351
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Paddock SW, Eliceiri KW. Laser scanning confocal microscopy: history, applications, and related optical sectioning techniques. Methods Mol Biol 2014; 1075:9-47. [PMID: 24052346 DOI: 10.1007/978-1-60761-847-8_2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Confocal microscopy is an established light microscopical technique for imaging fluorescently labeled specimens with significant three-dimensional structure. Applications of confocal microscopy in the biomedical sciences include the imaging of the spatial distribution of macromolecules in either fixed or living cells, the automated collection of 3D data, the imaging of multiple labeled specimens and the measurement of physiological events in living cells. The laser scanning confocal microscope continues to be chosen for most routine work although a number of instruments have been developed for more specific applications. Significant improvements have been made to all areas of the confocal approach, not only to the instruments themselves, but also to the protocols of specimen preparation, to the analysis, the display, the reproduction, sharing and management of confocal images using bioinformatics techniques.
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Affiliation(s)
- Stephen W Paddock
- Howard Hughes Medical Institute, Department of Molecular Biology, University of Wisconsin, Madison, WI, USA
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352
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Szmacinski H, Toshchakov V, Lakowicz JR. Application of phasor plot and autofluorescence correction for study of heterogeneous cell population. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:046017. [PMID: 24770662 PMCID: PMC4000004 DOI: 10.1117/1.jbo.19.4.046017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 03/09/2014] [Accepted: 03/25/2014] [Indexed: 05/22/2023]
Abstract
Protein-protein interactions in cells are often studied using fluorescence resonance energy transfer (FRET) phenomenon by fluorescence lifetime imaging microscopy (FLIM). Here, we demonstrate approaches to the quantitative analysis of FRET in cell population in a case complicated by a highly heterogeneous donor expression, multiexponential donor lifetime, large contribution of cell autofluorescence, and significant presence of unquenched donor molecules that do not interact with the acceptor due to low affinity of donor-acceptor binding. We applied a multifrequency phasor plot to visualize FRET FLIM data, developed a method for lifetime background correction, and performed a detailed time-resolved analysis using a biexponential model. These approaches were applied to study the interaction between the Toll Interleukin-1 receptor (TIR) domain of Toll-like receptor 4 (TLR4) and the decoy peptide 4BB. TLR4 was fused to Cerulean fluorescent protein (Cer) and 4BB peptide was labeled with Bodipy TMRX (BTX). Phasor displays for multifrequency FLIM data are presented. The analytical procedure for lifetime background correction is described and the effect of correction on FLIM data is demonstrated. The absolute FRET efficiency was determined based on the phasor plot display and multifrequency FLIM data analysis. The binding affinity between TLR4-Cer (donor) and decoy peptide 4BB-BTX (acceptor) was estimated in a heterogeneous HeLa cell population.
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Affiliation(s)
- Henryk Szmacinski
- University of Maryland School of Medicine, Department of Biochemistry and Molecular Biology, Baltimore, Maryland 21201
- Address all correspondence to: Henryk Szmacinski, E-mail:
| | - Vladimir Toshchakov
- University of Maryland School of Medicine, Department of Microbiology and Immunology, Baltimore, Maryland 21201
| | - Joseph R. Lakowicz
- University of Maryland School of Medicine, Department of Biochemistry and Molecular Biology, Baltimore, Maryland 21201
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353
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Liu Y, Liu Q, Yan Q, Shi L, Fang Y. Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model. Mol Biol Cell 2014; 25:1366-73. [PMID: 24554768 PMCID: PMC3983000 DOI: 10.1091/mbc.e13-09-0527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/27/2014] [Accepted: 02/13/2014] [Indexed: 01/08/2023] Open
Abstract
Protein-protein interactions play essential roles in regulating many biological processes. At the cellular level, many proteins form nuclear foci known as nuclear bodies in which many components interact with each other. Photobodies are nuclear bodies containing proteins for light-signaling pathways in plants. What initiates the formation of photobodies is poorly understood. Here we develop a nucleolar marker protein nucleolin2 (Nuc2)-based method called the nucleolus-tethering system (NoTS) by artificially tethering a protein of interest to the nucleolus to analyze the initiation of photobodies. A candidate initiator is evaluated by visualizing whether a protein fused with Nuc2 forms body-like structures at the periphery of the nucleolus, and other components are recruited to the de novo-formed bodies. The interaction between two proteins can also be revealed through relocation and recruitment of interacting proteins to the nucleolus. Using the NoTS, we test the interactions among components in photobodies. In addition, we demonstrate that components of photobodies such as CONSTITUTIVELY PHOTOMORPHOGENIC 1, photoreceptors, and transcription factors tethered to the nucleolus have the capacity to form body-like structures at the periphery of the nucleolus, which contain other components of photobodies, suggesting a self-organization model for the biogenesis of photobodies.
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Affiliation(s)
- Yin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingqing Yan
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Leilei Shi
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuda Fang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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354
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Baird L, Swift S, Llères D, Dinkova-Kostova AT. Monitoring Keap1-Nrf2 interactions in single live cells. Biotechnol Adv 2014; 32:1133-44. [PMID: 24681086 PMCID: PMC4165437 DOI: 10.1016/j.biotechadv.2014.03.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/10/2014] [Accepted: 03/10/2014] [Indexed: 12/30/2022]
Abstract
The transcription factor NF-E2 p45-related factor 2 (Nrf2) and its negative regulator Kelch-like ECH associated protein 1 (Keap1) control the expression of nearly 500 genes with diverse cytoprotective functions. Keap1, a substrate adaptor protein for Cullin3/Rbx1 ubiquitin ligase, normally continuously targets Nrf2 for degradation, but loses this ability in response to electrophiles and oxidants (termed inducers). Consequently, Nrf2 accumulates and activates transcription of its downstream target genes. Many inducers are phytochemicals, and cruciferous vegetables represent one of the richest sources of inducer activity among the most commonly used edible plants. Here we summarize the discovery of the isothiocyanate sulforaphane as a potent inducer which reacts with cysteine sensors of Keap1, leading to activation of Nrf2. We then describe the development of a quantitative Förster resonance energy transfer (FRET)-based methodology combined with multiphoton fluorescence lifetime imaging microscopy (FLIM) to investigate the interactions between Keap1 and Nrf2 in single live cells, and the effect of sulforaphane, and other cysteine-reactive inducers, on the dynamics of the Keap1–Nrf2 protein complex. We present the experimental evidence for the “cyclic sequential attachment and regeneration” or “conformation cycling” model of Keap1-mediated Nrf2 degradation. Finally, we discuss the implications of this mode of regulation of Nrf2 for achieving a fine balance under normal physiological conditions, and the consequences and mechanisms of disrupting this balance for tumor biology.
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Affiliation(s)
- Liam Baird
- Jacqui Wood Cancer Centre, Division of Cancer Research, Medical Research Institute, University of Dundee, Dundee DD1 9SY Scotland, UK
| | - Sam Swift
- Microscopy Facility, College of Life Sciences, University of Dundee, Dundee DD1 5EH Scotland, UK
| | - David Llères
- Institute of Molecular Genetics of Montpellier, 34293 Montpellier Cedex 5, France
| | - Albena T Dinkova-Kostova
- Jacqui Wood Cancer Centre, Division of Cancer Research, Medical Research Institute, University of Dundee, Dundee DD1 9SY Scotland, UK; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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355
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Saleh AA, Bhadra AK, Roy I. Cytotoxicity of mutant huntingtin fragment in yeast can be modulated by the expression level of wild type huntingtin fragment. ACS Chem Neurosci 2014; 5:205-15. [PMID: 24377263 PMCID: PMC3963126 DOI: 10.1021/cn400171d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/26/2013] [Indexed: 12/23/2022] Open
Abstract
Conflicting reports exist in the literature regarding the role of wild-type huntingtin in determining the toxicity of the aggregated, mutant huntingtin in Huntington's disease (HD). Some studies report the amelioration of toxicity of the mutant protein in the presence of the wild-type protein, while others indicate sequestration of the wild-type protein by mutant huntingtin. Over the years, yeast has been established as a valid model organism to study molecular changes associated with HD, especially at the protein level. We have used an inducible system to express human huntingtin fragments harboring normal (25Q) and pathogenic (103Q) polyglutamine lengths under the control of a galactose promoter in a yeast model of HD. We show that the relative expression level of each allele (wild-type/mutant) decides the cellular phenotype. When the expression level of wild-type huntingtin is high, an increase in the solubility of the mutant protein is observed. Fluorescence-recovery-after-photobleaching (FRAP) studies show that solubility reaches ∼94% in these cells. This leads to reduction in oxidative stress and cytotoxicity, and increases cell viability. In-cell FRET studies show that interaction between these proteins does not require the presence of a mediator. When the expression of wild-type huntingtin is low, it is sequestered into aggregates by the mutant protein. Even under these conditions, cytotoxicity is attenuated. Our findings indicate that the presence of wild-type huntingtin has a beneficial role even when its relative expression level is lower than that of the mutant protein.
