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Wu T, King MR, Farag M, Pappu RV, Lew MD. Single fluorogen imaging reveals distinct environmental and structural features of biomolecular condensates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525727. [PMID: 36747818 PMCID: PMC9900924 DOI: 10.1101/2023.01.26.525727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Recent computations suggest that biomolecular condensates that form via macromolecular phase separation are network fluids featuring spatially inhomogeneous organization of the underlying molecules. Computations also point to unique conformations of molecules at condensate interfaces. Here, we test these predictions using high-resolution structural characterizations of condensates formed by intrinsically disordered prion-like low complexity domains (PLCDs). We leveraged the localization and orientational preferences of freely diffusing fluorogens and the solvatochromic effect whereby specific fluorogens are turned on in response to the physic-chemical properties of condensate microenvironments to facilitate single-molecule tracking and super-resolution imaging. We deployed three different fluorogens to probe internal microenvironments and molecular organization of PLCD condensates. The spatiotemporal resolution and environmental sensitivity afforded by single-fluorogen imaging shows that the internal environments of condensates are more hydrophobic than coexisting dilute phases. Molecules within condensates are organized in a spatially inhomogeneous manner featuring slow-moving nanoscale molecular clusters or hubs that coexist with fast-moving molecules. Finally, molecules at interfaces of condensates are found to have distinct orientational preferences when compared to the interiors. Our findings, which affirm computational predictions, help provide a structural basis for condensate viscoelasticity and dispel the notion of protein condensates being isotropic liquids defined by uniform internal densities.
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Affiliation(s)
- Tingting Wu
- Department of Electrical and Systems Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Matthew R King
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Mina Farag
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Department of Biomedical Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Matthew D Lew
- Department of Electrical and Systems Engineering, Washington University in St. Louis, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
- Center for Biomolecular Condensates, James F. McKelvey School of Engineering, Washington University in St. Louis; St. Louis, MO 63130, USA
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2
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Ichikawa S, Ishikawa K, Miyakawa H, Kodama Y. Live-cell imaging of the chloroplast outer envelope membrane using fluorescent dyes. PLANT DIRECT 2022; 6:e462. [PMID: 36398034 PMCID: PMC9666008 DOI: 10.1002/pld3.462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/15/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
UNLABELLED Chloroplasts are organelles composed of sub-organellar compartments-stroma, thylakoids, and starch granules-and are surrounded by outer and inner envelope membranes (OEM and IEM, respectively). The chloroplast OEM and IEM play key roles not only as a barrier separating the chloroplast components from the cytosol but also in the interchange of numerous metabolites and proteins between the chloroplast interior and the cytosol. Fluorescent protein markers for the chloroplast OEM have been widely used to visualize the outermost border of chloroplasts. However, the use of marker proteins requires an established cellular genetic transformation method, which limits the plant species in which marker proteins can be used. Moreover, the high accumulation of OEM marker proteins often elicits abnormal morphological phenotypes of the OEM. Because the OEM can currently only be visualized using exogenous marker proteins, the behaviors of the chloroplast and/or its OEM remain unknown in wild-type cells of various plant species. Here, we visualized the OEM using live-cell staining with the fluorescent dyes rhodamine B and Nile red in several plant species, including crops. We propose rhodamine B and Nile red as new tools for visualizing the chloroplast OEM in living plant cells that do not require genetic transformation. SIGNIFICANCE STATEMENT We established a live-cell imaging method to visualize the chloroplast outer envelope membrane by staining living cells with fluorescent dyes. This method does not require genetic transformation and allows the observation of the chloroplast outer envelope membrane in various plant species.
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Affiliation(s)
- Shintaro Ichikawa
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
- Graduate School of Regional Development and CreativityUtsunomiya UniversityTochigiJapan
| | - Kazuya Ishikawa
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
| | - Hitoshi Miyakawa
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
- Graduate School of Regional Development and CreativityUtsunomiya UniversityTochigiJapan
| | - Yutaka Kodama
- Center for Bioscience Research and EducationUtsunomiya UniversityTochigiJapan
- Graduate School of Regional Development and CreativityUtsunomiya UniversityTochigiJapan
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3
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Sarkar S, De S. Brij Niosomes as Carriers for Sustained Drug Delivery─A Fluorescence-Based Approach to Probe the Niosomal Microenvironment. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:4521-4537. [PMID: 35377656 DOI: 10.1021/acs.langmuir.1c02996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Niosomes were prepared using a triad of polyoxyethylene alkyl ether surfactants. The focus was to elucidate the effects of varying alkyl chain length and varying hydrophilic headgroups on the structure of the niosomes, with an aim to design niosomes for efficient encapsulation and release of both hydrophobic and hydrophilic drugs. The phase transitions of the surfactants were ascertained by differential scanning calorimetry. It was found that the headgroup has a profound influence on the niosomal bilayer. Fluorescent probes Coumarin 153 (C-153) and 1,6-diphenyl-1,3,5-hexatriene were used to probe the structural integrity of the niosomal bilayer under stress conditions. Other aspects of the niosomes were probed by following the aggregation of the dyes fluorescein (FL) and Nile Red, red edge excitation shift, and fluorescence resonance energy transfer (FRET) between them. Fluorescence lifetime imaging microscopy provides proof of the exact location of the donor and acceptor dyes in the niosomes under FRET condition. It was also shown that the niosomes are efficient "carriers" for entrapment and controlled release of the chemotherapeutic drug 5-fluorouracil. It was found that a rigid niosomal bilayer leads to controlled drug release. The present work is relevant for the future use of these niosomes for cargo entrapment.
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Affiliation(s)
- Sudeshna Sarkar
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal 741235, India
| | - Swati De
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal 741235, India
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4
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Carravilla P, Dasgupta A, Zhurgenbayeva G, Danylchuk DI, Klymchenko AS, Sezgin E, Eggeling C. Long-term STED imaging of membrane packing and dynamics by exchangeable polarity-sensitive dyes. BIOPHYSICAL REPORTS 2021; 1:None. [PMID: 34939048 PMCID: PMC8651516 DOI: 10.1016/j.bpr.2021.100023] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/08/2021] [Indexed: 12/28/2022]
Abstract
Understanding the plasma membrane nanoscale organization and dynamics in living cells requires microscopy techniques with high spatial and temporal resolution that permit for long acquisition times and allow for the quantification of membrane biophysical properties, such as lipid ordering. Among the most popular super-resolution techniques, stimulated emission depletion (STED) microscopy offers one of the highest temporal resolutions, ultimately defined by the scanning speed. However, monitoring live processes using STED microscopy is significantly limited by photobleaching, which recently has been circumvented by exchangeable membrane dyes that only temporarily reside in the membrane. Here, we show that NR4A, a polarity-sensitive exchangeable plasma membrane probe based on Nile red, permits the super-resolved quantification of membrane biophysical parameters in real time with high temporal and spatial resolution as well as long acquisition times. The potential of this polarity-sensitive exchangeable dye is showcased by live-cell real-time three-dimensional STED recordings of bleb formation and lipid exchange during membrane fusion as well as by STED-fluorescence correlation spectroscopy experiments for the simultaneous quantification of membrane dynamics and lipid packing that correlate in model and live-cell membranes.
