de Los Angeles Ramirez
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain; Instituto de Nanosistemas, Universidad Nacional de San Martín (INS-UNSAM), Av. 25 de Mayo 1021, San Martín, Buenos Aires, Argentina
| | - Paolin Rocio Caceres-Velez
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain
| | - Maria Grazia Ortore
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Damien Dupin
- CIDETEC Nanomedicine, Paseo Miramón, 196, 20014 Donostia-San Sebastián, Spain
| | - Patrizia Andreozzi
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain.
| | - Sergio E Moya
- CICbiomaGUNE - Soft Matter Nanotechnology Group, Paseo Miramón n° 182, Edificio C, 20014 Donostia-San Sebastián, Spain.
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6
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Ng XW, Sampath K, Wohland T. Fluorescence Correlation and Cross-Correlation Spectroscopy in Zebrafish. Methods Mol Biol 2019; 1863:67-105. [PMID: 30324593 DOI: 10.1007/978-1-4939-8772-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
There has been increasing interest in biophysical studies on live organisms to gain better insights into physiologically relevant biological events at the molecular level. Zebrafish (Danio rerio) is a viable vertebrate model to study such events due to its genetic and evolutionary similarities to humans, amenability to less invasive fluorescence techniques owing to its transparency and well-characterized genetic manipulation techniques. Fluorescence techniques used to probe biomolecular dynamics and interactions of molecules in live zebrafish embryos are therefore highly sought-after to bridge molecular and developmental events. Fluorescence correlation and cross-correlation spectroscopy (FCS and FCCS) are two robust techniques that provide molecular level information on dynamics and interactions respectively. Here, we detail the steps for applying confocal FCS and FCCS, in particular single-wavelength FCCS (SW-FCCS), in live zebrafish embryos, beginning with sample preparation, instrumentation, calibration, and measurements on the FCS/FCCS instrument and ending with data analysis.
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Affiliation(s)
- Xue Wen Ng
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
| | - Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Thorsten Wohland
- Department of Chemistry and Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
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7
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Di Silvio D, Silvestri A, Lay L, Polito L, Moya SE. Impact of ConcanavalinA affinity in the intracellular fate of Protein Corona on Glucosamine Au nanoparticles. Sci Rep 2018; 8:9046. [PMID: 29899359 PMCID: PMC5998083 DOI: 10.1038/s41598-018-27418-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/25/2018] [Indexed: 01/12/2023] Open
Abstract
Biological fate and toxicity of nanoparticles (NPs) are connected to the interaction between NPs and the protein corona (PC) spontaneously forming around NPs in biological matrixes. PC is a dynamic entity that confers biological identity to NPs. In this work, fluorescence cross-correlation spectroscopy (FCCS) is used to study the impact of specific interactions between the NP surface and proteins on the intracellular fate of PC. The stability of the PC formed around glucosamide-functionalized Au-NPs from ConcanavalinA (ConA) or Bovine Serum Albumin (BSA) is characterized by FCCS. The NPs show higher affinity for ConA and competitive assays show that ConA easily exchanges BSA. A549 cells are exposed to glucosamide-functionalized Au-NPs with preformed ConA and BSA PCs. Intracellularly the frequency of cross-correlation for Au NPs with ConA PC remains constant to a 70% value until 24 h while for BSA it decreases to a 15% during the same period. FCCS measurements in several locations in the cell point out a different level of aggregation for the NPs with either ConA or BSA PCs. Our results show that the affinity of NPs functionalized with a ligand with affinity for a specific protein in bulk is retained intracellularly influencing NP fate and translocation.
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Affiliation(s)
- Desirè Di Silvio
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Paseo Miramon, 182, 20014, San Sebastian, Spain
| | - Alessandro Silvestri
- CNR - ISTM, Nanotechnology Lab., Via G. Fantoli 16/15, Milan, Italy
- Department of Chemistry, University of Milan, Via C. Golgi 19, Milan, Italy
- Max-Planck Institute of Colloids and Interfaces, Potsdam-Golm, 14476, Germany
| | - Luigi Lay
- Department of Chemistry, University of Milan, Via C. Golgi 19, Milan, Italy
- CRC Materiali Polimerici (LaMPo), University of Milan, Via C. Golgi 19, 20133, Milan, Italy
| | - Laura Polito
- CNR - ISTM, Nanotechnology Lab., Via G. Fantoli 16/15, 20138, Milan, Italy
| | - Sergio E Moya
- Soft Matter Nanotechnology Group, CIC biomaGUNE, Paseo Miramon, 182, 20014, San Sebastian, Spain.
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8
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Schwille P. There and back again: from the origin of life to single molecules. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 47:493-498. [PMID: 29569181 PMCID: PMC5982444 DOI: 10.1007/s00249-018-1295-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/08/2018] [Accepted: 03/13/2018] [Indexed: 11/27/2022]
Abstract
What is life? There is hardly a more fundamental question raised by aspiring researchers, and one less prone to ever be answered in a scientifically satisfying way. In the long, productive and highly influential period of research following his Nobel-recognised work on relaxation kinetics, Manfred Eigen made seminal contributions towards a quantifiable definition of life, with a strong focus on its evolutionary character. In the last years of his time as an active researcher, however, he devoted himself to another, purely experimental topic: the detection and analysis of single biomolecules in aqueous solution. In this short review, I will give an overview of the groundbreaking contributions to the field of single molecule research made by Eigen and coworkers, and show that both, in its intrinsic motivation, and in its consequences, single molecule research strongly relates to the question of the physical-chemical essence of life. In fact, research on living systems with single molecule sensitivity will always refer the researcher to the question of the simplest possible representation, and thus the origin, of any biological phenomenon.
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Affiliation(s)
- Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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9
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Su D, Hu X, Dong C, Ren J. Determination of Caspase-3 Activity and Its Inhibition Constant by Combination of Fluorescence Correlation Spectroscopy with a Microwell Chip. Anal Chem 2017; 89:9788-9796. [DOI: 10.1021/acs.analchem.7b01735] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Di Su
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiaocai Hu
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chaoqing Dong
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Jicun Ren
- School of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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10
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Szilvay AM, Sarria SV, Mannelqvist M, Aasland R, Furnes C. Proteolytic activity assayed by subcellular localization switching of a substrate. Biochem Biophys Rep 2016; 8:23-28. [PMID: 28955937 PMCID: PMC5613695 DOI: 10.1016/j.bbrep.2016.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/27/2016] [Accepted: 07/13/2016] [Indexed: 10/24/2022] Open
Abstract
An approach to assay proteolytic activity in vivo by altering the subcellular localization of a labelled substrate was demonstrated. The assay included a protein shuttling between different cellular compartments and a site-specific recombinant protease. The shuttle protein used was the human immunodeficiency virus type 1 (HIV-1) Rev protein tandemly fused to the enhanced green fluorescent protein (EGFP) and the red fluorescent protein (RFP), while the protease was the site-specific protease VP24 from the herpes simplex virus type 1 (HSV-1). The fluorescent proteins in the Rev fusion protein were separated by a cleavage site specific for the VP24 protease. When co-expressed in COS-7 cells proteolysis was observed by fluorescence microscopy as a shift from a predominantly cytoplasmic localization of the fusion protein RevEGFP to a nuclear localization while the RFP part of the fusion protein remained in the cytoplasm. The cleavage of the fusion protein by VP24 was confirmed by Western blot analysis. The activity of VP24, when tagged N-terminally by the Myc-epitope, was found to be comparable to VP24. These results demonstrates that the activity and localization of a recombinantly expressed protease can be assessed by protease-mediated cleavage of fusion proteins containing a specific protease cleavage site.