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Affiliation(s)
- Aliabbas Ahmedbhai Saleh
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ankan Kumar Bhadra
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
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356
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Vogel SS, van der Meer BW, Blank PS. Estimating the distance separating fluorescent protein FRET pairs. Methods 2014; 66:131-8. [PMID: 23811334 PMCID: PMC3964137 DOI: 10.1016/j.ymeth.2013.06.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/11/2013] [Accepted: 06/18/2013] [Indexed: 11/17/2022] Open
Abstract
Förster resonance energy transfer (FRET) describes a physical phenomenon widely applied in biomedical research to estimate separations between biological molecules. Routinely, genetic engineering is used to incorporate spectral variants of the green fluorescent protein (GFPs), into cellular expressed proteins. The transfer efficiency or rate of energy transfer between donor and acceptor FPs is then assayed. As appreciable FRET occurs only when donors and acceptors are in close proximity (1-10nm), the presence of FRET may indicate that the engineered proteins associate as interacting species. For a homogeneous population of FRET pairs the separations between FRET donors and acceptors can be estimated from a measured FRET efficiency if it is assumed that donors and acceptors are randomly oriented and rotate extensively during their excited state (dynamic regime). Unlike typical organic fluorophores, the rotational correlation-times of FPs are typically much longer than their fluorescence lifetime; accordingly FPs are virtually static during their excited state. Thus, estimating separations between FP FRET pairs is problematic. To overcome this obstacle, we present here a simple method for estimating separations between FPs using the experimentally measured average FRET efficiency. This approach assumes that donor and acceptor fluorophores are randomly oriented, but do not rotate during their excited state (static regime). This approach utilizes a Monte-Carlo simulation generated look-up table that allows one to estimate the separation, normalized to the Förster distance, from the average FRET efficiency. Assuming a dynamic regime overestimates the separation significantly (by 10% near 0.5 and 30% near 0.75 efficiencies) compared to assuming a static regime, which is more appropriate for estimates of separations between FPs.
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Affiliation(s)
- Steven S Vogel
- Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 5625 Fishers Lane, Room TS-06F: MSC 9411, Bethesda, MD 20892-9413, USA.
| | - B Wieb van der Meer
- Department of Physics and Astronomy, Western Kentucky University, 1906 College Heights Blvd. #11077, Bowling Green, KY 42101-1077, USA
| | - Paul S Blank
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Dr, Room 10D14: MSC 1855, Bethesda, MD 20892-1855, USA
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357
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Kraft LJ, Nguyen TA, Vogel SS, Kenworthy AK. Size, stoichiometry, and organization of soluble LC3-associated complexes. Autophagy 2014; 10:861-77. [PMID: 24646892 PMCID: PMC4768459 DOI: 10.4161/auto.28175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MAP1LC3B, an ortholog of yeast Atg8 and a member of the family of proteins formerly also known as ATG8 in mammals (LC3B henceforth in the text), functions in autophagosome formation and autophagy substrate recruitment. LC3 exists in both a soluble (autophagosome-independent) form as well as a lipid modified form that becomes tightly incorporated into autophagosomal membranes. Although LC3 is known to associate with tens of proteins, relatively little is known about soluble LC3 aside from its interactions with the LC3 lipid conjugation machinery. In previous studies we found autophagosome-independent GFP-LC3B diffuses unusually slowly for a protein of its size, suggesting it may constitutively associate with a high molecular weight complex, form homo-oligomers or aggregates, or reversibly bind microtubules or membranes. To distinguish between these possibilities, we characterized the size, stoichiometry, and organization of autophagosome-independent LC3B in living cells and in cytoplasmic extracts using fluorescence recovery after photobleaching (FRAP) and fluorescence polarization fluctuation analysis (FPFA). We found that the diffusion of LC3B was unaffected by either mutational disruption of its lipid modification or microtubule depolymerization. Brightness and homo-FRET analysis indicate LC3B does not homo-oligomerize. However, mutation of specific residues on LC3B required for binding other proteins and mRNA altered the effective hydrodynamic radius of the protein as well as its stoichiometry. We conclude that when not bound to autophagosomes, LC3B associates with a multicomponent complex with an effective size of ~500 kDa in the cytoplasm. These findings provide new insights into the nature of soluble LC3B and illustrate the power of FRAP and FPFA to investigate the emergent properties of protein complexes in the autophagy pathway.
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Affiliation(s)
- Lewis J Kraft
- Chemical and Physical Biology Program; Department of Molecular Physiology and Biophysics; Department of Cell and Developmental Biology; Vanderbilt University Medical Center; Nashville, TN USA
| | - Tuan A Nguyen
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology; National Institute on Alcohol Abuse and Alcoholism; National Institutes of Health; Rockville, MD USA
| | - Steven S Vogel
- Section on Cellular Biophotonics, Laboratory of Molecular Physiology; National Institute on Alcohol Abuse and Alcoholism; National Institutes of Health; Rockville, MD USA
| | - Anne K Kenworthy
- Chemical and Physical Biology Program; Department of Molecular Physiology and Biophysics; Department of Cell and Developmental Biology; Vanderbilt University Medical Center; Nashville, TN USA
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358
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Petersson EJ, Goldberg JM, Wissner RF. On the use of thioamides as fluorescence quenching probes for tracking protein folding and stability. Phys Chem Chem Phys 2014; 16:6827-37. [PMID: 24598971 DOI: 10.1039/c3cp55525a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our laboratory has developed thioamide analogs of the natural amino acids as minimally-perturbing fluorescence quenching probes that can be placed at many locations in a protein sequence. We have shown that the mechanism of quenching can be either Förster resonance energy transfer (FRET) or photoinduced electron transfer (PET), depending on the identity of the donor fluorophore. Furthermore, we have shown that one can use a combination of semi-synthetic methods to label full-sized proteins with fluorophore-thioamide pairs. These probes can be used to study protein-protein interactions, protein folding or misfolding, and proteolysis.
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Affiliation(s)
- E James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA.
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359
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Algar WR, Kim H, Medintz IL, Hildebrandt N. Emerging non-traditional Förster resonance energy transfer configurations with semiconductor quantum dots: Investigations and applications. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2013.07.015] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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360
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Abstract
The use of fluorescent proteins (FPs) in modern cell biology and microscopy has had an extraordinary impact on our ability to investigate dynamic processes in living cells. FPs are unique in that fluorescence is encoded solely by the primary amino acid sequence of the FP and does not require enzymatic modification or cofactors. This genetically encoded fluorescence enables the expression of FPs in diverse cells and organisms and the detection of that fluorescence in living systems. This chapter focuses on microscopy-based applications of FP detection to monitor protein localization, dynamics, interaction, and the cellular environment.
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361
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Rajendran M, Yapici E, Miller LW. Lanthanide-based imaging of protein-protein interactions in live cells. Inorg Chem 2014; 53:1839-53. [PMID: 24144069 PMCID: PMC3944735 DOI: 10.1021/ic4018739] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In order to deduce the molecular mechanisms of biological function, it is necessary to monitor changes in the subcellular location, activation, and interaction of proteins within living cells in real time. Förster resonance energy-transfer (FRET)-based biosensors that incorporate genetically encoded, fluorescent proteins permit high spatial resolution imaging of protein-protein interactions or protein conformational dynamics. However, a nonspecific fluorescence background often obscures small FRET signal changes, and intensity-based biosensor measurements require careful interpretation and several control experiments. These problems can be overcome by using lanthanide [Tb(III) or Eu(III)] complexes as donors and green fluorescent protein (GFP) or other conventional fluorophores as acceptors. Essential features of this approach are the long-lifetime (approximately milliseconds) luminescence of Tb(III) complexes and time-gated luminescence microscopy. This allows pulsed excitation, followed by a brief delay, which eliminates nonspecific fluorescence before the detection of Tb(III)-to-GFP emission. The challenges of intracellular delivery, selective protein labeling, and time-gated imaging of lanthanide luminescence are presented, and recent efforts to investigate the cellular uptake of lanthanide probes are reviewed. Data are presented showing that conjugation to arginine-rich, cell-penetrating peptides (CPPs) can be used as a general strategy for the cellular delivery of membrane-impermeable lanthanide complexes. A heterodimer of a luminescent Tb(III) complex, Lumi4, linked to trimethoprim and conjugated to nonaarginine via a reducible disulfide linker rapidly (∼10 min) translocates into the cytoplasm of Maden Darby canine kidney cells from the culture medium. With this reagent, the intracellular interaction between GFP fused to FK506 binding protein 12 (GFP-FKBP12) and the rapamycin binding domain of mTOR fused to Escherichia coli dihydrofolate reductase (FRB-eDHFR) were imaged at high signal-to-noise ratio with fast (1-3 s) image acquisition using a time-gated luminescence microscope. The data reviewed and presented here show that lanthanide biosensors enable fast, sensitive, and technically simple imaging of protein-protein interactions in live cells.