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Affiliation(s)
- Pablo Carravilla
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Anindita Dasgupta
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
| | - Gaukhar Zhurgenbayeva
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
| | - Dmytro I. Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Andrey S. Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, Illkirch, France
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian Eggeling
- Leibniz Institute of Photonic Technology e.V., Jena, Germany
- Faculty of Physics and Astronomy, Institute of Applied Optics and Biophysics, Friedrich Schiller University Jena, Jena, Germany
- Jena School for Microbial Communication, Friedrich Schiller University Jena, Jena, Germany
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Jena Center for Soft Matter, Jena, Germany
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5
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The potential of fluorescent dyes-comparative study of Nile red and three derivatives for the detection of microplastics. Anal Bioanal Chem 2021; 413:1059-1071. [PMID: 33415434 DOI: 10.1007/s00216-020-03066-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 10/22/2022]
Abstract
During the last years, microplastics in the environment came to the fore in environmental science research. For an appropriate risk assessment, it is essential to know the levels of microplastic contamination in the environment. In the field of microplastic detection, extensive research has been carried out in recent years. While common methods such as Raman spectroscopy and pyrolysis GC-MS are time-consuming and require trained staff and expensive equipment, there is the need for a cheap and easily applicable method. Staining microplastics with the fluorescent dye Nile red (NR) has a high potential to fulfill these criteria. In our work, we tested Nile red and newly developed derivatives, with the aim of achieving greater selectivity for plastic particles and more intense fluorescence. In addition, the influence of using different solvents and water at different pH values in the dyeing process was investigated by analyzing solid sample fluorescence spectra of dyed microplastics and natural particles. Finally, the method developed from the acquired knowledge was tested for sea salt. Graphical abstract.
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6
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Valero M, Hu W, Houston JE, Dreiss CA. Solubilisation of salicylate in F127 micelles: Effect of pH and temperature on morphology and interactions with cyclodextrin. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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7
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Swain J, Mishra J, Ghosh G, Mishra AK. Quantification of micropolarity and microviscosity of aggregation and salt-induced gelation of sodium deoxycholate (NaDC) using Nile red fluorescence. Photochem Photobiol Sci 2019; 18:2773-2781. [DOI: 10.1039/c9pp00293f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nile red fluorescence properties can be used for the estimation of micropolarity and microviscosity of the gel medium.
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Affiliation(s)
- Jitendriya Swain
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai 600 036
- India
| | - Jhili Mishra
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai 600 036
- India
| | - Goutam Ghosh
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai 600 036
- India
| | - Ashok Kumar Mishra
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai 600 036
- India
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8
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Bhuiya S, Haque L, Das S. Association of iminium and alkanolamine forms of the benzo[c]phenanthridine alkaloid chelerythrine with human serum albumin: photophysical, thermodynamic and theoretical approach. NEW J CHEM 2018. [DOI: 10.1039/c7nj02972a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Association of isoforms of chelerythrine (CHL) with HSA.
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Affiliation(s)
- Sutanwi Bhuiya
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| | - Lucy Haque
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
| | - Suman Das
- Department of Chemistry
- Jadavpur University
- Kolkata 700 032
- India
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9
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Zhdanova NG, Maksimov EG, Arutyunyan AM, Fadeev VV, Shirshin EA. Tyrosine fluorescence probing of conformational changes in tryptophan-lacking domain of albumins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:223-229. [PMID: 27918933 DOI: 10.1016/j.saa.2016.11.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/17/2016] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
We addressed the possibility of using tyrosine (Tyr) fluorescence for monitoring conformational changes of proteins which are undetectable via tryptophan (Trp) fluorescence. The model objects, human (HSA) and bovine (BSA) serum albumins, contain one and two Trp residues, respectively, while Tyr is more uniformly distributed over their structure. The results of the investigation of albumins interaction with ethanol using intrinsic Trp and Tyr steady-state and time-resolved picosecond fluorescence indicated the presence of an intermediate at 10% (v/v) of ethanol in solution, that was supported by the results of extrinsic fluorescence measurements with the Nile Red dye. Based on the comparison of HSA and BSA Trp and Tyr fluorescence, it was suggested that conformational changes at low ethanol concentration are located in the domain III of albumins, which lacks tryptophan residues. The sensitivity of Tyr fluorescence to domain III alterations was further verified by studying albumins interaction with GdnHCl.
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Affiliation(s)
- N G Zhdanova
- Department of Physics, M.V. Lomonosov Moscow State University, 119991, Russia.
| | - E G Maksimov
- Department of Biology, M.V. Lomonosov Moscow State University, 119991, Russia
| | - A M Arutyunyan
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Russia
| | - V V Fadeev
- Department of Physics, M.V. Lomonosov Moscow State University, 119991, Russia
| | - E A Shirshin
- Department of Physics, M.V. Lomonosov Moscow State University, 119991, Russia.
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10
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Booth EA, Thorner J. A FRET-based method for monitoring septin polymerization and binding of septin-associated proteins. Methods Cell Biol 2016; 136:35-56. [PMID: 27473902 DOI: 10.1016/bs.mcb.2016.03.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Much about septin function has been inferred from in vivo studies using mainly genetic methods, and much of what we know about septin organization has been obtained through examination of static structures in vitro primarily by electron microscopy. Deeper mechanistic insight requires real-time analysis of the dynamics of the assembly of septin-based structures and how other proteins associate with them. We describe here a Förster resonance energy transfer (FRET)-based approach for measuring in vitro the rate and extent of filament formation from septin complexes, binding of other proteins to septin structures, and the apparent affinities of these interactions. FRET is particularly well suited for interrogating protein-protein interactions, especially on a rapid timescale; the spectral change provides an unambiguous indication of whether two elements within the system under study are associating and serves as a molecular-level "ruler" because it is very sensitive to the separation between the donor and acceptor fluorophores over biologically relevant distances (≤10nm). The necessary procedures involve generation of appropriate cysteine-less and single cysteine-containing septin variants, expression and purification of the heterooctameric complexes containing them, efficient labeling of the purified complexes with desired fluorophores, fluorimetric measurement of FRET, and appropriate safeguards and controls in data acquisition and analysis. Our methods can be used to interrogate the effects of buffer conditions, small molecules, and septin-binding proteins on septin filament assembly or stability; determine the effect of alternative septin subunits, mutational alterations, or posttranslational modifications on assembly; and, delineate the location of septin-binding proteins.
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Affiliation(s)
- E A Booth
- University of California, Berkeley, CA, United States
| | - J Thorner
- University of California, Berkeley, CA, United States
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11
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Herrera MG, Veuthey TV, Dodero VI. Self-organization of gliadin in aqueous media under physiological digestive pHs. Colloids Surf B Biointerfaces 2016; 141:565-575. [PMID: 26897550 DOI: 10.1016/j.colsurfb.2016.02.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 02/02/2016] [Accepted: 02/08/2016] [Indexed: 12/22/2022]
Abstract
Here we showed that gliadin, a complex protein system related to celiac disease and other human diseases, is spontaneously self-organized in a very dilute solution at pH 3.0 and 7.0 in water under low ionic strength (10mM NaCl). The spontaneous self-organization at pH 3.0 increases the apparent solubility due to the formation of finite sized aggregates, such as those formed in the micellization of amphiphilic molecules. Switching the pH from 3.0 to 7.0 lead to a phase separation, however part of the nano-particles are stable remaining disperse in water after centrifugation. Also, beside the pH change led to changes in protein composition and concentration, we determined that the secondary structure of both system is the same. Moreover, Tyrs are slightly more buried and Trps are slightly more exposed to water at pH 7.0 than those at pH 3.0. Electron microscopy techniques showed that both gliadin systems are composed of nanostructures and in the case of pH 7.0 amorphous microaggregates were found, too. Only nanostructures at pH 3.0 showed a micromolar binding affinity to Nile red probe, suggesting the presence of accessible hydrophobic patches which are not more accessible at pH 7.0. All our results suggest that gliadin is able to self-organized at pH 3.0 forming protein micelles type nanostructures (ζ=+13, 42 ± 1.55 mV), meanwhile at 7.0 the decrease of superficial charge to ζ of +4, 78 ± 0.48 mV led to the formation of stable colloidal nanoparticles, unable to interact with Nile red probe. Our findings may open new perspectives for the understanding of gliadin ability to avoid proteolysis, to reach and cross the intestinal lumen and to trigger different immunological disorders.