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Affiliation(s)
- Anne-Marie Szilvay
- Department of Molecular Biology, University of Bergen, HIB, Post-box 7800, N-5020 Bergen, Norway
| | | | - Monica Mannelqvist
- Department of Molecular Biology, University of Bergen, HIB, Post-box 7800, N-5020 Bergen, Norway.,Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, HIB, Post-box 7800, N-5020 Bergen, Norway
| | - Rein Aasland
- Department of Molecular Biology, University of Bergen, HIB, Post-box 7800, N-5020 Bergen, Norway
| | - Clemens Furnes
- Department of Molecular Biology, University of Bergen, HIB, Post-box 7800, N-5020 Bergen, Norway.,Centre for Organelle Research (CORE), University of Stavanger, Norway
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11
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Isokane M, Walter T, Mahen R, Nijmeijer B, Hériché JK, Miura K, Maffini S, Ivanov MP, Kitajima TS, Peters JM, Ellenberg J. ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores. J Cell Biol 2016; 212:647-59. [PMID: 26953350 PMCID: PMC4792069 DOI: 10.1083/jcb.201408089] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/11/2016] [Indexed: 12/15/2022] Open
Abstract
The spindle assembly checkpoint (SAC) ensures genome stability during cell division. Here, a new essential SAC factor, ARHGEF17, is characterized by quantitative imaging, biochemical, and biophysical experiments, which show that it targets the checkpoint kinase Mps1 to kinetochores. To prevent genome instability, mitotic exit is delayed until all chromosomes are properly attached to the mitotic spindle by the spindle assembly checkpoint (SAC). In this study, we characterized the function of ARHGEF17, identified in a genome-wide RNA interference screen for human mitosis genes. Through a series of quantitative imaging, biochemical, and biophysical experiments, we showed that ARHGEF17 is essential for SAC activity, because it is the major targeting factor that controls localization of the checkpoint kinase Mps1 to the kinetochore. This mitotic function is mediated by direct interaction of the central domain of ARHGEF17 with Mps1, which is autoregulated by the activity of Mps1 kinase, for which ARHGEF17 is a substrate. This mitosis-specific role is independent of ARHGEF17’s RhoGEF activity in interphase. Our study thus assigns a new mitotic function to ARHGEF17 and reveals the molecular mechanism for a key step in SAC establishment.
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Affiliation(s)
- Mayumi Isokane
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Thomas Walter
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Robert Mahen
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bianca Nijmeijer
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jean-Karim Hériché
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kota Miura
- Centre for Molecular and Cellular Imaging, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Miroslav Penchev Ivanov
- Molecular and Cellular Biology, Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Tomoya S Kitajima
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jan-Michael Peters
- Molecular and Cellular Biology, Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
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12
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Hendrix J, Baumgärtel V, Schrimpf W, Ivanchenko S, Digman MA, Gratton E, Kräusslich HG, Müller B, Lamb DC. Live-cell observation of cytosolic HIV-1 assembly onset reveals RNA-interacting Gag oligomers. J Cell Biol 2015; 210:629-46. [PMID: 26283800 PMCID: PMC4539982 DOI: 10.1083/jcb.201504006] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Analysis of the cytosolic HIV-1 Gag fraction in live cells via advanced fluctuation imaging methods reveals potential nucleation steps before membrane-assisted Gag assembly. Assembly of the Gag polyprotein into new viral particles in infected cells is a crucial step in the retroviral replication cycle. Currently, little is known about the onset of assembly in the cytosol. In this paper, we analyzed the cytosolic HIV-1 Gag fraction in real time in live cells using advanced fluctuation imaging methods and thereby provide detailed insights into the complex relationship between cytosolic Gag mobility, stoichiometry, and interactions. We show that Gag diffuses as a monomer on the subsecond timescale with severely reduced mobility. Reduction of mobility is associated with basic residues in its nucleocapsid (NC) domain, whereas capsid (CA) and matrix (MA) domains do not contribute significantly. Strikingly, another diffusive Gag species was observed on the seconds timescale that oligomerized in a concentration-dependent manner. Both NC- and CA-mediated interactions strongly assist this process. Our results reveal potential nucleation steps of cytosolic Gag fractions before membrane-assisted Gag assembly.
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Affiliation(s)
- Jelle Hendrix
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Viola Baumgärtel
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Waldemar Schrimpf
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Sergey Ivanchenko
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
| | - Michelle A Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697 Development Biology Center Optical Biology Core Facility, University of California, Irvine, Irvine, CA 92697
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697 Development Biology Center Optical Biology Core Facility, University of California, Irvine, Irvine, CA 92697
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, D-69120 Heidelberg, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Ludwig Maximilian University of Munich, D-81377 Munich, Germany NanoSystems Initiative Munich (NIM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Munich Center for Integrated Protein Science (CiPSM), Ludwig Maximilian University of Munich, D-81377 Munich, Germany Center for Nanoscience (CeNS), Ludwig Maximilian University of Munich, D-81377 Munich, Germany
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13
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Hendrix J, van Heertum B, Vanstreels E, Daelemans D, De Rijck J. Dynamics of the ternary complex formed by c-Myc interactor JPO2, transcriptional co-activator LEDGF/p75, and chromatin. J Biol Chem 2014; 289:12494-506. [PMID: 24634210 DOI: 10.1074/jbc.m113.525964] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Lens epithelium-derived growth factor (LEDGF/p75) is a transcriptional co-activator involved in targeting human immunodeficiency virus (HIV) integration and the development of MLL fusion-mediated acute leukemia. A previous study revealed that LEDGF/p75 dynamically scans the chromatin, and upon interaction with HIV-1 integrase, their complex is locked on chromatin. At present, it is not known whether LEDGF/p75-mediated chromatin locking is typical for interacting proteins. Here, we employed continuous photobleaching and fluorescence correlation and cross-correlation spectroscopy to investigate in vivo chromatin binding of JPO2, a LEDGF/p75- and c-Myc-interacting protein involved in transcriptional regulation. In the absence of LEDGF/p75, JPO2 performs chromatin scanning inherent to transcription factors. However, whereas the dynamics of JPO2 chromatin binding are decelerated upon interaction with LEDGF/p75, very strong locking of their complex onto chromatin is absent. Similar results were obtained with the domesticated transposase PogZ, another cellular interaction partner of LEDGF/p75. We furthermore show that diffusive JPO2 can oligomerize; that JPO2 and LEDGF/p75 interact directly and specifically in vivo through the specific interaction domain of JPO2 and the C-terminal domain of LEDGF/p75, comprising the integrase-binding domain; and that modulation of JPO2 dynamics requires a functional PWWP domain in LEDGF/p75. Our results suggest that the dynamics of the LEDGF/p75-chromatin interaction depend on the specific partner and that strong chromatin locking is not a property of all LEDGF/p75-binding proteins.