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Affiliation(s)
- Megha Rajendran
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607
| | - Engin Yapici
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607
| | - Lawrence W. Miller
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607
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362
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Adam V. Phototransformable fluorescent proteins: which one for which application? Histochem Cell Biol 2014; 142:19-41. [PMID: 24522394 DOI: 10.1007/s00418-014-1190-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2014] [Indexed: 01/10/2023]
Abstract
In these last two decades , fluorescent proteins (FPs) have become highly valued imaging tools for cell biology, owing to their compatibility with living samples, their low levels of invasiveness and the possibility to specifically fuse them to a variety of proteins of interest. Remarkably, the recent development of phototransformable fluorescent proteins (PTFPs) has made it possible to conceive optical imaging experiments that were unimaginable only a few years ago. For example, it is nowadays possible to monitor intra- or intercellular trafficking, to optically individualize single cells in tissues or to observe single molecules in live cells. The tagging specificity brought by these genetically encoded highlighters leads to constant progress in the engineering of increasingly powerful, versatile and non-cytotoxic FPs. This review is focused on the recent developments of PTFPs and highlights their contribution to studies within cells, tissues and even living organisms. The aspects of single-molecule localization microscopy, intracellular tracking of photoactivated molecules, applications of PTFPs in biotechnology/optobiology and complementarities between PTFPs and other microscopy techniques are particularly discussed.
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Affiliation(s)
- Virgile Adam
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, F-38000, Grenoble, France,
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363
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Mehrotra N, Nichols J, Ramachandran R. Alternate pleckstrin homology domain orientations regulate dynamin-catalyzed membrane fission. Mol Biol Cell 2014; 25:879-90. [PMID: 24478459 PMCID: PMC3952856 DOI: 10.1091/mbc.e13-09-0548] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The isolated dynamin PH domain is an assembly-independent sensor of membrane curvature but not a curvature generator. In full-length dynamin, the PH alternates between two different orientations on the membrane surface during the GTP hydrolysis cycle, causing dramatic fluctuations in the diameter of dynamin polymers. The self-assembling GTPase dynamin catalyzes endocytic vesicle scission via membrane insertion of its pleckstrin homology (PH) domain. However, the molecular mechanisms underlying PH domain–dependent membrane fission remain obscure. Membrane-curvature–sensing and membrane-curvature–generating properties have been attributed, but it remains to be seen whether the PH domain is involved in either process independent of dynamin self-assembly. Here, using multiple fluorescence spectroscopic and microscopic techniques, we demonstrate that the isolated PH domain does not act to bend membranes but instead senses high membrane curvature through hydrophobic insertion into the membrane bilayer. Furthermore, we use a complementary set of short- and long-distance Förster resonance energy transfer approaches to distinguish PH-domain orientation from proximity at the membrane surface in full-length dynamin. We reveal, in addition to the GTP-sensitive “hydrophobic mode,” the presence of an alternate, GTP-insensitive “electrostatic mode” of PH domain–membrane interactions that retains dynamin on the membrane surface during the GTP hydrolysis cycle. Stabilization of this alternate orientation produces dramatic variations in the morphology of membrane-bound dynamin spirals, indicating that the PH domain regulates membrane fission through the control of dynamin polymer dynamics.
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Affiliation(s)
- Niharika Mehrotra
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH 44106
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364
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Yurlova L, Derks M, Buchfellner A, Hickson I, Janssen M, Morrison D, Stansfield I, Brown CJ, Ghadessy FJ, Lane DP, Rothbauer U, Zolghadr K, Krausz E. The fluorescent two-hybrid assay to screen for protein-protein interaction inhibitors in live cells: targeting the interaction of p53 with Mdm2 and Mdm4. ACTA ACUST UNITED AC 2014; 19:516-25. [PMID: 24476585 DOI: 10.1177/1087057113518067] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Protein-protein interactions (PPIs) are attractive but challenging targets for drug discovery. To overcome numerous limitations of the currently available cell-based PPI assays, we have recently established a fully reversible microscopy-assisted fluorescent two-hybrid (F2H) assay. The F2H assay offers a fast and straightforward readout: an interaction-dependent co-localization of two distinguishable fluorescent signals at a defined spot in the nucleus of mammalian cells. We developed two reversible F2H assays for the interactions between the tumor suppressor p53 and its negative regulators, Mdm2 and Mdm4. We then performed a pilot F2H screen with a subset of compounds, including small molecules (such as Nutlin-3) and stapled peptides. We identified five cell-penetrating compounds as potent p53-Mdm2 inhibitors. However, none exhibited intracellular activity on p53-Mdm4. Live cell data generated by the F2H assays enable the characterization of stapled peptides based on their ability to penetrate cells and disrupt p53-Mdm2 interaction as well as p53-Mdm4 interaction. Here, we show that the F2H assays enable side-by-side analysis of substances' dual Mdm2-Mdm4 activity. In addition, they are suitable for testing various types of compounds (e.g., small molecules and peptidic inhibitors) and concurrently provide initial data on cellular toxicity. Furthermore, F2H assays readily allow real-time visualization of PPI dynamics in living cells.
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365
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Legartová S, Stixová L, Laur O, Kozubek S, Sehnalová P, Bártová E. Nuclear Structures Surrounding Internal Lamin Invaginations. J Cell Biochem 2014; 115:476-87. [DOI: 10.1002/jcb.24681] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/23/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Soňa Legartová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Lenka Stixová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Oskar Laur
- Emory University School of Medicine; Emory University; Atlanta Georgia 30322
| | - Stanislav Kozubek
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
| | - Eva Bártová
- Institute of Biophysics; Academy of Sciences of the Czech Republic; 612 65 Brno Czech Republic
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366
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Voss S, Zhao L, Chen X, Gerhard F, Wu YW. Generation of an intramolecular three-color fluorescence resonance energy transfer probe by site-specific protein labeling. J Pept Sci 2014; 20:115-20. [PMID: 24395760 DOI: 10.1002/psc.2590] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/20/2013] [Accepted: 10/24/2013] [Indexed: 12/23/2022]
Abstract
Fluorescence resonance energy transfer (FRET) is a valuable tool for studying protein structure, folding and interactions. The steep distance dependence of the FRET efficiency requires the donor and acceptor to be in close proximity (1-7.5 nm) to exhibit sufficient energy transfer. One possibility to overcome this limitation is the usage of a FRET cascade that utilizes more than one FRET pair. Essential for realizing this FRET cascade is the site-specific introduction of multiple fluorophores to a given protein, which remains a great challenge. In this study, orthogonal labeling techniques, including fluorescent protein tagging, oxime ligation and kinetically controlled cysteine conjugation, are employed to introduce three fluorophores at specific sites of Rab1b GTPase, yielding a triple-labeled FRET probe. The generated protein probe exhibits efficient energy transfer from the primary donor enhanced green fluorescent protein over the intermediate acceptor rhodamine to the final acceptor Dy630. The labeling strategy opens up a new avenue for multi-color labeling of proteins, facilitating long-distance FRET studies.
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Affiliation(s)
- Stephanie Voss
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Lei Zhao
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Xi Chen
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Frank Gerhard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Yao-Wen Wu
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227, Dortmund, Germany.,Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
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367
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Murayama T, Kobayashi T. Purification of recombinant proteins with a multifunctional GFP tag. Methods Mol Biol 2014; 1177:151-161. [PMID: 24943321 DOI: 10.1007/978-1-4939-1034-2_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Green fluorescent protein (GFP) is the most widespread fluorescent reporter for cellular localization and interaction of proteins. Because GFP itself is not the protein purification tag, protein purification is generally carried out with the aid of additional affinity tags. We have recently engineered a "multifunctional GFP" (mfGFP), a variant of enhanced GFP (EGFP), in which multiple affinity tags are inserted in tandem into an internal loop of EGFP. The mfGFP can be used as a fluorescent reporter and an affinity tag, and is compatible with various expression systems in prokaryotic and eukaryotic cells. Herein, we describe detailed procedures for the expression and purification of mfGFP fusion proteins in mammalian cells. A method for tandem affinity purification using two different tags within mfGFP is also described.