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Affiliation(s)
- María G Herrera
- Departamento de Química-INQUISUR, Universidad Nacional del Su- CONICET, Av. Alem 1253, Bahía Blanca, Argentina
| | - Tania V Veuthey
- Departamento de Química-INQUISUR, Universidad Nacional del Su- CONICET, Av. Alem 1253, Bahía Blanca, Argentina
| | - Verónica I Dodero
- Departamento de Química-INQUISUR, Universidad Nacional del Su- CONICET, Av. Alem 1253, Bahía Blanca, Argentina; Universität Bielefeld, Fakultät für Chemie, Organische Chemie, Universitätsstr. 25, 33615 Bielefeld, Germany.
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12
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Booth EA, Vane EW, Dovala D, Thorner J. A Förster Resonance Energy Transfer (FRET)-based System Provides Insight into the Ordered Assembly of Yeast Septin Hetero-octamers. J Biol Chem 2015; 290:28388-28401. [PMID: 26416886 PMCID: PMC4653696 DOI: 10.1074/jbc.m115.683128] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Indexed: 12/21/2022] Open
Abstract
Prior studies in both budding yeast (Saccharomyces cerevisiae) and in human cells have established that septin protomers assemble into linear hetero-octameric rods with 2-fold rotational symmetry. In mitotically growing yeast cells, five septin subunits are expressed (Cdc3, Cdc10, Cdc11, Cdc12, and Shs1) and assemble into two types of rods that differ only in their terminal subunit: Cdc11-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Cdc11 and Shs1-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Shs1. EM analysis has shown that, under low salt conditions, the Cdc11-capped rods polymerize end to end to form long paired filaments, whereas Shs1-capped rods form arcs, spirals, and rings. To develop a facile method to study septin polymerization in vitro, we exploited our previous work in which we generated septin complexes in which all endogenous cysteine (Cys) residues were eliminated by site-directed mutagenesis, except an introduced E294C mutation in Cdc11 in these experiments. Mixing samples of a preparation of such single-Cys containing Cdc11-capped rods that have been separately derivatized with organic dyes that serve as donor and acceptor, respectively, for FRET provided a spectroscopic method to monitor filament assembly mediated by Cdc11-Cdc11 interaction and to measure its affinity under specified conditions. Modifications of this same FRET scheme also allow us to assess whether Shs1-capped rods are capable of end to end association either with themselves or with Cdc11-capped rods. This FRET approach also was used to follow the binding to septin filaments of a septin-interacting protein, the type II myosin-binding protein Bni5.
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Affiliation(s)
- Elizabeth A Booth
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Eleanor W Vane
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Dustin Dovala
- Program in Microbial Pathogenesis and Host Defense, Department of Microbiology and Immunology, University of California School of Medicine, San Francisco, California 94158-2200
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics, and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202.
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13
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Nithianantham S, Le S, Seto E, Jia W, Leary J, Corbett KD, Moore JK, Al-Bassam J. Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics. eLife 2015. [PMID: 26208336 PMCID: PMC4574351 DOI: 10.7554/elife.08811] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microtubule dynamics and polarity stem from the polymerization of
αβ-tubulin heterodimers. Five conserved tubulin cofactors/chaperones
and the Arl2 GTPase regulate α- and β-tubulin assembly into
heterodimers and maintain the soluble tubulin pool in the cytoplasm, but their
physical mechanisms are unknown. Here, we reconstitute a core tubulin chaperone
consisting of tubulin cofactors TBCD, TBCE, and Arl2, and reveal a cage-like
structure for regulating αβ-tubulin. Biochemical assays and electron
microscopy structures of multiple intermediates show the sequential binding of
αβ-tubulin dimer followed by tubulin cofactor TBCC onto this chaperone,
forming a ternary complex in which Arl2 GTP hydrolysis is activated to alter
αβ-tubulin conformation. A GTP-state locked Arl2 mutant inhibits
ternary complex dissociation in vitro and causes severe defects in microtubule
dynamics in vivo. Our studies suggest a revised paradigm for tubulin cofactors and
Arl2 functions as a catalytic chaperone that regulates soluble
αβ-tubulin assembly and maintenance to support microtubule
dynamics. DOI:http://dx.doi.org/10.7554/eLife.08811.001 Cells contain a network of protein filaments called microtubules. These filaments are
involved in many biological processes; for example, they help cells keep the right
shape, and they help to transport proteins and other materials inside cells. Two proteins called α-tubulin and β-tubulin are the building blocks of
microtubules. The filaments are very dynamic structures that can rapidly change
length as individual tubulin units are either added or removed to the filament ends.
Several proteins known as tubulin cofactors and an enzyme called Arl2 help to build a
vast pool of tubulin units that are able attach to the microtubules. These
units—called αβ-tubulin—are formed by α-tubulin
and β-tubulin binding to each other, but it not clear exactly what roles the
tubulin cofactors and Arl2 play in this process. Nithianantham et al. used a combination of microscopy and biochemical techniques to
study how the tubulin cofactors and Arl2 are organised, and their role in the
assembly of microtubules in yeast. The experiments show that Arl2 and two tubulin
cofactors associate with each other to form a stable ‘complex’ that has
a cage-like structure. A molecule of αβ-tubulin binds to the complex,
followed by another cofactor called TBCC. This activates the enzyme activity of Arl2,
which releases the energy needed to alter the shape of the αβ-tubulin.
Nithianantham et al. also found that yeast cells with a mutant form of Arl2 that
lacked enzyme activity had problems forming microtubules. Together, these findings show that the tubulin cofactors and Arl2 form a complex that
regulates the assembly and maintenance of αβ-tubulin. The next
challenge is to understand how this regulation influences the way that microtubules
grow and shrink inside cells. DOI:http://dx.doi.org/10.7554/eLife.08811.002
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Affiliation(s)
- Stanley Nithianantham
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Sinh Le
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Elbert Seto
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Weitao Jia
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Julie Leary
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Jawdat Al-Bassam
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
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14
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Location, dynamics and solvent relaxation of a nile red-based phase-sensitive fluorescent membrane probe. Chem Phys Lipids 2014; 183:1-8. [DOI: 10.1016/j.chemphyslip.2014.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 11/20/2022]
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15
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Spectral and aggregative properties of two oxazine dyes in aqueous solutions containing structure-breaking and multifunctional additives. J Mol Liq 2014. [DOI: 10.1016/j.molliq.2013.12.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Wang Z, Sun J, Jia X. Self-immolative nanoparticles triggered by hydrogen peroxide and pH. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/pola.27203] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhijian Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Jianbo Sun
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
| | - Xinru Jia
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering; Peking University; Beijing 100871 China
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17
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Stirling DP, Cummins K, Mishra M, Teo W, Yong VW, Stys P. Toll-like receptor 2-mediated alternative activation of microglia is protective after spinal cord injury. Brain 2013; 137:707-23. [DOI: 10.1093/brain/awt341] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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18
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Méndez-Pérez M, Vaz B, García-Río L, Pérez-Lorenzo M. Polymeric premicelles as efficient lipophilic nanocarriers: extending drug uptake to the submicellar regime. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11251-11259. [PMID: 23926963 DOI: 10.1021/la4022273] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A multitechnique investigation on the self-assembly behavior of a biocompatible polymer in the high dilution regime is reported herein. The obtained results unambiguously reveal the existence of premicellar structures that may further extend the efficiency of traditional polymeric micelles as drug-delivery vehicles. Such an expansion in the excipient capacity arises from (i) the increased drug retention of submicellar assemblies due to their higher resistance to dilution and therefore to their improved circulation time and (ii) the superior carrier permeability of these premicellar aggregates as a result of their smaller size, which makes these drug vehicles more effectively targeted to the tumors through the so-called enhanced permeability and retention effect. The uptake ability of the polymeric premicelles described in this work has been tested through the use of Nile Red as drug model given its intermediate lipophilicity (log P ≈ 3-5) similar to that of potent chemotherapy agents and its microenvironment-sensitive fluorescence properties relevant for localization purposes. Thus, it has been found that an efficient drug encapsulation can be achieved under conditions well below the normally required critical micelle concentration. These results may constitute a promising strategy in order to develop new and more efficient polymeric formulations in drug delivery technology.