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Affiliation(s)
- Jelle Hendrix
- From the Laboratory for Photochemistry and Spectroscopy, Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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14
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Biomolecular dynamics and binding studies in the living cell. Phys Life Rev 2014; 11:1-30. [DOI: 10.1016/j.plrev.2013.11.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022]
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15
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Dornblut C, Quinn N, Monajambashi S, Prendergast L, van Vuuren C, Münch S, Deng W, Leonhardt H, Cardoso MC, Hoischen C, Diekmann S, Sullivan KF. A CENP-S/X complex assembles at the centromere in S and G2 phases of the human cell cycle. Open Biol 2014; 4:130229. [PMID: 24522885 PMCID: PMC3938055 DOI: 10.1098/rsob.130229] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The functional identity of centromeres arises from a set of specific nucleoprotein particle subunits of the centromeric chromatin fibre. These include CENP-A and histone H3 nucleosomes and a novel nucleosome-like complex of CENPs -T, -W, -S and -X. Fluorescence cross-correlation spectroscopy and Förster resonance energy transfer (FRET) revealed that human CENP-S and -X exist principally in complex in soluble form and retain proximity when assembled at centromeres. Conditional labelling experiments show that they both assemble de novo during S phase and G2, increasing approximately three- to fourfold in abundance at centromeres. Fluorescence recovery after photobleaching (FRAP) measurements documented steady-state exchange between soluble and assembled pools, with CENP-X exchanging approximately 10 times faster than CENP-S (t1/2 ∼ 10 min versus 120 min). CENP-S binding to sites of DNA damage was quite distinct, with a FRAP half-time of approximately 160 s. Fluorescent two-hybrid analysis identified CENP-T as a uniquely strong CENP-S binding protein and this association was confirmed by FRET, revealing a centromere-bound complex containing CENP-S, CENP-X and CENP-T in proximity to histone H3 but not CENP-A. We propose that deposition of the CENP-T/W/S/X particle reveals a kinetochore-specific chromatin assembly pathway that functions to switch centromeric chromatin to a mitosis-competent state after DNA replication. Centromeres shuttle between CENP-A-rich, replication-competent and H3-CENP-T/W/S/X-rich mitosis-competent compositions in the cell cycle.
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Affiliation(s)
- Carsten Dornblut
- Molecular Biology, FLI, Beutenbergstrasse 11, Jena 07745, Germany
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16
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A fluorescence correlation spectroscopy-based enzyme assay for human Dicer. Methods Mol Biol 2013. [PMID: 24166306 DOI: 10.1007/978-1-62703-703-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We used fluorescence correlation spectroscopy (FCS) to establish an in vitro assay to investigate RNase activity of human Dicer (Werner et al., Biol Chem 393(3):187-193). FCS allows investigating the interactions of different particles due to their differing diffusion mobility, provided that one of the interacting partners exhibit a fluorescence label. In our case we used a fluorophore-labeled double-stranded RNA (dsRNA) as substrate to monitor Dicer activity. The dsRNA was cleaved by the enzyme resulting in a five-nucleotide-short single-stranded RNA (ssRNA) fragment carrying the fluorophore, which could be distinguished from the substrate and unlabeled second product by FCS. Furthermore, we refer to additional (control) experiments to confirm obtained data.
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17
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Affiliation(s)
- Jens Michaelis
- Biophysics
Institute, Faculty of Natural Sciences, Ulm University, Albert-Einstein-Allee
11, 89081 Ulm, Germany
- Center
for Integrated Protein Science Munich (CIPSM), Department
of Chemistry and Biochemistry, Munich University, Butenandtstrasse 5-13, 81377 München, Germany
| | - Barbara Treutlein
- Department
of Bioengineering, Stanford University, James H. Clark Center, E-300, 318
Campus Drive, Stanford, California 94305-5432, United States
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18
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Weidemann T, Schwille P. Dual-color fluorescence cross-correlation spectroscopy with continuous laser excitation in a confocal setup. Methods Enzymol 2013; 518:43-70. [PMID: 23276535 DOI: 10.1016/b978-0-12-388422-0.00003-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Fluorescence correlation spectroscopy evaluates local signal fluctuations arising from stochastic movements of fluorescent particles in solution. The measured fluctuating signal is correlated in time and analyzed with appropriate model functions containing the parameters that describe the underlying molecular behavior. The dual-color extension, fluorescence cross-correlation spectroscopy (FCCS) allows for a comparison between spectrally well-separated channels to extract codiffusion events that reflect interactions between differently labeled molecules. In addition to solution measurements, FCCS can be applied with subcellular resolution and is therefore a very promising approach for a quantitative biochemical assessment of molecular networks in living cells. To derive thermodynamic and kinetic reaction parameters, the influence of a number of other factors like background noise, illumination intensity profiles, photophysical processes, and cross talk between the channels have to be treated. Here, we provide a roadmap to derive binding reaction data with dual-color FCCS using continuous wave laser excitation, as it is now accessible with many state-of-the-art confocal microscopes.
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Affiliation(s)
- Thomas Weidemann
- Biophysics/BIOTEC, Technische Universität Dresden, Dresden, Germany.
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19
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Eskat A, Deng W, Hofmeister A, Rudolphi S, Emmerth S, Hellwig D, Ulbricht T, Döring V, Bancroft JM, McAinsh AD, Cardoso MC, Meraldi P, Hoischen C, Leonhardt H, Diekmann S. Step-wise assembly, maturation and dynamic behavior of the human CENP-P/O/R/Q/U kinetochore sub-complex. PLoS One 2012; 7:e44717. [PMID: 23028590 PMCID: PMC3445539 DOI: 10.1371/journal.pone.0044717] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/06/2012] [Indexed: 11/18/2022] Open
Abstract
Kinetochores are multi-protein megadalton assemblies that are required for attachment of microtubules to centromeres and, in turn, the segregation of chromosomes in mitosis. Kinetochore assembly is a cell cycle regulated multi-step process. The initial step occurs during interphase and involves loading of the 15-subunit constitutive centromere associated complex (CCAN), which contains a 5-subunit (CENP-P/O/R/Q/U) sub-complex. Here we show using a fluorescent three-hybrid (F3H) assay and fluorescence resonance energy transfer (FRET) in living mammalian cells that CENP-P/O/R/Q/U subunits exist in a tightly packed arrangement that involves multifold protein-protein interactions. This sub-complex is, however, not pre-assembled in the cytoplasm, but rather assembled on kinetochores through the step-wise recruitment of CENP-O/P heterodimers and the CENP-P, -O, -R, -Q and -U single protein units. SNAP-tag experiments and immuno-staining indicate that these loading events occur during S-phase in a manner similar to the nucleosome binding components of the CCAN, CENP-T/W/N. Furthermore, CENP-P/O/R/Q/U binding to the CCAN is largely mediated through interactions with the CENP-N binding protein CENP-L as well as CENP-K. Once assembled, CENP-P/O/R/Q/U exchanges slowly with the free nucleoplasmic pool indicating a low off-rate for individual CENP-P/O/R/Q/U subunits. Surprisingly, we then find that during late S-phase, following the kinetochore-binding step, both CENP-Q and -U but not -R undergo oligomerization. We propose that CENP-P/O/R/Q/U self-assembles on kinetochores with varying stoichiometry and undergoes a pre-mitotic maturation step that could be important for kinetochores switching into the correct conformation necessary for microtubule-attachment.