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Affiliation(s)
- Takashi Murayama
- Department of Cellular and Molecular Pharmacology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan,
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368
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In situ techniques for protein analysis in tumor tissue. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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369
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Kim SY, Lee MJ, Na YR, Kim SY, Yang EG. Visualization of Hypoxia-Inducible Factor 1α-p300 Interactions in Live Cells by Fluorescence Resonance Energy Transfer. J Cell Biochem 2013; 115:271-80. [DOI: 10.1002/jcb.24659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 08/14/2013] [Indexed: 11/09/2022]
Affiliation(s)
- So Yeon Kim
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology; Seoul 136-791 Republic of Korea
| | - Myong Jin Lee
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology; Seoul 136-791 Republic of Korea
| | - Yu-Ran Na
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology; Seoul 136-791 Republic of Korea
| | - Sang Yoon Kim
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology; Seoul 136-791 Republic of Korea
| | - Eun Gyeong Yang
- Center for Theragnosis, Biomedical Research Institute; Korea Institute of Science and Technology; Seoul 136-791 Republic of Korea
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370
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Speight LC, Muthusamy AK, Goldberg JM, Warner JB, Wissner RF, Willi TS, Woodman BF, Mehl RA, Petersson EJ. Efficient synthesis and in vivo incorporation of acridon-2-ylalanine, a fluorescent amino acid for lifetime and Förster resonance energy transfer/luminescence resonance energy transfer studies. J Am Chem Soc 2013; 135:18806-14. [PMID: 24303933 DOI: 10.1021/ja403247j] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein conformational change because it is a long lifetime, visible wavelength fluorophore that is small enough to be incorporated during ribosomal biosynthesis. Incorporation of Acd into proteins expressed in Escherichia coli requires efficient chemical synthesis to produce large quantities of the amino acid and the generation of a mutant aminoacyl tRNA synthetase that can selectively charge the amino acid onto a tRNA. Here, we report the synthesis of Acd in 87% yield over five steps from Tyr and the identification of an Acd synthetase by screening candidate enzymes previously evolved from Methanococcus janaschii Tyr synthetase for unnatural amino acid incorporation. Furthermore, we characterize the photophysical properties of Acd, including quenching interactions with select natural amino acids and Förster resonance energy transfer (FRET) interactions with common fluorophores such as methoxycoumarin (Mcm). Finally, we demonstrate the value of incorporation of Acd into proteins, using changes in Acd fluorescence lifetimes, Mcm/Acd FRET, or energy transfer to Eu(3+) to monitor protein folding and binding interactions.
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Affiliation(s)
- Lee C Speight
- University of Pennsylvania , Department of Chemistry, 231 South 34th Street, Philadelphia, Pennsylvania, 19104-6323, United States
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371
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Cole RW, Thibault M, Bayles CJ, Eason B, Girard AM, Jinadasa T, Opansky C, Schulz K, Brown CM. International test results for objective lens quality, resolution, spectral accuracy and spectral separation for confocal laser scanning microscopes. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:1653-1668. [PMID: 24103552 DOI: 10.1017/s1431927613013470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As part of an ongoing effort to increase image reproducibility and fidelity in addition to improving cross-instrument consistency, we have proposed using four separate instrument quality tests to augment the ones we have previously reported. These four tests assessed the following areas: (1) objective lens quality, (2) resolution, (3) accuracy of the wavelength information from spectral detectors, and (4) the accuracy and quality of spectral separation algorithms. Data were received from 55 laboratories located in 18 countries. The largest source of errors across all tests was user error which could be subdivided between failure to follow provided protocols and improper use of the microscope. This truly emphasizes the importance of proper rigorous training and diligence in performing confocal microscopy experiments and equipment evaluations. It should be noted that there was no discernible difference in quality between confocal microscope manufactures. These tests, as well as others previously reported, will help assess the quality of confocal microscopy equipment and will provide a means to track equipment performance over time. From 62 to 97% of the data sets sent in passed the various tests demonstrating the usefulness and appropriateness of these tests as part of a larger performance testing regiment.
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Affiliation(s)
- Richard W Cole
- New York State Department of Health, Wadsworth Center, P.O. Box 509, Albany, NY 12201, USA
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372
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Espenel C, Acharya BR, Kreitzer G. A biosensor of local kinesin activity reveals roles of PKC and EB1 in KIF17 activation. ACTA ACUST UNITED AC 2013; 203:445-55. [PMID: 24189273 PMCID: PMC3824023 DOI: 10.1083/jcb.201305023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We showed previously that the kinesin-2 motor KIF17 regulates microtubule (MT) dynamics and organization to promote epithelial differentiation. How KIF17 activity is regulated during this process remains unclear. Several kinesins, including KIF17, adopt compact and extended conformations that reflect autoinhibited and active states, respectively. We designed biosensors of KIF17 to monitor its activity directly in single cells using fluorescence lifetime imaging to detect Förster resonance energy transfer. Lifetime data are mapped on a phasor plot, allowing us to resolve populations of active and inactive motors in individual cells. Using this biosensor, we demonstrate that PKC contributes to the activation of KIF17 and that this is required for KIF17 to stabilize MTs in epithelia. Furthermore, we show that EB1 recruits KIF17 to dynamic MTs, enabling its accumulation at MT ends and thus promoting MT stabilization at discrete cellular domains.
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Affiliation(s)
- Cedric Espenel
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY 10021
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373
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Müller SM, Galliardt H, Schneider J, Barisas BG, Seidel T. Quantification of Förster resonance energy transfer by monitoring sensitized emission in living plant cells. FRONTIERS IN PLANT SCIENCE 2013; 4:413. [PMID: 24194740 PMCID: PMC3810607 DOI: 10.3389/fpls.2013.00413] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/29/2013] [Indexed: 05/20/2023]
Abstract
Förster resonance energy transfer (FRET) describes excitation energy exchange between two adjacent molecules typically in distances ranging from 2 to 10 nm. The process depends on dipole-dipole coupling of the molecules and its probability of occurrence cannot be proven directly. Mostly, fluorescence is employed for quantification as it represents a concurring process of relaxation of the excited singlet state S1 so that the probability of fluorescence decreases as the probability of FRET increases. This reflects closer proximity of the molecules or an orientation of donor and acceptor transition dipoles that facilitates FRET. Monitoring sensitized emission by 3-Filter-FRET allows for fast image acquisition and is suitable for quantifying FRET in dynamic systems such as living cells. In recent years, several calibration protocols were established to overcome to previous difficulties in measuring FRET-efficiencies. Thus, we can now obtain by 3-filter FRET FRET-efficiencies that are comparable to results from sophisticated fluorescence lifetime measurements. With the discovery of fluorescent proteins and their improvement toward spectral variants and usability in plant cells, the tool box for in vivo FRET-analyses in plant cells was provided and FRET became applicable for the in vivo detection of protein-protein interactions and for monitoring conformational dynamics. The latter opened the door toward a multitude of FRET-sensors such as the widely applied Ca(2+)-sensor Cameleon. Recently, FRET-couples of two fluorescent proteins were supplemented by additional fluorescent proteins toward FRET-cascades in order to monitor more complex arrangements. Novel FRET-couples involving switchable fluorescent proteins promise to increase the utility of FRET through combination with photoactivation-based super-resolution microscopy.
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Affiliation(s)
- Sara M. Müller
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld UniversityBielefeld, Germany
| | - Helena Galliardt
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld UniversityBielefeld, Germany
| | - Jessica Schneider
- Bioinformatic Resource Facility, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - B. George Barisas
- Chemistry Department, Colorado State UniversityFort Collins, CO, USA
| | - Thorsten Seidel
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld UniversityBielefeld, Germany
- *Correspondence: Thorsten Seidel, Dynamic Cell Imaging, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33501 Bielefeld, Germany e-mail:
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374
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Grünberg R, Burnier JV, Ferrar T, Beltran-Sastre V, Stricher F, van der Sloot AM, Garcia-Olivas R, Mallabiabarrena A, Sanjuan X, Zimmermann T, Serrano L. Engineering of weak helper interactions for high-efficiency FRET probes. Nat Methods 2013; 10:1021-7. [PMID: 23995386 DOI: 10.1038/nmeth.2625] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/20/2013] [Indexed: 12/19/2022]
Abstract
Fluorescence resonance energy transfer (FRET)-based detection of protein interactions is limited by the very narrow range of FRET-permitting distances. We show two different strategies for the rational design of weak helper interactions that co-recruit donor and acceptor fluorophores for a more robust detection of bimolecular FRET: (i) in silico design of electrostatically driven encounter complexes and (ii) fusion of tunable domain-peptide interaction modules based on WW or SH3 domains. We tested each strategy for optimization of FRET between (m)Citrine and mCherry, which do not natively interact. Both approaches yielded comparable and large increases in FRET efficiencies with little or no background. Helper-interaction modules can be fused to any pair of fluorescent proteins and could, we found, enhance FRET between mTFP1 and mCherry as well as between mTurquoise2 and mCitrine. We applied enhanced helper-interaction FRET (hiFRET) probes to study the binding between full-length H-Ras and Raf1 as well as the drug-induced interaction between Raf1 and B-Raf.