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Affiliation(s)
- María Méndez-Pérez
- Center for Research in Biological Chemistry and Molecular Materials, Universidade de Santiago de Compostela , 15782 Santiago de Compostela, Spain
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19
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Figueira-González M, Francisco V, García-Río L, Marques EF, Parajó M, Rodríguez-Dafonte P. Self-Aggregation Properties of Ionic Liquid 1,3-Didecyl-2-methylimidazolium Chloride in Aqueous Solution: From Spheres to Cylinders to Bilayers. J Phys Chem B 2013; 117:2926-37. [DOI: 10.1021/jp3117962] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- María Figueira-González
- Centro Singular de Investigación
en Química Biológica y Materiales Moleculares, Department
of Physical Chemistry, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Vitor Francisco
- Centro Singular de Investigación
en Química Biológica y Materiales Moleculares, Department
of Physical Chemistry, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Luis García-Río
- Centro Singular de Investigación
en Química Biológica y Materiales Moleculares, Department
of Physical Chemistry, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Eduardo F. Marques
- Centro de Investigação
em Química, Department of Chemistry and Biochemistry, Faculty
of Sciences, University of Porto, Rua do
Campo Alegre, 687, 4169-007 Porto, Portugal
| | - Mercedes Parajó
- Centro Singular de Investigación
en Química Biológica y Materiales Moleculares, Department
of Physical Chemistry, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Pedro Rodríguez-Dafonte
- Centro Singular de Investigación
en Química Biológica y Materiales Moleculares, Department
of Physical Chemistry, University of Santiago de Compostela, 15782, Santiago de Compostela, Spain
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20
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Wang Z, Gao M, Sun J, Liang D, Jia X. Photoresponsive Dendronized Copolymers of Styrene and Maleic Anhydride Pendant with Poly(amidoamine) Dendrons as Side Groups. Macromolecules 2013. [DOI: 10.1021/ma302358t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Zhijian Wang
- Beijing National Laboratory for Molecular Sciences, Key
Laboratory of Polymer Chemistry and Physics of the Ministry of Education,
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Min Gao
- Beijing National Laboratory for Molecular Sciences, Key
Laboratory of Polymer Chemistry and Physics of the Ministry of Education,
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jianbo Sun
- Beijing National Laboratory for Molecular Sciences, Key
Laboratory of Polymer Chemistry and Physics of the Ministry of Education,
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Dehai Liang
- Beijing National Laboratory for Molecular Sciences, Key
Laboratory of Polymer Chemistry and Physics of the Ministry of Education,
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xinru Jia
- Beijing National Laboratory for Molecular Sciences, Key
Laboratory of Polymer Chemistry and Physics of the Ministry of Education,
College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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21
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Pickup JC, Khan F, Zhi ZL, Coulter J, Birch DJS. Fluorescence intensity- and lifetime-based glucose sensing using glucose/galactose-binding protein. J Diabetes Sci Technol 2013; 7:62-71. [PMID: 23439161 PMCID: PMC3692217 DOI: 10.1177/193229681300700108] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We review progress in our laboratories toward developing in vivo glucose sensors for diabetes that are based on fluorescence labeling of glucose/galactose-binding protein. Measurement strategies have included both monitoring glucose-induced changes in fluorescence resonance energy transfer and labeling with the environmentally sensitive fluorophore, badan. Measuring fluorescence lifetime rather than intensity has particular potential advantages for in vivo sensing. A prototype fiber-optic-based glucose sensor using this technology is being tested.
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Affiliation(s)
- John C Pickup
- Diabetes Research Group, King’s College London School of Medicine, Guy’s Hospital, London, United Kingdom.
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22
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Gilani AG, Hosseini SE, Moghadam M, Alizadeh E. Excited state electric dipole moment of nile blue and brilliant cresyl blue: a comparative study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 89:231-237. [PMID: 22261111 DOI: 10.1016/j.saa.2011.12.063] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 12/18/2011] [Accepted: 12/21/2011] [Indexed: 05/31/2023]
Abstract
A solvatochromic study on the photophysical properties of two cationic oxazine dyes (brilliant cresyl blue and nile blue) was carried out. The electronic absorption and emission spectra of the dyes were recorded in various organic solvents with different polarity. The ground and the excited state dipole moments of the dyes were estimated from solvatochromic shift method. The solvent dependent spectral shifts in absorption and fluorescence spectra were analyzed by the Katritzky and Kamlet-Taft multi-parameter scales. This work is characterized by detailed quantitative studies on the nature and extent of solvent-solute interactions.
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Affiliation(s)
- A Ghanadzadeh Gilani
- Department of Chemistry, Faculty of Science, University of Guilan, Rasht 41335, Iran.
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23
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Dsouza RN, Pischel U, Nau WM. Fluorescent dyes and their supramolecular host/guest complexes with macrocycles in aqueous solution. Chem Rev 2011; 111:7941-80. [PMID: 21981343 DOI: 10.1021/cr200213s] [Citation(s) in RCA: 797] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Roy N Dsouza
- School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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24
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Heider EC, Peterson EM, Barhoum M, Gericke KH, Harris JM. Quantitative fluorescence microscopy to determine molecular occupancy of phospholipid vesicles. Anal Chem 2011; 83:5128-36. [PMID: 21648957 DOI: 10.1021/ac200129n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Encapsulation of molecules in phospholipid vesicles provides unique opportunities to study chemical reactions in small volumes as well as the behavior of individual proteins, enzymes, and ribozymes in a confined region without requiring a tether to immobilize the molecule to a surface. These experiments generally depend on generating a predictable loading of vesicles with small numbers of target molecules and thus raise a significant measurement challenge, namely, to quantify molecular occupancy of vesicles at the single-molecule level. In this work, we describe an imaging experiment to measure the time-dependent fluorescence from individual dye molecules encapsulated in ~130 nm vesicles that are adhered to a glass surface. For determining a fit of the molecular occupancy data to a Poisson model, it is critical to count empty vesicles in the population since these dominate the sample when the mean occupancy is small, λ ≤ ~1. Counting empty vesicles was accomplished by subsequently labeling all the vesicles with a lipophilic dye and reimaging the sample. By counting both the empty vesicles and those containing fluors, and quantifying the number of fluors present, we demonstrate a self-consistent Poisson distribution of molecular occupancy for well-solvated molecules, as well as anomalies due to aggregation of dye, which can arise even at very low solution concentrations. By observation of many vesicles in parallel in an image, this approach provides quantitative information about the distribution of molecular occupancy in a population of vesicles.