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Affiliation(s)
| | - Wen Deng
- Department of Biology II, Center for Integrated Protein Science, Ludwig Maximilians University Munich, Planegg-Martinsried, Munich, Germany
| | | | | | | | | | | | | | - James M. Bancroft
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Andrew D. McAinsh
- Centre for Mechanochemical Cell Biology, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | | | | | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science, Ludwig Maximilians University Munich, Planegg-Martinsried, Munich, Germany
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20
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Chlastakova I, Liskova M, Kudelova J, Dubska L, Kleparnik K, Matalova E. Dynamics of caspase-3 activation and inhibition in embryonic micromasses evaluated by a photon-counting chemiluminescence approach. In Vitro Cell Dev Biol Anim 2012; 48:545-9. [PMID: 22976371 DOI: 10.1007/s11626-012-9542-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 07/31/2012] [Indexed: 12/01/2022]
Abstract
Caspases are key enzymatic components of the intracellular apoptotic machinery, and their role in mammalian systems is often studied using fluoromethylketone (FMK) inhibitors. Despite many advantages of such approach, efficiency of the inhibitor and membrane permeability speed are often questioned. This work therefore focuses on an exact evaluation of caspase-3 FMK inhibition dynamics in camptothecin-induced mesenchymal micromasses. Two parameters of caspase-3 FMK inhibitor were investigated: first, the stability of the inhibitory potential in the time course of cultivation and, simultaneously, the dynamics of caspase-3 FMK inhibition after camptothecin-induced apoptosis peak. A photon-counting chemiluminescence approach was applied for quantification of active caspase-3. The sensitivity of the photon-counting method allowed for evaluation of active caspase-3 concentration in femtogram amounts per cell. The inhibitor penetrated the cells within the first minute after its application, and the peak of caspase-3 started to decline to the blank level after 30 min. The inhibitory effect of the FMK inhibitor was unchanged during the entire 48 h of cultivation.
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Affiliation(s)
- I Chlastakova
- Institute of Animal Physiology and Genetics CAS, v.v.i., Brno, Czech Republic
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21
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Factors affecting the quantification of biomolecular interactions by fluorescence cross-correlation spectroscopy. Biophys J 2012; 102:1174-83. [PMID: 22404940 DOI: 10.1016/j.bpj.2012.01.040] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 01/13/2012] [Accepted: 01/23/2012] [Indexed: 01/11/2023] Open
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is used to determine interactions and dissociation constants (K(d)s) of biomolecules. The determination of a K(d) depends on the accurate measurement of the auto- and cross-correlation function (ACF and CCF) amplitudes. In the case of complete binding, the ratio of the CCF/ACF amplitudes is expected to be 1. However, measurements performed on tandem fluorescent proteins (FPs), in which two different FPs are linked, yield CCF/ACF amplitude ratios of ~0.5 or less for different FCCS schemes. We use single wavelength FCCS and pulsed interleaved excitation FCCS to measure various tandem FPs constituted of different red and green FPs and determine the causes for this suboptimal ratio. The main causes for the reduced CCF/ACF amplitude ratio are differences in observation volumes for the different labels, the existence of dark FPs due to maturation problems, photobleaching, and to a lesser extent Förster (or fluorescence) resonance energy transfer between the labels. We deduce the fraction of nonfluorescent proteins for EGFP, mRFP, and mCherry as well as the differences in observation volumes. We use this information to correct FCCS measurements of the interaction of Cdc42, a small Rho-GTPase, with its effector IQGAP1 in live cell measurements to obtain a label-independent value for the K(d).
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22
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Proteins on the move: insights gained from fluorescent protein technologies. Nat Rev Mol Cell Biol 2011; 12:656-68. [PMID: 21941275 DOI: 10.1038/nrm3199] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Proteins are always on the move, and this may occur through diffusion or active transport. The realization that the regulation of signal transduction is highly dynamic in space and time has stimulated intense interest in the movement of proteins. Over the past decade, numerous new technologies using fluorescent proteins have been developed, allowing us to observe the spatiotemporal dynamics of proteins in living cells. These technologies have greatly advanced our understanding of protein dynamics, including protein movement and protein interactions.
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23
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Hayakawa EH, Furutani M, Matsuoka R, Takakuwa Y. Comparison of protein behavior between wild-type and G601S hERG in living cells by fluorescence correlation spectroscopy. J Physiol Sci 2011; 61:313-9. [PMID: 21573751 PMCID: PMC10717380 DOI: 10.1007/s12576-011-0150-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 04/17/2011] [Indexed: 11/24/2022]
Abstract
The human ether-a-go-go-related gene (hERG) protein is a cardiac potassium channel. Mutations in hERG can result in reductions in membrane channel current, cardiac repolarization, prolongation of QT intervals, and lethal arrhythmia. In the last decade, it has been found that some mutants of hERG involved in long QT syndrome exhibit intracellular protein trafficking defects, while other mutants sort to the membrane but cannot form functional channels. Due to the close relationship between intracellular trafficking and functional protein expression, we aimed to measure differences in protein behavior/motion between wild-type and mutant hERG by directly analyzing the fluorescence fluctuations of green fluorescent protein-labeled proteins using fluorescence correlation spectroscopy (FCS). Our data imply that FCS can be applied as a new diagnostic tool to assess whether the defect in a particular mutant channel protein involves aberrant intracellular trafficking.
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Affiliation(s)
- Eri H. Hayakawa
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Present Address: Laboratory of Medical Zoology and Parasitology, Department of Infection and Immunity, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498 Japan
| | - Michiko Furutani
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Department of Pediatric Cardiology, Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Rumiko Matsuoka
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Department of Pediatric Cardiology, Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
| | - Yuichi Takakuwa
- International Research and Educational Institute for Integrated Medical Sciences (IREIIMS), Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
- Department of Biochemistry, Tokyo Women’s Medical University, 8-1 Kawata-cho, Shinjuku-ku, Tokyo, 162-8666 Japan
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24
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Tian Y, Martinez MM, Pappas D. Fluorescence correlation spectroscopy: a review of biochemical and microfluidic applications. APPLIED SPECTROSCOPY 2011; 65:115A-124A. [PMID: 21396180 PMCID: PMC3071976 DOI: 10.1366/10-06224] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Over the years fluorescence correlation spectroscopy (FCS) has proven to be a useful technique that has been utilized in several fields of study. Although FCS initially suffered from poor signal-to-noise ratios, the incorporation of confocal microscopy has overcome this drawback and transformed FCS into a sensitive technique with high figures of merit. In addition, tandem methods have evolved to include dual-color cross-correlation, total internal reflection fluorescence correlation, and fluorescence lifetime correlation spectroscopy combined with time-correlated single-photon counting. In this review, we discuss several applications of FSC for biochemical, microfluidic, and cellular investigations.
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Affiliation(s)
- Yu Tian
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Michelle M. Martinez
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
| | - Dimitri Pappas
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409
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25
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Mazouchi A, Liu B, Bahram A, Gradinaru CC. On the performance of bioanalytical fluorescence correlation spectroscopy measurements in a multiparameter photon-counting microscope. Anal Chim Acta 2011; 688:61-9. [PMID: 21296206 DOI: 10.1016/j.aca.2011.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 12/10/2010] [Accepted: 01/04/2011] [Indexed: 11/26/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) data acquisition and analysis routines were developed and implemented in a home-built, multiparameter photon-counting microscope. Laser excitation conditions were investigated for two representative fluorescent probes, Rhodamine110 and enhanced green fluorescent protein (EGFP). Reliable local concentrations and diffusion constants were obtained by fitting measured FCS curves, provided that the excitation intensity did not exceed 20% of the saturation level for each fluorophore. Accurate results were obtained from FCS measurements for sample concentrations varying from pM to μM range, as well as for conditions of high background signals. These experimental constraints were found to be determined by characteristics of the detection system and by the saturation behavior of the fluorescent probes. These factors actually limit the average number of photons that can be collected from a single fluorophore passing through the detection volume. The versatility of our setup and the data analysis capabilities were tested by measuring the mobility of EGFP in the nucleus of Drosophila cells under conditions of high concentration and molecular crowding. As a bioanalytical application, we studied by FCS the binding affinity of a novel peptide-based drug to the cancer-regulating STAT3 protein and corroborated the results with fluorescence polarization analysis derived from the same photon data.