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Affiliation(s)
- Raik Grünberg
- 1] EMBL/CRG Systems Biology Research Unit, Center for Genomic Regulation, Barcelona, Spain. [2] Pompeu Fabra University, Barcelona, Spain. [3] Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, Canada
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375
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Zhang C, Ye BC. Real-time measurement of quorum-sensing signal autoinducer 3OC6HSL by a FRET-based nanosensor. Bioprocess Biosyst Eng 2013; 37:849-55. [DOI: 10.1007/s00449-013-1055-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 09/06/2013] [Indexed: 11/30/2022]
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376
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Berthelot V, Steinmetz V, Alvarez LA, Houée-Levin C, Merola F, Rusconi F, Erard M. An analytical workflow for the molecular dissection of irreversibly modified fluorescent proteins. Anal Bioanal Chem 2013; 405:8789-98. [PMID: 24026516 DOI: 10.1007/s00216-013-7326-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/08/2013] [Accepted: 07/11/2013] [Indexed: 12/01/2022]
Abstract
Owing to their ability to be genetically expressed in live cells, fluorescent proteins have become indispensable markers in cellular and biochemical studies. These proteins can undergo a number of covalent chemical modifications that may affect their photophysical properties. Among other mechanisms, such covalent modifications may be induced by reactive oxygen species (ROS), as generated along a variety of biological pathways or through the action of ionizing radiations. In a previous report [1], we showed that the exposure of cyan fluorescent protein (ECFP) to amounts of (•)OH that mimic the conditions of intracellular oxidative bursts (associated with intense ROS production) leads to observable changes in its photophysical properties in the absence of any direct oxidation of the ECFP chromophore. In the present work, we analyzed the associated structural modifications of the protein in depth. Following the quantified production of (•)OH, we devised a complete analytical workflow based on chromatography and mass spectrometry that allowed us to fully characterize the oxidation events. While methionine, tyrosine, and phenylalanine were the only amino acids that were found to be oxidized, semi-quantitative assessment of their oxidation levels showed that the protein is preferentially oxidized at eight residue positions. To account for the preferred oxidation of a few, poorly accessible methionine residues, we propose a multi-step reaction pathway supported by data from pulsed radiolysis experiments. The described experimental workflow is widely generalizable to other fluorescent proteins, and opens the door to the identification of crucial covalent modifications that affect their photophysics.
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Affiliation(s)
- Vivien Berthelot
- Laboratoire de Chimie Physique, UMR CNRS 8000, Building 350, 91405, Orsay Cedex, France
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377
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Chang Y, Cai C, Li L, Miao J, Ucakturk E, Li G, Ly M, Linhardt RJ. Ultrasensitive detection and quantification of acidic disaccharides using capillary electrophoresis and quantum dot-based fluorescence resonance energy transfer. Anal Chem 2013; 85:9356-62. [PMID: 23985015 DOI: 10.1021/ac402242v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid and highly sensitive detection of the carbohydrate components of glycoconjugates is critical for advancing glycobiology. Fluorescence (or Förster) resonance energy transfer (FRET) is commonly used in detection of DNA, in protein structural biology, and in protease assays but is less frequently applied to glycan analysis due to difficulties in inserting two fluorescent tags into small glycan structures. We report an ultrasensitive method for the detection and quantification of a chondroitin sulfate disaccharide based on FRET, involving a CdSe-ZnS core-shell nanocrystal quantum dot (QD) streptavidin conjugate donor and a Cy5 acceptor. The disaccharide was doubly labeled with biotin and Cy5. QDs then served to concentrate the target disaccharide, enhancing the overall energy transfer efficiency, with unlinked QDs and Cy5 hydrazide producing nearly zero background signal in capillary electrophoresis using laser-induced fluorescence detection with two different band-pass filters. This method is generally applicable to the ultrasensitive analysis of acidic glycans and offers promise for the high-throughput disaccharide analysis of glycosaminoglycans.
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Affiliation(s)
- Yuqing Chang
- Department of Chemistry and Chemical Biology, ‡Chemical and Biological Engineering, §Biology, and ∥Biomedical Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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378
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Solez K, Bernier A, Crichton J, Graves H, Kuttikat P, Lockwood R, Marovitz WF, Monroe D, Pallen M, Pandya S, Pearce D, Saleh A, Sandhu N, Sergi C, Tuszynski J, Waugh E, White J, Woodside M, Wyndham R, Zaiane O, Zakus D. Bridging the gap between the technological singularity and mainstream medicine: highlighting a course on technology and the future of medicine. Glob J Health Sci 2013; 5:112-25. [PMID: 24171879 PMCID: PMC4776857 DOI: 10.5539/gjhs.v5n6p112] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 09/09/2013] [Indexed: 11/17/2022] Open
Abstract
The "technological singularity" is defined as that putative point in time forecasted to occur in the mid twenty-first century when machines will become smarter than humans, leading humans and machines to merge. It is hypothesized that this event will have a profound influence on medicine and population health. This work describes a new course on Technology and the Future of Medicine developed by a diverse, multi-disciplinary group of faculty members at a Canadian university. The course began as a continuous professional learning course and was later established as a recognized graduate course. We describe the philosophy of the course, the barriers encountered in course development, and some of the idiosyncratic solutions that were developed to overcome these, including the use of YouTube audience retention analytics. We hope that this report might provide a useful template for other institutions attempting to set up similar programs.
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379
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Gholami Z, Brunsveld L, Hanley Q. PNA-induced assembly of fluorescent proteins using DNA as a framework. Bioconjug Chem 2013; 24:1378-86. [PMID: 23848261 DOI: 10.1021/bc400202s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Controlled alignment of proteins on molecular frameworks requires the development of facile and orthogonal chemical approaches and molecular scaffolds. In this work, protein-PNA conjugates are brought forward as new chemical components allowing efficient assembly and alignment on DNA scaffolds. Site-selective monomeric teal fluorescent protein (mTFP)-peptide nucleic acid (PNA) (mTFP-PNA) conjugation was achieved by covalent linkage of the PNA to the protein through expressed protein ligation (EPL). A DNA beacon, with 6-Fam and Dabcyl at its ends, acts as a framework to create an assembled hetero-FRET system with the mTFP-PNA conjugate. Using fluorescence intensity, frequency domain lifetime measurements, and anisotropy measurements, the system was shown to produce FRET as indicated by decreased donor intensity, decreased donor lifetime, and increased donor anisotropy. Extension of the DNA scaffold allowed for the assembly of multiple mTFP-PNA constructs. Efficient formation of protein dimers and oligomers on the DNA-PNA frameworks could be shown, as visualized via size exclusion chromatography (SEC) and electrophoresis (SDS-PAGE). Assembly of multiple proteins in a row induced homo-FRET for the mTFP-PNA's assembled on the DNA scaffolds. The oligonucleotide framework allows an induced and controllable assembly of proteins by fusing them to PNAs directed to align on DNA scaffolds.
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Affiliation(s)
- Zahra Gholami
- School of Science and Technology, Nottingham Trent University , Clifton Lane, Nottingham NG11 8NS, United Kingdom
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380
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Chang JC, Rosenthal SJ. A Bright Light to Reveal Mobility: Single Quantum Dot Tracking Reveals Membrane Dynamics and Cellular Mechanisms. J Phys Chem Lett 2013; 4:2858-2866. [PMID: 28626534 PMCID: PMC5473254 DOI: 10.1021/jz401071g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This perspective describes recent progress in single quantum dot techniques, with an emphasis on their applications in exploring membrane dynamics and cellular mechanisms. In these cases, conventional population measurements, such as fluorescence recovery after photobleaching, yield only a mean value on an ensemble or bulk collection of molecules, where the behavior of individual proteins and vehicles is missing. In recent years, the single quantum dot imaging approach has been introduced as a sub-category of single molecule fluorescent techniques to reveal single protein/vehicle dynamics in real-time. One of the major advantages of using single quantum dots is the high signal-to-noise ratio originating from their unique photophysical properties such as extraordinarily high molar extinction coefficients and large effective Stokes shifts. In addition to a brief overview on the principle of single quantum dot imaging techniques, we highlight recent discoveries and discuss future directions in the field.
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Affiliation(s)
- Jerry C. Chang
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Sandra J. Rosenthal
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
- Department of Pharmacology, Chemical and Biomolecular Engineering, Physics and Astronomy, and Vanderbilt Institute of Nanoscale Science and Engineering, Vanderbilt University, Nashville, TN 37235
- Department of Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
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381
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Warren SC, Margineanu A, Alibhai D, Kelly DJ, Talbot C, Alexandrov Y, Munro I, Katan M, Dunsby C, French PMW. Rapid global fitting of large fluorescence lifetime imaging microscopy datasets. PLoS One 2013; 8:e70687. [PMID: 23940626 PMCID: PMC3734241 DOI: 10.1371/journal.pone.0070687] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 06/20/2013] [Indexed: 12/18/2022] Open
Abstract
Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset). This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC) or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis of live cell homo-FRET data. A software package implementing this algorithm, FLIMfit, is available under an open source licence through the Open Microscopy Environment.