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Affiliation(s)
- Emily C Heider
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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25
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Mach H, Arvinte T. Addressing new analytical challenges in protein formulation development. Eur J Pharm Biopharm 2011; 78:196-207. [DOI: 10.1016/j.ejpb.2011.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Revised: 02/24/2011] [Accepted: 03/02/2011] [Indexed: 12/15/2022]
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26
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Schibel AEP, Heider EC, Harris JM, White HS. Fluorescence microscopy of the pressure-dependent structure of lipid bilayers suspended across conical nanopores. J Am Chem Soc 2011; 133:7810-5. [PMID: 21542629 DOI: 10.1021/ja1117182] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Glass and fused-quartz nanopore membranes containing a single conically shaped pore are promising solid supports for lipid bilayer ion-channel recordings due to the high inherent stability of lipid bilayers suspended across the nanopore orifice, as well as the favorable electrical properties of glass and fused quartz. Fluorescence microscopy is used here to investigate the structure of the suspended lipid bilayer as a function of the pressure applied across a fused-quartz nanopore membrane. When a positive pressure is applied across the bilayer, from the nanopore interior relative to the exterior bulk solution, insertion or reconstitution of operative ion channels (e.g., α-hemolysin (α-HL) and gramicidin) in the bilayer is observed; conversely, reversing the direction of the applied pressure results in loss of all channel activity, although the bilayer remains intact. The dependence of the bilayer structure on pressure was explored by imaging the fluorescence intensity from Nile red dye doped into suspended 1,2-diphytanoyl-sn-glycero-3-phosphocholine bilayers, while simultaneously recording the activity of an α-HL channel. The fluorescence images suggest that a positive pressure results in compression of the bilayer leaflets and an increase in the bilayer curvature, making it suitable for ion-channel formation and activity. At negative pressure, the fluorescence images are consistent with separation of the lipid leaflets, resulting in the observed loss of the ion-channel activity. The fluorescence data indicate that the changes in the pressure-induced bilayer structure are reversible, consistent with the ability to repeatedly switch the ion-channel activity on and off by applying positive and negative pressures, respectively.
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Affiliation(s)
- Anna E P Schibel
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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27
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Lu Y, Porterfield R, Thunder T, Paige MF. An ensemble and single-molecule fluorescence microscopy investigation of phase-separated monolayer films stained with Nile Red. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:216-223. [PMID: 21115390 DOI: 10.1016/j.saa.2010.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 09/08/2010] [Accepted: 09/29/2010] [Indexed: 05/30/2023]
Abstract
Phase-separated Langmuir-Blodgett monolayer films prepared from mixtures of arachidic acid (C19H39COOH) and perfluorotetradecanoic acid (C13F27COOH) were stained via spin-casting with the polarity sensitive phenoxazine dye Nile Red, and characterized using a combination of ensemble and single-molecule fluorescence microscopy measurements. Ensemble fluorescence microscopy and spectromicroscopy showed that Nile Red preferentially associated with the hydrogenated domains of the phase-separated films, and was strongly fluorescent in these areas of the film. These measurements, in conjunction with single-molecule fluorescence imaging experiments, also indicated that a small sub-population of dye molecules localizes on the perfluorinated regions of the sample, but that this sub-population is spectroscopically indistinguishable from that associated with the hydrogenated domains. The relative importance of selective dye adsorption and local polarity sensitivity of Nile Red for staining applications in phase-separated LB films as well as in cellular environments is discussed in context of the experimental results.
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Affiliation(s)
- Yin Lu
- Department of Chemistry, University of Saskatchewan 110 Science Place, Saskatoon, SK S7N 5C9, Canada
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28
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Pande A, Ghosh KS, Banerjee PR, Pande J. Increase in surface hydrophobicity of the cataract-associated P23T mutant of human gammaD-crystallin is responsible for its dramatically lower, retrograde solubility. Biochemistry 2010; 49:6122-9. [PMID: 20553008 DOI: 10.1021/bi100664s] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cataract-associated Pro23 to Thr (P23T) mutation in human gammaD-crystallin (HGD) has a variety of phenotypes and is geographically widespread. Therefore, there is considerable interest in understanding the molecular basis of cataract formation due to this mutation. We showed earlier [Pande, A., et al. (2005) Biochemistry 44, 2491-2500] that the probable basis of opacity in this case is the severely compromised, retrograde solubility and aggregation of P23T relative to HGD. The dramatic solubility change occurs even as the structure of the mutant protein remains essentially unchanged in vitro. We proposed that the retrograde solubility and aggregation of P23T were mediated by net hydrophobic, protein-protein interactions. On the basis of these initial findings for P23T and related mutants, and the subsequent finding that they show atypical phase behavior [McManus, J. J., et al. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 16856-16861], we concluded that the protein clusters formed in solutions of the mutant proteins were held together by net hydrophobic, anisotropic interactions. Here we show, using chemical probes, that the surface hydrophobicities of these mutants are inversely related to their solubility. Furthermore, by probing the isolated N-terminal domains of HGD and P23T directly, we find that the increase in the surface hydrophobicity of P23T is localized in the N-terminal domain. Modeling studies suggest the presence of sticky patches on the surface of the N-terminal domain that could be engaged in the formation of protein clusters via hydrophobic protein-protein interactions. This work thus provides direct evidence of the dominant role played by net hydrophobic and anisotropic protein-protein interactions in the aggregation of P23T.
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Affiliation(s)
- Ajay Pande
- Department of Chemistry, Life Sciences Research Building, University at Albany, State University of New York, Albany, New York 12222, USA
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29
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Wolff J. Plasma membrane tubulin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1415-33. [PMID: 19328773 DOI: 10.1016/j.bbamem.2009.03.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/13/2009] [Accepted: 03/19/2009] [Indexed: 01/17/2023]
Abstract
The association of tubulin with the plasma membrane comprises multiple levels of penetration into the bilayer: from integral membrane protein, to attachment via palmitoylation, to surface binding, and to microtubules attached by linker proteins to proteins in the membrane. Here we discuss the soundness and weaknesses of the chemical and biochemical evidence marshaled to support these associations, as well as the mechanisms by which tubulin or microtubules may regulate functions at the plasma membrane.
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Affiliation(s)
- J Wolff
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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30
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Hawe A, Sutter M, Jiskoot W. Extrinsic fluorescent dyes as tools for protein characterization. Pharm Res 2008; 25:1487-99. [PMID: 18172579 PMCID: PMC2440933 DOI: 10.1007/s11095-007-9516-9] [Citation(s) in RCA: 858] [Impact Index Per Article: 53.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 12/05/2007] [Indexed: 11/16/2022]
Abstract
Noncovalent, extrinsic fluorescent dyes are applied in various fields of protein analysis, e.g. to characterize folding intermediates, measure surface hydrophobicity, and detect aggregation or fibrillation. The main underlying mechanisms, which explain the fluorescence properties of many extrinsic dyes, are solvent relaxation processes and (twisted) intramolecular charge transfer reactions, which are affected by the environment and by interactions of the dyes with proteins. In recent time, the use of extrinsic fluorescent dyes such as ANS, Bis-ANS, Nile Red, Thioflavin T and others has increased, because of their versatility, sensitivity and suitability for high-throughput screening. The intention of this review is to give an overview of available extrinsic dyes, explain their spectral properties, and show illustrative examples of their various applications in protein characterization.