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Affiliation(s)
- Amir Mazouchi
- Department of Physics, Institute for Optical Sciences, University of Toronto, Toronto, Canada
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26
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Fluorescence Correlation and Cross-Correlation Spectroscopy Using Fluorescent Proteins for Measurements of Biomolecular Processes in Living Organisms. FLUORESCENT PROTEINS II 2011. [DOI: 10.1007/4243_2011_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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27
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Roy S, Dixit CK, Woolley R, MacCraith BD, O'Kennedy R, McDonagh C. Novel multiparametric approach to elucidate the surface amine-silanization reaction profile on fluorescent silica nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18125-18134. [PMID: 21069990 DOI: 10.1021/la103212d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This Article addresses the important issue of the characterization of surface functional groups for optical bioassay applications. We use a model system consisting of spherical dye-doped silica nanoparticles (NPs) that have been functionalized with amine groups whereby the encapsulated cyanine-based near-infrared dye fluorescence acts as a probe of the NP surface environment. This facilitates the identification of the optimum deposition parameters for the formation of a stable ordered amine monolayer and also elucidates the functionalization profile of the amine-silanization process. Specifically, we use a novel approach where the techniques of fluorescence correlation spectroscopy (FCS) and fluorescence lifetime measurement (FL) are used in conjunction with the more conventional analytical techniques of zeta potential measurement and Fourier transfer infrared spectroscopy (FTIR). The dynamics of the ordering of the amine layer in different stages of the reaction have been characterized by FTIR, FL, and FCS. The results indicate an optimum reaction time for the formation of a stable amine layer, which is optimized for further biomolecular conjugation, whereas extended reaction times lead to a disordered cross-linked layer. The results have been validated using an immunoglobulin (IgG) plate-based direct binding assay where the maximum number of IgG-conjugated aminated NPs were captured by immobilized anti-IgG antibodies for the NP sample corresponding to the optimized amine-silanization condition. Importantly, these results point to the potential of FCS and FL as useful analytical tools in diverse fields such as characterization of surface functionalization.
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Affiliation(s)
- Shibsekhar Roy
- National Biophotonics and Imaging Platform, School of Physical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
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28
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Li N, Henry E, Guiot E, Rigolet P, Brochon JC, Xi XG, Deprez E. Multiple Escherichia coli RecQ helicase monomers cooperate to unwind long DNA substrates: a fluorescence cross-correlation spectroscopy study. J Biol Chem 2010; 285:6922-36. [PMID: 20048388 DOI: 10.1074/jbc.m109.069286] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The RecQ family helicases catalyze the DNA unwinding reaction in an ATP hydrolysis-dependent manner. We investigated the mechanism of DNA unwinding by the Escherichia coli RecQ helicase using a new sensitive helicase assay based on fluorescence cross-correlation spectroscopy (FCCS) with two-photon excitation. The FCCS-based assay can be used to measure the unwinding activity under both single and multiple turnover conditions with no limitation related to the size of the DNA strands constituting the DNA substrate. We found that the monomeric helicase was sufficient to perform the unwinding of short DNA substrates. However, a significant increase in the activity was observed using longer DNA substrates, under single turnover conditions, originating from the simultaneous binding of multiple helicase monomers to the same DNA molecule. This functional cooperativity was strongly dependent on several factors, including DNA substrate length, the number and size of single-stranded 3'-tails, and the temperature. Regarding the latter parameter, a strong cooperativity was observed at 37 degrees C, whereas only modest or no cooperativity was observed at 25 degrees C regardless of the nature of the DNA substrate. Consistently, the functional cooperativity was found to be tightly associated with a cooperative DNA binding mode. We also showed that the cooperative binding of helicase to the DNA substrate indirectly accounts for the sigmoidal dependence of unwinding activity on ATP concentration, which also occurs only at 37 degrees C but not at 25 degrees C. Finally, we further examined the influences of spontaneous DNA rehybridization (after helicase translocation) and the single-stranded DNA binding property of helicase on the unwinding activity as detected in the FCCS assay.
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Affiliation(s)
- Na Li
- Laboratoire de Biologie et Pharmacologie Appliquées, CNRS UMR8113, Ecole Normale Supérieure Cachan, Institut d'Alembert, 61 Avenue du Président Wilson, 94235 Cachan, France
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29
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Vámosi G, Damjanovich S, Szöllosi J, Vereb G. Measurement of molecular mobility with fluorescence correlation spectroscopy. ACTA ACUST UNITED AC 2009; Chapter 2:Unit2.15. [PMID: 19816923 DOI: 10.1002/0471142956.cy0215s50] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a fluctuation method established three decades ago, whose application to cellular systems became popular in the last decade. Fluctuations of fluorescence emission are observed from a small, femtoliter to sub-femtoliter, usually confocal volume at high time resolution. A time-dependent autocorrelation function is generated and evaluated to obtain time constants of photophysical and photochemical reactions, as well as of molecular diffusion and in the observation volume. Molecules in various subcellular compartments-including the nucleus, the cytoplasm, and the membrane-can be observed after labeling them with antibodies, ligands, or fluorescent proteins. The anomaly of diffusion, the local concentration, and the average fluorescence per diffusing particle can also be determined, all of which can be characteristic of molecular interactions. A two-color version of FCS, fluorescence cross-correlation spectroscopy, can also be applied to observe co-diffusion, i.e., stable association of two distinct molecular species in their cellular environment.
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Affiliation(s)
- György Vámosi
- Cell Biology and Signaling Research Group of the Hungarian Academy of Sciences, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
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30
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Early detection of apoptosis in living cells by fluorescence correlation spectroscopy. Anal Bioanal Chem 2009; 396:1177-85. [DOI: 10.1007/s00216-009-3298-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 11/02/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
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31
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Nuclear import and assembly of influenza A virus RNA polymerase studied in live cells by fluorescence cross-correlation spectroscopy. J Virol 2009; 84:1254-64. [PMID: 19906916 DOI: 10.1128/jvi.01533-09] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intracellular transport and assembly of the subunits of the heterotrimeric RNA-dependent RNA polymerase constitute a key component of the replication cycle of influenza virus. Recent results suggest that efficient polymerase assembly is a limiting factor in the viability of reassortant viruses. The mechanism of nuclear import and assembly of the three polymerase subunits, PB1, PB2, and PA, is still controversial, yet it is clearly of great significance in understanding the emergence of new strains with pandemic potential. In this study, we systematically investigated the interactions between the polymerase subunits and their localization in living cells by fluorescence cross-correlation spectroscopy (FCCS) and quantitative confocal microscopy. We could show that PB1 and PA form a dimer in the cytoplasm, which is imported into the nucleus separately from PB2. Once in the nucleus, the PB1/PA dimer associates with PB2 to form the trimeric polymerase. Photon-counting histogram analysis revealed that trimeric polymerase complexes can form higher-order oligomers in the nucleus. We furthermore demonstrate that impairing the nuclear import of PB2 by mutating its nuclear localization signal leads to abnormal formation of the trimeric polymerase in the cytoplasm. Taken together, our results demonstrate which of the previously discussed influenza virus polymerase transport models operates in live cells. Our study sheds light on the interplay between the nuclear import of the subunits and the assembly of the influenza virus polymerase and provides a methodological framework to analyze the effects of different host range mutations in the future.