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Affiliation(s)
- Sean C Warren
- Department of Chemistry, Institute for Chemical Biology, Imperial College London, London, United Kingdom.
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382
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Zhang C, Wei ZH, Ye BC. Quantitative monitoring of 2-oxoglutarate in Escherichia coli cells by a fluorescence resonance energy transfer-based biosensor. Appl Microbiol Biotechnol 2013; 97:8307-16. [PMID: 23893310 DOI: 10.1007/s00253-013-5121-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 06/07/2013] [Accepted: 07/10/2013] [Indexed: 11/25/2022]
Abstract
2-Oxoglutarate (2OG) is a metabolite from the highly conserved Krebs cycle and not only plays a critical role in metabolism but also acts as a signaling molecule in a variety of organisms. Environmental inorganic nitrogen is reduced to ammonium by microorganisms, whose metabolic pathways involve the conversion of 2OG to glutamate and glutamine. Tracking of 2OG in real time would be useful for studies on cell metabolism and signal transduction. Here, we developed a genetically encoded 2OG biosensor based on fluorescent resonance energy transfer by inserting the functional 2OG-binding domain GAF of the NifA protein between the fluorescence resonance energy transfer (FRET) pair YFP/CFP. The dynamic range of the sensors is 100 μM to 10 mM, which appeared identical to the physiological range observed in E. coli. We optimized the peptide lengths of the binding domain to obtain a sensor with a maximal ratio change of 0.95 upon 2OG binding and demonstrated the feasibility of this sensor for the visualization of metabolites both in vitro and in vivo.
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Affiliation(s)
- Chang Zhang
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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383
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A Sensitized Emission Based Calibration of FRET Efficiency for Probing the Architecture of Macromolecular Machines. Cell Mol Bioeng 2013; 6:369-382. [PMID: 24319499 PMCID: PMC3843746 DOI: 10.1007/s12195-013-0290-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 07/02/2013] [Indexed: 01/24/2023] Open
Abstract
Macromolecular machines participate in almost every cell biological function. These machines can take the form of well-defined protein structures such as the kinetochore, or more loosely organized protein assemblies like the endocytic coat. The protein architecture of these machines—the arrangement of multiple copies of protein subunits at the nanoscale, is necessary for understanding their cell biological function and biophysical mechanism. Defining this architecture in vivo presents a major challenge. High density of protein molecules within macromolecular machines severely limits the effectiveness of super-resolution microscopy. However, this density is ideal for Forster Resonance Energy Transfer (FRET), which can determine the proximity between neighboring molecules. Here, we present a simple FRET quantitation scheme that calibrates a standard epifluorescence microscope for measuring donor–acceptor separations. This calibration can be used to deduce FRET efficiency fluorescence intensity measurements. This method will allow accurate determination of FRET efficiency over a wide range of values and FRET pair number. It will also allow dynamic FRET measurements with high spatiotemporal resolution under cell biological conditions. Although the poor maturation efficiency of genetically encoded fluorescent proteins presents a challenge, we show that its effects can be alleviated. To demonstrate this methodology, we probe the in vivo architecture of the γ-Tubulin Ring. Our technique can be applied to study the architecture and dynamics of a wide range of macromolecular machines.
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384
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Lee JH, Song E, Lee SG, Kim BG. High-throughput screening for transglutaminase activities using recombinant fluorescent proteins. Biotechnol Bioeng 2013; 110:2865-73. [PMID: 23740563 DOI: 10.1002/bit.24970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/28/2013] [Accepted: 05/28/2013] [Indexed: 01/20/2023]
Abstract
Since detailed evaluation of specific transglutaminases (TGs) from various species requires identification of their substrate specificities, rapid substrate screening method by measurement of their relative activities is in great demand. Here, a novel evaluation method of TG activity was developed using two recombinant fluorescent proteins (FPs), that is, eYFP and DsRed, tagged with TG substrate peptides. By cross-linking the two FPs based on the tagged target peptide sequences at their C-terminus, the expression of co-transformed TG allows quenching of the yellow fluorescence intensities. It was shown that the degree of in vivo fluorescent quenching by the TG activity agrees well with its in vitro reaction data, suggesting that this system can be used to identify relative substrate specificity of TGs for target peptide sequences. Using this method, the lysine substrates of TGs from Bacillus species (BTG) were evaluated, and the newly selected pentapeptide, KTKTN showed almost the same reactivity with the well-known hexa-lysine (K₆) substrate for BTG reaction.
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Affiliation(s)
- Jae-Hun Lee
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Kwanak-Gu, Seoul, South Korea; Institute of Bioengineering, Seoul National University, Kwanak-Gu, Seoul, South Korea
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385
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Synergizing nucleic acid aptamers with 1-dimensional nanostructures as label-free field-effect transistor biosensors. Biosens Bioelectron 2013; 50:278-93. [PMID: 23872609 DOI: 10.1016/j.bios.2013.06.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/06/2013] [Accepted: 06/17/2013] [Indexed: 01/04/2023]
Abstract
Since the introduction by Gold et al. in 1990, nucleic acid aptamers had evolved to become a true contender in biosensors for protein and cell detections. Aptamers are short strands of synthetically designed DNA or RNA oligonucleotides that can be self-assembled into unique 3-dimensional structures and can bind to different proteins, cells or even small molecules at a high level of specificity and affinity. In recent years, there had been many reports in literature in using aptamers in place of conventional antibodies as capture biomolecules on the surface. This is mainly due to the better thermal stability properties and ease in production. Consequently, also these characteristics allowed the aptamers to find use in field effect transistors (FETs) based upon 1D nanostructured (1D-NS) as label-free biosensing. In terms of designing label-free platforms for biosensors applications, 1D-NS FET had been an attractive option due to reported high sensitivities toward protein targets arising from the large surface area for detection as well as to their label-free nature. Since the first aptamer-based 1D-NS FET biosensor had surfaced in 2005, there had been many more improvements in the overall design and sensitivity in recent years. In this review, the latest developments in synergizing these two interesting areas of research (aptamers and 1D-NS FET) will be discussed for a range of different nanowire types as well as for the detection results.
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386
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Sun Y, Rombola C, Jyothikumar V, Periasamy A. Förster resonance energy transfer microscopy and spectroscopy for localizing protein-protein interactions in living cells. Cytometry A 2013; 83:780-93. [PMID: 23813736 DOI: 10.1002/cyto.a.22321] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Revised: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/15/2022]
Abstract
The fundamental theory of Förster resonance energy transfer (FRET) was established in the 1940s. Its great power was only realized in the past 20 years after different techniques were developed and applied to biological experiments. This success was made possible by the availability of suitable fluorescent probes, advanced optics, detectors, microscopy instrumentation, and analytical tools. Combined with state-of-the-art microscopy and spectroscopy, FRET imaging allows scientists to study a variety of phenomena that produce changes in molecular proximity, thereby leading to many significant findings in the life sciences. In this review, we outline various FRET imaging techniques and their strengths and limitations; we also provide a biological model to demonstrate how to investigate protein-protein interactions in living cells using both intensity- and fluorescence lifetime-based FRET microscopy methods.
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Affiliation(s)
- Yuansheng Sun
- The W.M. Keck Center for Cellular Imaging (KCCI), Department of Biology, Physical and Life Sciences Building, University of Virginia, Charlottesville, Virginia
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387
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Mohsin M, Abdin MZ, Nischal L, Kardam H, Ahmad A. Genetically encoded FRET-based nanosensor for in vivo measurement of leucine. Biosens Bioelectron 2013; 50:72-7. [PMID: 23835220 DOI: 10.1016/j.bios.2013.06.028] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/31/2013] [Accepted: 06/11/2013] [Indexed: 01/08/2023]
Abstract
Besides fundamental role in protein synthesis, leucine has metabolic roles as energy substrates, precursors for synthesis of other amino acids and as a modulator of muscle protein synthesis via the insulin-signaling pathway. Leucine concentration in cell and tissue is temporally dynamic as the metabolism of leucine is regulated through multiple enzymes and transporters. Assessment of cell-type specific activities of transporters and enzymes by physical fractionation is extremely challenging. Therefore, a method of reporting leucine dynamics at the cellular level is highly desirable. Given this, we developed a series of genetically encoded nanosensors for real-time in vivo measurement of leucine at cellular level. A leucine binding periplasmic binding protein (LivK) of Escherichia coli K12 was flanked with CFP (cyan fluorescent protein) and YFP (yellow fluorescent protein) at N-terminus and C-terminus, respectively. The constructed nanosensors allowed in vitro determination of fluorescence resonance energy transfer (FRET) changes in a concentration-dependent manner. These sensors were found to be specific to leucine, and stable to pH-changes within a physiological range. Genetically encoded sensors can be targeted to a specific cell type, and allow dynamic measurement of leucine concentration in bacterial and yeast cells.