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Affiliation(s)
- Andrea Hawe
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Marc Sutter
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
- Novartis Pharma AG, WSJ-316.4.14, CH-4056 Basel, Switzerland
| | - Wim Jiskoot
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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31
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Frade VH, Sousa MJ, Moura JC, Gonçalves MST. Synthesis, characterisation and antimicrobial activity of new benzo[a]phenoxazine based fluorophores. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.09.108] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Gao F, Mei E, Lim M, Hochstrasser RM. Probing lipid vesicles by bimolecular association and dissociation trajectories of single molecules. J Am Chem Soc 2007; 128:4814-22. [PMID: 16594718 DOI: 10.1021/ja058098a] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Vesicles prepared by DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) and SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid molecules having sizes smaller than the diffraction-limited focused laser beam have been used to confine single molecules in the laser focus. The confinement of single molecules in a volume smaller than the focused laser beam leads to a Gaussian distribution of single molecule fluorescence intensity. The interactions of single Nile Red molecules with DMPC and SOPC lipid bilayers were studied by single molecule fluorescence confocal microscopy. Nile Red molecules were observed to associate with and dissociate from individual DMPC and SOPC vesicles adsorbed on a glass surface, generating on-and-off fluctuations in a fluorescence signal representing a very low noise two-state trajectory. Off-time statistics were used to investigate the mean radius of the vesicles and the size distribution functions. The means of the on-time distributions of Nile Red in DMPC and SOPC vesicles were significantly different. The association and dissociation reactions of single Nile Red molecules with a vesicle have been studied. Features of the bimolecular interaction between the probe Nile Red and the vesicle were evaluated from the uncorrelated mean on-time and vesicle radius distributions, and the linear Nile Red concentration dependence of the mean off-time. Nile Red is shown to be a useful probe of the structural fluctuations and heterogeneity of these membrane structures, and it is a useful model with which to directly study a diffusion-influenced reversible bimolecular reaction.
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Affiliation(s)
- Feng Gao
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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33
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Mukherjee S, Kombrabail M, Krishnamoorthy G, Chattopadhyay A. Dynamics and heterogeneity of bovine hippocampal membranes: role of cholesterol and proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2130-44. [PMID: 17618864 DOI: 10.1016/j.bbamem.2007.05.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 05/05/2007] [Accepted: 05/29/2007] [Indexed: 12/14/2022]
Abstract
The structural and dynamic consequence of alterations in membrane lipid composition (specifically cholesterol) in neuronal membranes is poorly understood. Previous work from our laboratory has established bovine hippocampal membranes as a convenient natural source for studying neuronal receptors. In this paper, we have explored the role of cholesterol and proteins in the dynamics and heterogeneity of bovine hippocampal membranes using fluorescence lifetime distribution analysis of the environment-sensitive fluorescent probe Nile Red incorporated into such membranes by the maximum entropy method (MEM), and time-resolved fluorescence anisotropy measurements. The peak position and the width of the lifetime distribution of Nile Red show a progressive reduction with increasing cholesterol depletion from native hippocampal membranes indicating that the extent of heterogeneity decreases with decrease in membrane cholesterol content. This is accompanied by a concomitant decrease of the fluorescence anisotropy and rotational correlation time. Our results point out that the microenvironment experienced by Nile Red is relatively insensitive to the presence of proteins in hippocampal membranes. Interestingly, Nile Red lifetime distribution in liposomes of lipid extracts is similar to that of native membranes indicating that proteins do not contribute significantly to the high level of heterogeneity observed in native membranes. These results could be relevant in understanding the neuronal diseases characterized by defective membrane lipid metabolism.
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Affiliation(s)
- Soumi Mukherjee
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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34
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Sutter M, Oliveira S, Sanders NN, Lucas B, van Hoek A, Hink MA, Visser AJWG, De Smedt SC, Hennink WE, Jiskoot W. Sensitive spectroscopic detection of large and denatured protein aggregates in solution by use of the fluorescent dye Nile red. J Fluoresc 2007; 17:181-92. [PMID: 17294134 PMCID: PMC1915606 DOI: 10.1007/s10895-007-0156-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 01/02/2007] [Indexed: 11/09/2022]
Abstract
The fluorescent dye Nile red was used as a probe for the sensitive detection of large, denatured aggregates of the model protein β-galactosidase (E. coli) in solution. Aggregates were formed by irreversible heat denaturation of β-galactosidase below and above the protein’s unfolding temperature of 57.4°C, and the presence of aggregates in heated solutions was confirmed by static light scattering. Interaction of Nile red with β-galactosidase aggregates led to a shift of the emission maximum (λmax) from 660 to 611 nm, and to an increase of fluorescence intensity. Time-resolved fluorescence and fluorescence correlation spectroscopy (FCS) measurements showed that Nile red detected large aggregates with hydrodynamic radii around 130 nm. By steady-state fluorescence measurements, it was possible to detect 1 nM of denatured and aggregated β-galactosidase in solution. The comparison with size exclusion chromatography (SEC) showed that native β-galactosidase and small aggregates thereof had no substantial effect on the fluorescence of Nile red. Large aggregates were not detected by SEC, because they were excluded from the column. The results with β-galactosidase demonstrate the potential of Nile red for developing complementary analytical methods that overcome the size limitations of SEC, and can detect the formation of large protein aggregates at early stages.
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Affiliation(s)
- Marc Sutter
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
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35
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Mukherjee S, Raghuraman H, Chattopadhyay A. Membrane localization and dynamics of Nile Red: Effect of cholesterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:59-66. [PMID: 16934217 DOI: 10.1016/j.bbamem.2006.07.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Revised: 07/07/2006] [Accepted: 07/14/2006] [Indexed: 11/29/2022]
Abstract
The organization and dynamics of the hydrophobic fluorescent probe Nile Red incorporated in DOPC vesicles containing varying amounts of cholesterol has been monitored utilizing fluorescence-based approaches which include the red edge excitation shift (REES) approach and the parallax method for depth determination. Our results show that the fluorescence emission maximum, intensity, polarization, and lifetime of Nile Red vary with the cholesterol content of the membrane. Interestingly, Nile Red exhibits significant REES independent of the presence of cholesterol. This indicates that Nile Red is localized in a motionally restricted environment in the membrane. This is supported by analysis of membrane penetration depth of Nile Red using the parallax method which points out to a membrane interfacial localization of Nile Red. These results could be useful in analyzing membrane organization and heterogeneity in natural membranes using Nile Red.
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Affiliation(s)
- Soumi Mukherjee
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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Descalzo AB, Dolores Marcos M, Monte C, Martínez-Máñez R, Rurack K. Mesoporous silica materials with covalently anchored phenoxazinone dyes as fluorescent hybrid materials for vapour sensing. ACTA ACUST UNITED AC 2007. [DOI: 10.1039/b707473e] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kim SY, Semyonov AN, Twieg RJ, Horwich AL, Frydman J, Moerner WE. Probing the sequence of conformationally induced polarity changes in the molecular chaperonin GroEL with fluorescence spectroscopy. J Phys Chem B 2006; 109:24517-25. [PMID: 16375456 PMCID: PMC1414071 DOI: 10.1021/jp0534232] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic interactions play a major role in binding non-native substrate proteins in the central cavity of the bacterial chaperonin GroEL. The sequence of local conformational changes by which GroEL and its cofactor GroES assist protein folding can be explored using the polarity-sensitive fluorescence probe Nile Red. A specific single-cysteine mutant of GroEL (Cys261), whose cysteine is located inside the central cavity at the apical region of the protein, was covalently labeled with synthetically prepared Nile Red maleimide (NR). Bulk fluorescence spectra of Cys261-NR were measured to examine the effects of binding of the stringent substrate, malate dehydrogenase (MDH), GroES, and nucleotide on the local environment of the probe. After binding denatured substrate, the fluorescence intensity increased by 32 +/- 7%, suggesting enhanced hydrophobicity at the position of the label. On the other hand, in the presence of ATP, the fluorescence intensity decreased by 13 +/- 3%, implying increased local polarity. To explore the sequence of local polarity changes, substrate, GroES, and various nucleotides were added in different orders; the resulting changes in emission intensity provide insight into the sequence of conformational changes occurring during GroEL-mediated protein folding.