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32
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Miller AE, Hollars CW, Lane SM, Laurence TA. Fluorescence cross-correlation spectroscopy as a universal method for protein detection with low false positives. Anal Chem 2009; 81:5614-22. [PMID: 19522509 DOI: 10.1021/ac9001645] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specific, quantitative, and sensitive protein detection with minimal sample preparation is an enduring need in biology and medicine. Protein detection assays ideally provide quick, definitive measurements that use only small amounts of material. Fluorescence cross-correlation spectroscopy (FCCS) has been proposed and developed as a protein detection assay for several years. Here, we combine several recent advances in FCCS apparatus and analysis to demonstrate it as an important method for sensitive, quantitative, information-rich protein detection with low false positives. The addition of alternating laser excitation (ALEX) to FCCS along with a method to exclude signals from occasional aggregates leads to a very low rate of false positives, allowing the detection and quantification of the concentrations of a wide variety of proteins. We detect human chorionic gonadotropin (hCG) using an antibody-based sandwich assay and quantitatively compare our results with calculations based on binding equilibrium equations. Furthermore, using our aggregate exclusion method, we detect smaller oligomers of the prion protein PrP by excluding bright signals from large aggregates.
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Affiliation(s)
- Abigail E Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
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33
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Shi X, Foo YH, Sudhaharan T, Chong SW, Korzh V, Ahmed S, Wohland T. Determination of dissociation constants in living zebrafish embryos with single wavelength fluorescence cross-correlation spectroscopy. Biophys J 2009; 97:678-86. [PMID: 19619483 DOI: 10.1016/j.bpj.2009.05.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Revised: 04/27/2009] [Accepted: 05/01/2009] [Indexed: 10/20/2022] Open
Abstract
The quantification of biological interactions is very important in life sciences. Here we report for the first time, to our knowledge, the determination of a biomolecular dissociation constant (K(D)) in living zebrafish embryos at physiological protein expression levels. For that purpose, we extend the application of single wavelength fluorescence cross-correlation spectroscopy into small organisms and measure the interaction of Cdc42, a small Rho-GTPase, and IQGAP1, an actin-binding scaffolding protein. Cdc42 and IQGAP1 were labeled with monomeric red fluorescent protein and enhanced green fluorescent protein, respectively. Both fluorophores were excited at a single wavelength of 514 nm, simplifying the fluorescence spectroscopy measurements and allowing quantification. For the determination of the interaction, we used two Cdc42 mutants, the constitutively active Cdc42(G12V) which is in a predominantly GTP-bound form and the dominant-negative GDP-bound Cdc42(T17N). While Cdc42(G12V) binds to IQGAP1 with an apparent K(D) of approximately 100 nM, Cdc42(T17N) has at least a one-order-of-magnitude lower affinity for the same protein. As a comparison, we measure the same protein-protein interactions in Chinese hamster ovary cell cultures but observe significant differences in protein mobility and K(D) from the zebrafish measurements, supporting the notion that bimolecular interactions depend on the biological system under investigation and are best performed under physiologically relevant conditions.
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Affiliation(s)
- Xianke Shi
- Department of Chemistry, National University of Singapore, Singapore
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34
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Digman MA, Gratton E. Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2009; 1:273-282. [PMID: 20835996 PMCID: PMC3086279 DOI: 10.1002/wsbm.5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This article focuses on methods based on fluctuation correlation spectroscopy to determine the formation of protein complexes in living cells. We present the principles of the fluctuation method applied to cells. We discuss the novelty and the promises of this approach. The emphasis is in the discussion of the underlying statistical assumptions of the image correlation spectroscopy analysis rather than in reviewing applications of the method. Although one example of the application of the fluctuation method is given, this article also contains simulations that are better suited to illustrate and support the basic assumptions of the method.
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Affiliation(s)
- Michelle A. Digman
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
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35
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Nakata H, Ohtsuki T, Sisido M. A protease inhibitor discovery method using fluorescence correlation spectroscopy with position-specific labeled protein substrates. Anal Biochem 2009; 390:121-5. [PMID: 19394304 DOI: 10.1016/j.ab.2009.03.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Revised: 03/19/2009] [Accepted: 03/26/2009] [Indexed: 11/25/2022]
Abstract
We developed novel substrates for protease activity evaluation by fluorescence correlation spectroscopy (FCS). Substrates were labeled in a position-specific manner with a fluorophore near the N terminus and included a C-terminal, 30 kDa, highly soluble protein (elongation factor Ts [EF-Ts]). The C-terminal protein enhanced the substrate peptide solubility and increased the molecular weight, enabling sensitive detection by FCS. Using the labeled substrates, caspase-3 and matrix metalloproteinase-9 (MMP-9) activities were confirmed by FCS. To demonstrate the suitability of this FCS-based assay for high-throughput screening, we screened various chemical compounds for MMP-9 inhibitors. The screening results confirmed the inhibitory activity of one compound and also revealed another potential MMP-9 inhibitor. Thus, this combination of position-specific labeled protein substrates and FCS may serve as a useful tool for evaluating activities of various proteases and for protease inhibitor screening.
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Affiliation(s)
- Hidetaka Nakata
- Department of Bioscience and Biotechnology, Okayama University, Okayama 700-8530, Japan
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36
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Werner A, Konarev PV, Svergun DI, Hahn U. Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering. Anal Biochem 2009; 389:52-62. [PMID: 19303859 DOI: 10.1016/j.ab.2009.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2009] [Accepted: 03/12/2009] [Indexed: 01/14/2023]
Abstract
Using fluorescence correlation spectroscopy (FCS), we have established an in vitro assay to study RNA dynamics by analyzing fluorophore binding RNA aptamers at the single molecule level. The RNA aptamer SRB2m, a minimized variant of the initially selected aptamer SRB-2, has a high affinity to the disulfonated triphenylmethane dye sulforhodamine B. A mobility shift of sulforhodamine B after binding to SRB2m was measured. In contrast, patent blue V (PBV) is visible only if complexed with SRB2m due to increased molecular brightness and minimal background. With small angle X-ray scattering (SAXS), the three-dimensional structure of the RNA aptamer was characterized at low resolution to analyze the effect of fluorophore binding. The aptamer and sulforhodamine B-aptamer complex was found to be predominantly dimeric in solution. Interaction of PBV with SRB2m led to a dissociation of SRB2m dimers into monomers. Radii of gyration and hydrodynamic radii, gained from dynamic light scattering, FCS, and fluorescence cross-correlation experiments, led to comparable conclusions. Our study demonstrates how RNA-aptamer fluorophore complexes can be simultaneously structurally and photophysically characterized by FCS. Furthermore, fluorophore binding RNA aptamers provide a tool for visualizing single RNA molecules.