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Affiliation(s)
- Mohd Mohsin
- Molecular Ecology Laboratory, Department of Botany, Faculty of Science, Hamdard University, New Delhi 110062, India
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388
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Pletneva NV, Pletnev VZ, Souslova E, Chudakov DM, Lukyanov S, Martynov VI, Arhipova S, Artemyev I, Wlodawer A, Dauter Z, Pletnev S. Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:1005-12. [PMID: 23695245 PMCID: PMC3663121 DOI: 10.1107/s0907444913004034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/09/2013] [Indexed: 11/10/2022]
Abstract
The yellow fluorescent protein phiYFPv (λem(max) ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow-orange range (535-555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The `yellow' chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.
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Affiliation(s)
- Nadya V. Pletneva
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir Z. Pletnev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ekaterina Souslova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry M. Chudakov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Sergey Lukyanov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russian Federation
| | - Vladimir I. Martynov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Svetlena Arhipova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Igor Artemyev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
| | - Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, IL 60439, USA
- Basic Research Program, SAIC-Frederick, 9700 South Cass Avenue, Argonne, IL 60439, USA
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389
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Wang Z, Zhang K, Shen Y, Smith J, Bloch S, Achilefu S, Wooley KL, Taylor JS. Imaging mRNA expression levels in living cells with PNA·DNA binary FRET probes delivered by cationic shell-crosslinked nanoparticles. Org Biomol Chem 2013; 11:3159-67. [PMID: 23538604 PMCID: PMC3687806 DOI: 10.1039/c3ob26923j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Optical imaging of gene expression through the use of fluorescent antisense probes targeted to the mRNA has been an area of great interest. The main obstacles to developing highly sensitive antisense fluorescent imaging agents have been the inefficient intracellular delivery of the probes and high background signal from unbound probes. Binary antisense probes have shown great promise as mRNA imaging agents because a signal can only occur if both probes are bound simultaneously to the mRNA target site. Selecting an accessible binding site is made difficult by RNA folding and protein binding in vivo and the need to bind two probes. Even more problematic, has been a lack of methods for efficient cytoplasmic delivery of the probes that would be suitable for eventual applications in vivo in animals. Herein we report the imaging of iNOS mRNA expression in live mouse macrophage cells with PNA·DNA binary FRET probes delivered by a cationic shell crosslinked knedel-like nanoparticle (cSCK). We first demonstrate that FRET can be observed on in vitro transcribed mRNA with both the PNA probes and the PNA·DNA hybrid probes. We then demonstrate that the FRET signal can be observed in live cells when the hybrid probes are transfected with the cSCK, and that the strength of the FRET signal is sequence specific and depends on the mRNA expression level.
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Affiliation(s)
- Zhenghui Wang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
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390
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Zeug A, Woehler A, Neher E, Ponimaskin EG. Quantitative intensity-based FRET approaches--a comparative snapshot. Biophys J 2013. [PMID: 23199910 DOI: 10.1016/j.bpj.2012.09.031] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Förster resonance energy transfer (FRET) has become an important tool for analyzing different aspects of interactions among biological macromolecules in their native environments. FRET analysis has also been successfully applied to study the spatiotemporal regulation of various cellular processes using genetically encoded FRET-based biosensors. A variety of procedures have been described for measuring FRET efficiency or the relative abundance of donor-acceptor complexes, based on analysis of the donor fluorescence lifetime or the spectrally resolved fluorescence intensity. The latter methods are preferable if one wants to not only quantify the apparent FRET efficiencies but also calculate donor-acceptor stoichiometry and observe fast dynamic changes in the interactions among donor and acceptor molecules in live cells. This review focuses on a comparison of the available intensity-based approaches used to measure FRET. We discuss their strengths and weaknesses in terms of FRET quantification, and provide several examples of biological applications.
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Affiliation(s)
- André Zeug
- Cellular Neurophysiology, Center of Physiology, Hannover Medical School, Hannover, Germany
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391
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Watkins JL, Kim H, Markwardt ML, Chen L, Fromme R, Rizzo MA, Wachter RM. The 1.6 Å resolution structure of a FRET-optimized Cerulean fluorescent protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:767-73. [PMID: 23633585 PMCID: PMC3640468 DOI: 10.1107/s0907444913001546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 01/16/2013] [Indexed: 11/11/2022]
Abstract
Genetically encoded cyan fluorescent proteins (CFPs) bearing a tryptophan-derived chromophore are commonly used as energy-donor probes in Förster resonance energy transfer (FRET) experiments useful in live cell-imaging applications. In recent years, significant effort has been expended on eliminating the structural and excited-state heterogeneity of these proteins, which has been linked to undesirable photophysical properties. Recently, mCerulean3, a descendant of enhanced CFP, was introduced as an optimized FRET donor protein with a superior quantum yield of 0.87. Here, the 1.6 Å resolution X-ray structure of mCerulean3 is reported. The chromophore is shown to adopt a planar trans configuration at low pH values, indicating that the acid-induced isomerization of Cerulean has been eliminated. β-Strand 7 appears to be well ordered in a single conformation, indicating a loss of conformational heterogeneity in the vicinity of the chromophore. Although the side chains of Ile146 and Leu167 appear to exist in two rotamer states, they are found to be well packed against the indole group of the chromophore. The Ser65 reversion mutation allows improved side-chain packing of Leu220. A structural comparison with mTurquoise2 is presented and additional engineering strategies are discussed.
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Affiliation(s)
- Jennifer L. Watkins
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Hanseong Kim
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Michele L. Markwardt
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201-1559, USA
| | - Liqing Chen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
| | - Mark A. Rizzo
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201-1559, USA
| | - Rebekka M. Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
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392
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Wissner RF, Batjargal S, Fadzen CM, Petersson EJ. Labeling proteins with fluorophore/thioamide Förster resonant energy transfer pairs by combining unnatural amino acid mutagenesis and native chemical ligation. J Am Chem Soc 2013; 135:6529-40. [PMID: 23594264 DOI: 10.1021/ja4005943] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have recently shown that p-cyanophenylalanine (Cnf) and a thioamide can be used as a minimally perturbing Förster resonant energy transfer (FRET) pair to monitor protein conformation. We have also shown that thioamide analogues of natural amino acids can be incorporated into full-sized proteins through native chemical ligation. For intermolecular studies with Cnf/thioamide FRET pairs, Cnf can be incorporated into proteins expressed in Escherichia coli through unnatural amino acid mutagenesis using a Cnf-specific tRNA synthetase. For intramolecular studies, a Cnf-labeled protein fragment can be expressed in E. coli and then ligated to a thioamide-labeled peptide synthesized on solid phase. This combination of methods allows for rapid access to double-labeled proteins with a minimum of unnecessary chemical synthesis. We demonstrate the utility of this approach by studying the binding of peptides to the protein calmodulin and by determining the orientation of the N- and C-termini in the amyloidogenic protein α-synuclein.
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Affiliation(s)
- Rebecca F Wissner
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
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393
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Satori CP, Henderson MM, Krautkramer EA, Kostal V, Distefano MM, Arriaga EA. Bioanalysis of eukaryotic organelles. Chem Rev 2013; 113:2733-811. [PMID: 23570618 PMCID: PMC3676536 DOI: 10.1021/cr300354g] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chad P. Satori
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Michelle M. Henderson
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Elyse A. Krautkramer
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Vratislav Kostal
- Tescan, Libusina trida 21, Brno, 623 00, Czech Republic
- Institute of Analytical Chemistry ASCR, Veveri 97, Brno, 602 00, Czech Republic
| | - Mark M. Distefano
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
| | - Edgar A. Arriaga
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN, USA, 55455
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394
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Vincill ED, Clarin AE, Molenda JN, Spalding EP. Interacting glutamate receptor-like proteins in Phloem regulate lateral root initiation in Arabidopsis. THE PLANT CELL 2013; 25:1304-13. [PMID: 23590882 PMCID: PMC3663269 DOI: 10.1105/tpc.113.110668] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 03/29/2013] [Accepted: 04/04/2013] [Indexed: 05/18/2023]
Abstract
Molecular, genetic, and electrophysiological evidence indicates that at least one of the plant Glu receptor-like molecules, GLR3.4, functions as an amino acid-gated Ca²⁺channel at the plasma membrane. The aspect of plant physiology, growth, or development to which GLR3.4 contributes is an open question. Protein localization studies performed here provide important information. In roots, GLR3.4 and the related GLR3.2 protein were present primarily in the phloem, especially in the vicinity of the sieve plates. GLR3.3 was expressed in most cells of the growing primary root but was not enriched in the phloem, including the sieve plate area. GLR3.2 and GLR3.4 physically interacted with each other better than with themselves as evidenced by a biophotonic assay performed in human embryonic kidney cells and Nicotiana benthamiana leaf cells. GLR3.3 interacted poorly with itself or the other two GLRs. Mutations in GLR3.2, GLR3.4, or GLR3.2 and GLR3.4 caused the same and equally severe phenotype, namely, a large overproduction and aberrant placement of lateral root primordia. Loss of GLR3.3 did not affect lateral root primordia. These results support the hypothesis that apoplastic amino acids acting through heteromeric GLR3.2/GLR3.4 channels affect lateral root development via Ca²⁺ signaling in the phloem.