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Affiliation(s)
- So Yeon Kim
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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38
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Sherman DB, Pitner JB, Ambroise A, Thomas KJ. Synthesis of thiol-reactive, long-wavelength fluorescent phenoxazine derivatives for biosensor applications. Bioconjug Chem 2006; 17:387-92. [PMID: 16536470 DOI: 10.1021/bc050309d] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two environmentally sensitive, long-wavelength fluorescent phenoxazine derivatives, INR and IANR, were synthesized with linkers for conjugation to the thiol group of cysteine in binding proteins. The linkers were designed based on the attachment sites at two different positions on the phenoxazine, which were chosen in order to study the orientation of the dye with respect to the binding protein. Conjugation of the dyes to the S337C maltose binding protein (MBP) mutant provided conjugates of these dyes that are capable of detecting maltose with different sensitivities. The dye INR gave a 3-fold (+200%) change in fluorescence intensity upon maltose binding when conjugated to S337C MBP with a binding constant (K(d)) of 435 microM. The fluorescence change for IANR was only 20% and the K(d) was 1.4 mM. Conformational analysis of the dyes by molecular modeling suggested that the linker in IANR imparted greater conformational freedom to the dye, resulting in little change in environment between the open and the closed-form conformations. The linker in INR, on the other hand, showed restricted motion, which placed the dye in different environments in the open and closed forms of the protein. Thus, design and placement of the linker play a critical role in the performance of these dyes as environmentally sensitive probes.
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Affiliation(s)
- Douglas B Sherman
- BD Technologies, 21 Davis Drive, Research Triangle Park, North Carolina 27709, USA
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Thomas KJ, Sherman DB, Amiss TJ, Andaluz SA, Pitner JB. A long-wavelength fluorescent glucose biosensor based on bioconjugates of galactose/glucose binding protein and Nile Red derivatives. Diabetes Technol Ther 2006; 8:261-8. [PMID: 16800747 DOI: 10.1089/dia.2006.8.261] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Fluorescent biosensors based on galactose/glucose binding protein (GGBP) and environmentally sensitive derivatives of the phenoxazine dye Nile Red are described. These biosensors are proposed as the sensing platform for a minimally invasive, continuous glucose monitoring system that can be implanted under the skin and read transdermally using an external fluorometer. METHODS To construct the biosensors, the thiol-reactive Nile Red derivatives INR and IANR were prepared and conjugated to GGBP proteins possessing cysteine mutations that were designed for optimal site-specific fluorophore attachment. The attachment sites were selected to maximize the local environment change for attached dyes between the bound and unbound conformations of GGBP. RESULTS Fluorescence responses at the selected cysteine sites of GGBP upon binding to glucose showed that the conjugates typically yielded fluorescence emission around 640-650 nm with up to 50% changes in fluorescence intensity. Conjugate E149C/A213C/L238S INR GGBP also displayed glucose binding in the human physiological range (K (D) = 7.4 mM). CONCLUSIONS The phenoxazine derivatives fluoresced at longer wavelengths (>600 nm) approaching the near-infrared spectral window, where interference from scattering and tissue absorbance are minimal. Ultimately, we expect that monitoring systems based on GGBP and longwavelength dyes will be implanted for up to 6 months and can be used to transmit information through the skin to an external monitor.
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Affiliation(s)
- K Joseph Thomas
- BD Technologies, Research Triangle Park, North Carolina 27709, USA
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40
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Døssing A, Magnussen M, Frey AM. Crystal Structure and Optical Properties of a Lanthanum(
III
) Complex of the Solvatochromic Dye “Nile Red”. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Anders Døssing
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark, Fax: + 45‐35320133
| | - Magnus Magnussen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark, Fax: + 45‐35320133
| | - Anne Mette Frey
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark, Fax: + 45‐35320133
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41
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Tang J, Mei E, Green C, Kaplan J, DeGrado WF, Smith AB, Hochstrasser RM. Probing Structural Dynamics of Individual Calmodulin:Peptide Complexes in Hydrogels by Single-Molecule Confocal Microscopy. J Phys Chem B 2004. [DOI: 10.1021/jp0480798] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianyong Tang
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Erwen Mei
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Clive Green
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Justin Kaplan
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - William F. DeGrado
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Amos B. Smith
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Robin M. Hochstrasser
- Department of Chemistry and Department of Biophysics and Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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42
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Hazra P, Chakrabarty D, Chakraborty A, Sarkar N. Intramolecular charge transfer and solvation dynamics of Nile Red in the nanocavity of cyclodextrins. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.02.078] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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43
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De S, Girigoswami A. Fluorescence resonance energy transfer—a spectroscopic probe for organized surfactant media. J Colloid Interface Sci 2004; 271:485-95. [PMID: 14972626 DOI: 10.1016/j.jcis.2003.10.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 10/22/2003] [Indexed: 11/21/2022]
Abstract
Dyes commonly used as biological labels have been used to probe resonance energy transfer in organized media. In neat water, energy transfer between the dye pairs fluorescein (donor):Nile red (acceptor) and acridine orange (donor):Nile red (acceptor) has a very low probability of occurrence. This study shows that the rate constant of energy transfer increases by more than an order of magnitude in organized surfactant media, viz., micelles and reverse micelles of the surfactant Triton X-100. The reverse micelles provide a better medium for energy transfer than the micelles. The energy transfer studies also provide an idea about the location and proximity of donor and acceptor dyes within the various organized media. Assuming Poissonian statistics for dye distribution, the donor-acceptor distances within micelles and reverse micelles are determined from energy transfer parameters. Acridine orange has been found to function better as a donor than fluorescein. This may be due to steric and electrostatic factors.
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Affiliation(s)
- Swati De
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, 741235 West Bengal, India.
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44
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Beuria TK, Krishnakumar SS, Sahar S, Singh N, Gupta K, Meshram M, Panda D. Glutamate-induced assembly of bacterial cell division protein FtsZ. J Biol Chem 2003; 278:3735-41. [PMID: 12446699 DOI: 10.1074/jbc.m205760200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The polymerization of FtsZ is a finely regulated process that plays an essential role in the bacterial cell division process. However, only a few modulators of FtsZ polymerization are known. We identified monosodium glutamate as a potent inducer of FtsZ polymerization. In the presence of GTP, glutamate enhanced the rate and extent of polymerization of FtsZ in a concentration-dependent manner; approximately 90% of the protein was sedimented as polymer in the presence of 1 m glutamate. Electron micrographs of glutamate-induced polymers showed large filamentous structures with extensive bundling. Furthermore, glutamate strongly stabilized the polymers against dilution-induced disassembly, and it decreased the GTPase activity of FtsZ. Calcium induced FtsZ polymerization and bundling of FtsZ polymers; interestingly, although 1 m glutamate produced a larger light-scattering signal than produced by 10 mm calcium, the amount of polymer sedimented in the presence of 1 m glutamate and 10 mm calcium was similar. Thus, the increased light scattering in the presence of glutamate must be due to its ability to induce more extensive bundling of FtsZ polymers than calcium. The data suggest that calcium and glutamate might induce FtsZ polymerization by different mechanisms.