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Affiliation(s)
- Arne Werner
- Institute for Biochemistry and Molecular Biology, Department of Chemistry, Faculty of Mathematics, Informatics, and Natural Sciences, Hamburg University, D-20146 Hamburg, Germany
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37
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Analysis of membrane-localized binding kinetics with FRAP. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:627-38. [PMID: 18299825 DOI: 10.1007/s00249-008-0286-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 01/25/2008] [Accepted: 01/31/2008] [Indexed: 10/22/2022]
Abstract
Interactions between plasma membrane-associated proteins on interacting cells are critical for many important biological processes. Few experimental techniques, however, can accurately determine the association and the dissociation rates between such interacting pairs when the two molecules diffuse on apposing membranes or lipid bilayers. In this study, we give a theoretical description of how and when fluorescence recovery after photobleaching (FRAP) experiments can be used to quantify these reaction rates. We analyze the effect of binding on FRAP recovery curves with a reaction-diffusion model and systematically identify different regimes in the parameter space of the association and the dissociation constants for which the full model simplifies into equivalent one-parameter models. Based on this analysis, we propose an experimental protocol that may be used to identify the kinetic parameters of binding in the appropriate parameter regime. We present simulated experiments illustrating our protocol and lay down guidelines for parameter estimation.
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38
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Fujii F, Kinjo M. Detection of antigen protein by using fluorescence cross-correlation spectroscopy and quantum-dot-labeled antibodies. Chembiochem 2008; 8:2199-203. [PMID: 18033717 DOI: 10.1002/cbic.200700399] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fumihiko Fujii
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
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39
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Briddon SJ, Hill SJ. Pharmacology under the microscope: the use of fluorescence correlation spectroscopy to determine the properties of ligand-receptor complexes. Trends Pharmacol Sci 2007; 28:637-45. [PMID: 18001848 PMCID: PMC2148440 DOI: 10.1016/j.tips.2007.09.008] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 09/05/2007] [Accepted: 09/07/2007] [Indexed: 02/04/2023]
Abstract
Recent years have revealed a high degree of structural organisation in the way in which cell-surface receptors and their associated signalling complexes interact at a molecular level. Fluorescence-based techniques have been at the forefront of methodologies used to investigate this organisation and dissect the pharmacology of drug–receptor interactions at the single-cell level. One such technique, fluorescence correlation spectroscopy (FCS), in conjunction with a fluorescent ligand or receptor, is capable of providing quantitative information about the number of receptors and their mobilities within small areas of the cell membrane that approach the size of some signalling domains. This article describes the use of FCS to perform subcellular quantitative pharmacology, with particular reference to G-protein-coupled receptors (GPCRs). In conjunction with other forms of fluctuation analysis, such as two-colour cross-correlation FCS and molecular brightness analysis, FCS provides the first opportunity to investigate the domain-specific nature of GPCR pharmacology.
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40
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Bacia K, Schwille P. Practical guidelines for dual-color fluorescence cross-correlation spectroscopy. Nat Protoc 2007; 2:2842-56. [DOI: 10.1038/nprot.2007.410] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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41
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Fujii F, Horiuchi M, Ueno M, Sakata H, Nagao I, Tamura M, Kinjo M. Detection of prion protein immune complex for bovine spongiform encephalopathy diagnosis using fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy. Anal Biochem 2007; 370:131-41. [PMID: 17825783 DOI: 10.1016/j.ab.2007.07.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 07/03/2007] [Accepted: 07/06/2007] [Indexed: 11/20/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) and fluorescence cross-correlation spectroscopy (FCCS) are powerful techniques to measure molecular interactions with high sensitivity in homogeneous solution and living cells. In this study, we developed methods for the detection of prion protein (PrP) using FCS and FCCS. A combination of a fluorescent-labeled Fab' fragment and another anti-PrP monoclonal antibody (mAb) enabled us to detect recombinant bovine PrP (rBoPrP) using FCS because there was a significant difference in the diffusion coefficients between the labeled Fab' fragment and the trimeric immune complex consisting of rBoPrP, labeled Fab' fragment, and another anti-PrP mAb. On the other hand, FCCS detected rBoPrP using two mAbs labeled with different fluorescence dyes. The detection limit for PrP in FCCS was approximately threefold higher than that in FCS. The sensitivity of FCCS in detection of abnormal isoform of PrP (PrP(Sc)) was comparable to that of enzyme-linked immunosorbent assay (ELISA). Because FCS and FCCS detect the PrP immune complex in homogeneous solution of only microliter samples with a single mixing step and without any washing steps, these features of measurement may facilitate automating bovine spongiform encephalopathy diagnosis.
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Affiliation(s)
- Fumihiko Fujii
- Laboratory of Supramolecular Biophysics, Research Institute of Electronic Science, Hokkaido University, Sapporo 060-0818, Japan
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42
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Haustein E, Schwille P. Fluorescence correlation spectroscopy: novel variations of an established technique. ACTA ACUST UNITED AC 2007; 36:151-69. [PMID: 17477838 DOI: 10.1146/annurev.biophys.36.040306.132612] [Citation(s) in RCA: 372] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is one of the major biophysical techniques used for unraveling molecular interactions in vitro and in vivo. It allows minimally invasive study of dynamic processes in biological specimens with extremely high temporal and spatial resolution. By recording and correlating the fluorescence fluctuations of single labeled molecules through the exciting laser beam, FCS gives information on molecular mobility and photophysical and photochemical reactions. By using dual-color fluorescence cross-correlation, highly specific binding studies can be performed. These have been extended to four reaction partners accessible by multicolor applications. Alternative detection schemes shift accessible time frames to slower processes (e.g., scanning FCS) or higher concentrations (e.g., TIR-FCS). Despite its long tradition, FCS is by no means dated. Rather, it has proven to be a highly versatile technique that can easily be adapted to solve specific biological questions, and it continues to find exciting applications in biology and medicine.
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Affiliation(s)
- Elke Haustein
- BioTec TU Dresden, Institute for Biophysics, D-01307 Dresden, Germany.
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43
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Zhang L, Hong L, Yu Y, Bae SC, Granick S. Nanoparticle-assisted surface immobilization of phospholipid liposomes. J Am Chem Soc 2007; 128:9026-7. [PMID: 16834363 DOI: 10.1021/ja062620r] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phospholipid liposomes (100-200 nm diameter) are deposited onto solid substrates after stabilizing them against fusion with the solid by allowing charged nanoparticles to adsorb at approximately 25% surface coverage. The immobilized vesicles remain stable over a period of days. Epifluorescence imaging shows that they diffuse freely over surfaces with the same charge but adsorb tightly onto surfaces with opposite charge. Nanoparticle adsorption to surface patterns of opposite charge provides a facile method to create large-scale surface-supported arrays of intact liposomes. This surface attachment method is simple chemically and applies generally for solid surfaces that can be hydrophobic or hydrophilic. Offering routes to localize proteins and other vesicle-contained objects at surfaces in tailored spatial patterns, these immobilized liposome arrays may find diverse applications in the emerging field of nanobiotechnology.
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Affiliation(s)
- Liangfang Zhang
- Department of Chemical Engineering, University of Illinois, Urbana, Illinois 61801, USA
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44
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Hwang LC, Wohland T. Recent Advances in Fluorescence Cross-correlation Spectroscopy. Cell Biochem Biophys 2007; 49:1-13. [PMID: 17873335 DOI: 10.1007/s12013-007-0042-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Revised: 11/30/1999] [Accepted: 05/21/2007] [Indexed: 12/14/2022]
Abstract
Fluorescence cross-correlation spectroscopy (FCCS) is a method that measures the temporal fluorescence fluctuations coming from two differently labeled molecules diffusing through a small sample volume. Cross-correlation analysis of the fluorescence signals from separate detection channels extracts information of the dynamics of the dual-labeled molecules. FCCS has become an essential tool for the characterization of diffusion coefficients, binding constants, kinetic rates of binding, and determining molecular interactions in solutions and cells. By cross-correlating between two focal spots, flow properties could also be measured. Recent developments in FCCS have been targeted at using different experimental schemes to improve on the sensitivity and address their limitations such as cross-talk and alignment issues. This review presents an overview of the different excitation and detection methodologies used in FCCS and their biological applications. This is followed by a description of the fluorescent probes currently available for the different methods. This will introduce biological readers to FCCS and its related techniques and provide a starting point to selecting which experimental scheme is suitable for their type of biological study.