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Affiliation(s)
- Eric D Vincill
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706, USA
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395
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Cho EJ, Holback H, Liu KC, Abouelmagd SA, Park J, Yeo Y. Nanoparticle characterization: state of the art, challenges, and emerging technologies. Mol Pharm 2013; 10:2093-110. [PMID: 23461379 DOI: 10.1021/mp300697h] [Citation(s) in RCA: 195] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nanoparticles have received enormous attention as a promising tool to enhance target-specific drug delivery and diagnosis. Various in vitro and in vivo techniques are used to characterize a new system and predict its clinical efficacy. These techniques enable efficient comparison across nanoparticles and facilitate a product optimization process. On the other hand, we recognize their limitations as a prediction tool, due to inadequate applications and overly simplified test conditions. We provide a critical review of in vitro and in vivo techniques currently used for evaluation of nanoparticles and introduce emerging techniques and models that may be used complementarily.
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Affiliation(s)
- Eun Jung Cho
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47907, USA
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396
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Akhavan-Tafti H, Binger DG, Blackwood JJ, Chen Y, Creager RS, de Silva R, Eickholt RA, Gaibor JE, Handley RS, Kapsner KP, Lopac SK, Mazelis ME, McLernon TL, Mendoza JD, Odegaard BH, Reddy SG, Salvati M, Schoenfelner BA, Shapir N, Shelly KR, Todtleben JC, Wang G, Xie W. A homogeneous chemiluminescent immunoassay method. J Am Chem Soc 2013; 135:4191-4. [PMID: 23477541 DOI: 10.1021/ja312039k] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A new homogeneous chemiluminescent immunoassay method featuring the use of specific binding members separately labeled with an acridan-based chemiluminescent compound and a peroxidase is reported. Formation of an immunocomplex brings the chemiluminescent compound and the peroxidase into close proximity. Without any separation steps, a chemiluminescent signal is generated upon addition of a trigger solution, and the intensity is directly correlated to the quantity of the analyte.
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397
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A feasible add-on upgrade on a commercial two-photon FLIM microscope for optimal FLIM-FRET imaging of CFP-YFP pairs. J Fluoresc 2013; 23:543-9. [PMID: 23456419 DOI: 10.1007/s10895-013-1188-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 02/24/2013] [Indexed: 10/27/2022]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) based on time-correlated single photon counting (TCSPC) is a widely used method for fluorescence resonance energy transfer (FRET). Here we report a feasible add-on approach to upgrade a commercial two-photon FLIM microscope into a single-photon FLIM microscope which provides optimal FLIM-FRET imaging of FRET pairs consisting of cyan fluorescent proteins (CFPs) as the donor and yellow fluorescent proteins (YFPs) as the acceptor. The capability of the upgraded system is evaluated and discussed, and the imaging performance of the system is demonstrated using FLIM-FRET experiments with a representative CFP-YFP FRET pair (mCerulean-mCitrine).
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398
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Alamiry MAH, Bahaidarah E, Harriman A, Olivier JH, Ziessel R. Influence of applied pressure on the probability of electronic energy transfer across a molecular dyad. PURE APPL CHEM 2013. [DOI: 10.1351/pac-con-12-09-04] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A pair of covalently linked molecular dyads is described in which two disparate
boron dipyrromethene dyes are separated by a tolane-like spacer. Efficient
electronic energy transfer (EET) occurs across the dyad; the mechanism involves
important contributions from both Förster-type coulombic interactions and
Dexter-type electron exchange processes. The energy acceptor is equipped with
long paraffinic chains that favor aggregation at high concentration or at low
temperature. The aggregate displays red-shifted absorption and emission spectral
profiles, relative to the monomer, such that EET is less efficient because of a
weaker overlap integral. The donor unit is insensitive to applied pressure but
this is not so for the acceptor, which has extended π-conjugation associated
with appended styryl groups. Here, pressure reduces the effective π-conjugation
length, leading to a new absorption band at higher energy. With increasing
pressure, the overall EET probability falls but this effect is nonlinear and at
modest pressure there is only a small recovery of donor fluorescence. This
situation likely arises from compensatory phenomena such as restricted rotation
and decreased dipole screening by the solvent. However, the probability of EET
falls dramatically over the regime where the π-conjugation length is reduced
owing to the presumed conformational exchange. It appears that the
pressure-induced conformer is a poor energy acceptor.
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Affiliation(s)
- Mohammed A. H. Alamiry
- 1Molecular Photonics Laboratory, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Effat Bahaidarah
- 1Molecular Photonics Laboratory, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Anthony Harriman
- 1Molecular Photonics Laboratory, School of Chemistry, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jean-Hubert Olivier
- 2Laboratoire de Chimie Moléculaire et Spectroscopies Avancées LCOSA, Ecole Européenne de Chimie, Polymères et Matériaux, CNRS, UMR 7515 associé au CNRS, 25 rue Becquerel, 67087 Strasbourg Cedex 02, France
| | - Raymond Ziessel
- 2Laboratoire de Chimie Moléculaire et Spectroscopies Avancées LCOSA, Ecole Européenne de Chimie, Polymères et Matériaux, CNRS, UMR 7515 associé au CNRS, 25 rue Becquerel, 67087 Strasbourg Cedex 02, France
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399
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Wang S, Li KJ, Lin XW, Jiang CZ, Chen DH, Wu Q, Hua ZC. Using c-Fos/c-Jun as hetero-dimer interaction model to optimize donor to acceptor concentration ratio range for three-filter fluorescence resonance energy transfer (FRET) measurement. J Microsc 2013; 248:58-65. [PMID: 22971218 DOI: 10.1111/j.1365-2818.2012.03650.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sensitized emission FRET detection method based on three-filter fluorescence microscopy is widely used and more suitable for live cell FRET imaging and dynamic protein-protein interaction analysis. But when it is applied to detect two proteins interaction in living cells, this intensity-based detection method is complicated by many experimental factors such as spectral crosstalk and spectral bleed-through and variable donor to acceptor concentration ratio. There are several FRET algorithms developed recently to correct those factors in order to quantitatively gauge and compare FRET signals between different experimental groups. But the algorithms are often difficult to choose when they are applied to certain experiments. In this research, we use c-Fos/c-Jun as a simple hetero-dimer interaction model to quantitatively detect and compare the FRET signals based on the following widely used sensitized emission FRET algorithms: N(FRET) , FRET(N) , FR, FRET(R) , E(app) and E(EFF) . We optimized the donor to acceptor concentration ratio range for the above FRET algorithms and facilitate their use in accurate FRET signal determination based on the three-filter FRET microscopy.
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Affiliation(s)
- S Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, College of Life Sciences, Nanjing University, Nanjing, PR China
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400
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Zhang Y, Yang J. Design Strategies for Fluorescent Biodegradable Polymeric Biomaterials. J Mater Chem B 2013; 1:132-148. [PMID: 23710326 PMCID: PMC3660738 DOI: 10.1039/c2tb00071g] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The marriage of biodegradable polymer and fluorescent imaging has resulted in an important area of polymeric biomaterials: biodegradable fluorescent polymers. Researchers have put significant efforts on developing versatile fluorescent biomaterials due to their promising in biological/biomedical labeling, tracking, monitoring, imaging, and diagnostic applications, especially in drug delivery, tissue engineering, and cancer imaging applications. Biodegradable fluorescent polymers can function not only as implant biomaterials but also as imaging probes. Currently, there are two major classes of biodegradable polymers used as fluorescent materials. The first class is the combination of non-fluorescent biodegradable polymers and fluorescent agents such as organic dyes and quantum dots. Another class of polymers shows intrinsic photoluminescence as polymers by themselves carrying integral fluorescent chemical structures in or pendent to their polymer backbone, such as Green Fluorescent protein (GFP), and the recently developed biodegradable photoluminescent polymer (BPLP). Thus there is no need to conjugate or encapsulate additional fluorescent materials for the latter. In the present review, we will review the fluorescent biodegradable polymers with emphases on material fluorescence mechanism, design criteria for fluorescence, and their cutting-edge applications in biomedical engineering. We expect that this review will provide insightful discussion on the fluorescent biomaterial design and lead to innovations for the development of the next generation of fluorescent biomaterials and fluorescence-based biomedical technology.
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Affiliation(s)
- Yi Zhang
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76010
- Joint Biomedical Engineering Program, The University of Texas Southwestern Medical Center and The University of Texas at Arlington, Dallas, TX 75390
| | - Jian Yang
- Department of Bioengineering, Materials Research Institute, The Huck Institutes of The Life Sciences, The Pennsylvania State University, University Park, PA 16802
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