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Affiliation(s)
- Tushar K Beuria
- School of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India
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45
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Caplow M, Fee L. Dissociation of the tubulin dimer is extremely slow, thermodynamically very unfavorable, and reversible in the absence of an energy source. Mol Biol Cell 2002; 13:2120-31. [PMID: 12058074 PMCID: PMC117629 DOI: 10.1091/mbc.e01-10-0089] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The finding that exchange of tubulin subunits between tubulin dimers (alpha-beta + alpha'beta' <--> alpha'beta + alphabeta') does not occur in the absence of protein cofactors and GTP hydrolysis conflicts with the assumption that pure tubulin dimer and monomer are in rapid equilibrium. This assumption underlies the many physical chemical measurements of the K(d) for dimer dissociation. To resolve this discrepancy we used surface plasmon resonance to determine the rate constant for dimer dissociation. The half-time for dissociation was approximately 9.6 h with tubulin-GTP, 2.4 h with tubulin-GDP, and 1.3 h in the absence of nucleotide. A Kd equal to 10(-11) M was calculated from the measured rate for dissociation and an estimated rate for association. Dimer dissociation was found to be reversible, and dimer formation does not require GTP hydrolysis or folding information from protein cofactors, because 0.2 microM tubulin-GDP incubated for 20 h was eluted as dimer when analyzed by size exclusion chromatography. Because 20 h corresponds to eight half-times for dissociation, only monomer would be present if dissociation were an irreversible reaction and if dimer formation required GTP or protein cofactors. Additional evidence for a 10(-11) M K(d) was obtained from gel exclusion chromatography studies of 0.02-2 nM tubulin-GDP. The slow dissociation of the tubulin dimer suggests that protein tubulin cofactors function to catalyze dimer dissociation, rather than dimer assembly. Assuming N-site-GTP dissociation is from monomer, our results agree with the 16-h half-time for N-site GTP in vitro and 33 h half-life for tubulin N-site-GTP in CHO cells.
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Affiliation(s)
- Michael Caplow
- Department of Biochemistry, University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA.
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46
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Richter-Egger DL, Tesfai A, Tucker SA. Spectroscopic investigations of poly(propyleneimine)dendrimers using the solvatochromic probe phenol blue and comparisons to poly(amidoamine) dendrimers. Anal Chem 2001; 73:5743-51. [PMID: 11774916 DOI: 10.1021/ac0155355] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The physical and chemical properties of PPI dendrimers' interior were investigated using the fluorescent, solvatochromic probe phenol blue. In aqueous solutions of each generation studied, two discrete dye populations were clearly observed. PPI dendrimers were shown to form a tight, nonpolar association with the vast majority of available dye, within the dendrimer interior, near the core. In the steady-state fluorescence emission spectra, a microenvironment of decreasing polarity in increasingly larger-generation PPI dendrimers (up to G3) was seen for the associated probe. Each of the remaining larger-generation dendrimers provided a microenvironment of essentially equal polarity. Fluorescence anisotropy values for phenol blue in the PPI dendrimers demonstrated the dye's sensitivity to the changing molecular volumes of the dendrimer generations. Model compounds that mimicked PPI's surface groups and branching moieties were used to better define the associated dye's location. The mimics further confirmed that phenol blue was associated inside the dendrimer, where it did not interact with the dendrimer surface groups. The comparison of amine-terminated PPI and PAMAM dendrimers clearly demonstrated the effects of their structural differences and the ability of phenol blue to have sensed those differences, including the initiator core length, branching unit length, and branching unit chemical composition.
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Affiliation(s)
- D L Richter-Egger
- Department of Chemistry, University of Missouri-Columbia, 65211-7600, USA
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47
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Krishnamoorthy G, Dogra SK. Spectral characteristics of 2-(4'-N,N-dimethylaminophenyl)pyrido[3,4-d]imidazole in AOT/n-heptane/water reverse micelles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:2617-2628. [PMID: 11765789 DOI: 10.1016/s1386-1425(01)00438-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Spectral characteristics of 2-(4'-N,N-dimethylaminophenyl)pyrido[3,4-d]imidazole (DMAPPI) have been studied in AOT/n-heptane/water reverse micelles at w0 > or = 0. Absorption, fluorescence excitation and fluorescence spectra have revealed that the monocation (MC) of DMAPPI, protonated at the imidazole nitrogen (MC2) (Scheme 2) is present in the S0 state at w0 = 0, along with the MC, protonated at pyridine nitrogen (MC3) and only normal emission is observed from both MC2 and MC3. With increase in w0 (water amount), the equilibrium is shifted towards the MC, protonated at -NMe2 group (MC1) and MC3 in the S0 state. Biprotonic phototautomerism is observed in MC1 to generate MC2 in the S1 state. The twisted intramolecular charge transfer (TICT) emission replaces the normal emission in MC3. All the MCs are present near the anionic polar head group of AOT in the bound water region.
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48
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Richter-Egger DL, Landry JC, Tesfai A, Tucker SA. Spectroscopic Investigations of Polyamido Amine Starburst Dendrimers Using the Solvatochromic Probe Phenol Blue. J Phys Chem A 2001. [DOI: 10.1021/jp0100396] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dana L. Richter-Egger
- Department of Chemistry, University of Missouri∼Columbia, Columbia, Missouri 65211-7600
| | - Jeff C. Landry
- Department of Chemistry, University of Missouri∼Columbia, Columbia, Missouri 65211-7600
| | - Aaron Tesfai
- Department of Chemistry, University of Missouri∼Columbia, Columbia, Missouri 65211-7600
| | - Sheryl A. Tucker
- Department of Chemistry, University of Missouri∼Columbia, Columbia, Missouri 65211-7600
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49
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Epps DE, Sarver RW, Rogers JM, Herberg JT, Tomich PK. The ligand affinity of proteins measured by isothermal denaturation kinetics. Anal Biochem 2001; 292:40-50. [PMID: 11319816 DOI: 10.1006/abio.2001.5047] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An isothermal denaturation kinetic method was developed for identifying potential ligands of proteins and measuring their affinity. The method is suitable for finding ligands specific toward proteins of unknown function and for large-scale drug screening. It consists of analyzing the kinetics of isothermal denaturation of the protein-with and without the presence of potential specific ligands-as measured by long-wavelength fluorescent dyes whose quantum yield increases when bound to hydrophobic regions exposed upon unfolding of the proteins. The experimental procedure was developed using thymidylate kinase and stromelysin as target proteins. The kinetics of thermal unfolding of both of these enzymes were consistent with a pathway of two consecutive first-order rate-limiting steps. Reflecting the stabilizing effect of protein/ligand complexes, the presence of specific ligands decreased the value of the rate constants of both steps in a dose-dependent manner. The dependence of the rate constants on ligand concentration obeyed a simple binding isotherm, the analysis of which yielded an accurate equilibrium constant for ligand binding. The method was validated by comparing its results with those obtained under the same conditions by steady-state fluorescence spectroscopy, circular dichroism, and uv spectrophotometry: The corresponding rate constants were comparable for each of the analytical detection methods.
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Affiliation(s)
- D E Epps
- Pharmacia Corporation, 7000 Portage Road, Kalamazoo, Michigan 49001, USA
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50
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Krishna MMG. Excited-State Kinetics of the Hydrophobic Probe Nile Red in Membranes and Micelles. J Phys Chem A 1999. [DOI: 10.1021/jp984620m] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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