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Affiliation(s)
- Ling Chin Hwang
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore.
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45
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Keese M, Offterdinger M, Tischer C, Girod A, Lommerse PHM, Yagublu V, Magdeburg R, Bastiaens PIH. Quantitative imaging of apoptosis commitment in colorectal tumor cells. Differentiation 2007; 75:809-18. [PMID: 17511782 DOI: 10.1111/j.1432-0436.2007.00186.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We have studied caspase-3 activation by combined DNA damage induction and EGFR kinase inhibition in order to identify potential EGFR-mediated survival signals conferring resistance to apoptosis in human colorectal tumor cells. The onset of apoptosis was microscopically imaged with a newly developed caspase-3 substrate sensor based on EGFP and tHcred1, enabling us to monitor caspase-3 activation in cells by fluorescence lifetime imaging microscopy or fluorescence correlation spectroscopy. Both optical approaches provide parameters quantitatively reporting the ratio between cleaved and uncleaved sensor, thereby facilitating the comparison of caspase-3 activation between different cells. Using these methods, we show that EGFR kinase inhibitors sensitize colorectal SW-480 tumor cells for 5-fluorouracil-induced apoptosis, indicating that EGFR-mediated survival signaling contributes to apoptosis resistance via its intrinsic kinase activity.
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Affiliation(s)
- Michael Keese
- Chirurgische Klinik, Universitätsklinikum Mannheim, Mannheim, Germany
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46
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Abstract
Fluorescence correlation spectroscopy (FCS) is a technique that allows for an extremely sensitive determination of molecular diffusion properties, down to the level of single molecules. It thus provides an attractive alternative to FRAP, requiring much less laser power and lower concentrations of fluorophores. FCS has recently been applied on live cells, and in comparison on domain-forming model membrane systems, to systematically study the influence of cholesterol on local membrane structure by investigating the mobility of selected lipid probes. The findings demonstrate the ability of FCS to sensitively distinguish between different local lipid structures, and emphasize the value of model systems for understanding membrane dynamics in general.
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Affiliation(s)
- Kirsten Bacia
- Institute of Biophysics, Dresden University of Technology, Germany
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47
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Abstract
BACKGROUND The "inverse" problem is related to the determination of unknown causes on the bases of the observation of their effects. This is the opposite of the corresponding "direct" problem, which relates to the prediction of the effects generated by a complete description of some agencies. The solution of an inverse problem entails the construction of a mathematical model and takes the moves from a number of experimental data. In this respect, inverse problems are often ill-conditioned as the amount of experimental conditions available are often insufficient to unambiguously solve the mathematical model. Several approaches to solving inverse problems are possible, both computational and experimental, some of which are mentioned in this article. In this work, we will describe in details the attempt to solve an inverse problem which arose in the study of an intracellular signaling pathway. RESULTS Using the Genetic Algorithm to find the sub-optimal solution to the optimization problem, we have estimated a set of unknown parameters describing a kinetic model of a signaling pathway in the neuronal cell. The model is composed of mass action ordinary differential equations, where the kinetic parameters describe protein-protein interactions, protein synthesis and degradation. The algorithm has been implemented on a parallel platform. Several potential solutions of the problem have been computed, each solution being a set of model parameters. A sub-set of parameters has been selected on the basis on their small coefficient of variation across the ensemble of solutions. CONCLUSION Despite the lack of sufficiently reliable and homogeneous experimental data, the genetic algorithm approach has allowed to estimate the approximate value of a number of model parameters in a kinetic model of a signaling pathway: these parameters have been assessed to be relevant for the reproduction of the available experimental data.
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Affiliation(s)
- Ivan Arisi
- European Brain Research Institute, Via Fosso del Fiorano 64, Roma, Italy
| | - Antonino Cattaneo
- European Brain Research Institute, Via Fosso del Fiorano 64, Roma, Italy
- Lay Line Genomics SpA, S.Raffaele Science Park, Castel Romano, Italy
- International School of Advanced Studies (SISSA/ISAS), Biophysics Dept., Via Beirut 2-4, Trieste, Italy
| | - Vittorio Rosato
- ENEA, Casaccia Research Center, Computing and Modelling Unit, Via Anguillarese 301, S.Maria di Galeria, Italy
- Ylichron Srl, c/o ENEA, Casaccia Research Center, Via Anguillarese 301, S.Maria di Galeria, Italy
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48
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Fletcher KA, Fakayode SO, Lowry M, Tucker SA, Neal SL, Kimaru IW, McCarroll ME, Patonay G, Oldham PB, Rusin O, Strongin RM, Warner IM. Molecular fluorescence, phosphorescence, and chemiluminescence spectrometry. Anal Chem 2006; 78:4047-68. [PMID: 16771540 PMCID: PMC2662353 DOI: 10.1021/ac060683m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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49
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Kogure T, Karasawa S, Araki T, Saito K, Kinjo M, Miyawaki A. A fluorescent variant of a protein from the stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy. Nat Biotechnol 2006; 24:577-81. [PMID: 16648840 DOI: 10.1038/nbt1207] [Citation(s) in RCA: 231] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Accepted: 03/29/2006] [Indexed: 11/09/2022]
Abstract
Dual-color fluorescence cross-correlation spectroscopy (FCCS) is a promising technique for quantifying protein-protein interactions. In this technique, two different fluorescent labels are excited and detected simultaneously within a common measurement volume. Difficulties in aligning two laser lines and emission crossover between the two fluorophores, however, make this technique complex. To overcome these limitations, we developed a fluorescent protein with a large Stokes shift. This protein, named Keima, absorbs and emits light maximally at 440 nm and 620 nm, respectively. Combining a monomeric version of Keima with cyan fluorescent protein allowed dual-color FCCS with a single 458-nm laser line and complete separation of the fluorescent protein emissions. This FCCS approach enabled sensitive detection of proteolysis by caspase-3 and the association of calmodulin with calmodulin-dependent enzymes. In addition, Keima and a spectral variant that emits maximally at 570 nm might facilitate simultaneous multicolor imaging with single-wavelength excitation.
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Affiliation(s)
- Takako Kogure
- Laboratory for Cell Function and Dynamics, Advanced Technology Development Group, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama, 351-0198, Japan
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50
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Abstract
Cell biologists strive to characterize molecular interactions directly in the intracellular environment. The intrinsic resolution of optical microscopy, however, allows visualization of only coarse subcellular localization. By extracting information from molecular dynamics, fluorescence cross-correlation spectroscopy (FCCS) grants access to processes on a molecular scale, such as diffusion, binding, enzymatic reactions and codiffusion, and has become a valuable tool for studies in living cells. Here we review basic principles of FCCS and focus on seminal applications, including examples of intracellular signaling and trafficking. We consider FCCS in the context of fluorescence resonance energy transfer and multicolor imaging techniques and discuss application strategies and recent technical advances.
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Affiliation(s)
- Kirsten Bacia
- Institute of Biophysics, Dresden University of Technology, Tatzberg 47-51, D-01307 Dresden, Germany
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