51
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A Perspective on Data Processing in Super-resolution Fluorescence Microscopy Imaging. JOURNAL OF ANALYSIS AND TESTING 2018. [DOI: 10.1007/s41664-018-0076-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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52
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Kim J, Heo WD. Synergistic Ensemble of Optogenetic Actuators and Dynamic Indicators in Cell Biology. Mol Cells 2018; 41:809-817. [PMID: 30157546 PMCID: PMC6182222 DOI: 10.14348/molcells.2018.0295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022] Open
Abstract
Discovery of the naturally evolved fluorescent proteins and their genetically engineered biosensors have enormously contributed to current bioimaging techniques. These reporters to trace dynamic changes of intracellular protein activities have continuously transformed according to the various demands in biological studies. Along with that, light-inducible optogenetic technologies have offered scientists to perturb, control and analyze the function of intracellular machineries in spatiotemporal manner. In this review, we present an overview of the molecular strategies that have been exploited for producing genetically encoded protein reporters and various optogenetic modules. Finally, in particular, we discuss the current efforts for combined use of these reporters and optogenetic modules as a powerful tactic for the control and imaging of signaling events in cells and tissues.
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Affiliation(s)
- Jihoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141,
Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141,
Korea
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53
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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54
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Gao A, Wang M, Ding J. Ultrafasttrans-cisphotoisomerization of the neutral chromophore in green fluorescent proteins: Surface-hopping dynamics simulation. J Chem Phys 2018; 149:074304. [DOI: 10.1063/1.5043246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Aihua Gao
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Meishan Wang
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264025, China
| | - Junxia Ding
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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55
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Enhanced photon collection enables four dimensional fluorescence nanoscopy of living systems. Nat Commun 2018; 9:3281. [PMID: 30115928 PMCID: PMC6095837 DOI: 10.1038/s41467-018-05799-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/27/2018] [Indexed: 11/15/2022] Open
Abstract
The theoretically unlimited spatial resolution of fluorescence nanoscopy often comes at the expense of time, contrast and increased dose of energy for recording. Here, we developed MoNaLISA, for Molecular Nanoscale Live Imaging with Sectioning Ability, a nanoscope capable of imaging structures at a scale of 45–65 nm within the entire cell volume at low light intensities (W-kW cm−2). Our approach, based on reversibly switchable fluorescent proteins, features three distinctly modulated illumination patterns crafted and combined to gain fluorescence ON–OFF switching cycles and image contrast. By maximizing the detected photon flux, MoNaLISA enables prolonged (40–50 frames) and large (50 × 50 µm2) recordings at 0.3–1.3 Hz with enhanced optical sectioning ability. We demonstrate the general use of our approach by 4D imaging of organelles and fine structures in epithelial human cells, colonies of mouse embryonic stem cells, brain cells, and organotypic tissues. Super-resolution microscopy often suffers from low contrast and slow recording times. Here the authors present an optical implementation which makes the fluorescent proteins’ ON–OFF switching cycles more efficient, enhancing contrast and spatio-temporal resolution in 3D cell and tissue imaging.
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56
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Vetschera P, Mishra K, Fuenzalida-Werner JP, Chmyrov A, Ntziachristos V, Stiel AC. Characterization of Reversibly Switchable Fluorescent Proteins in Optoacoustic Imaging. Anal Chem 2018; 90:10527-10535. [DOI: 10.1021/acs.analchem.8b02599] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Paul Vetschera
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Chair of Biological Imaging, Technische Universität München, D-80333 München, Germany
| | - Kanuj Mishra
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | | | - Andriy Chmyrov
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Center for Translational Cancer Research, Technische Universität München, D-81675 München, Germany
| | - Vasilis Ntziachristos
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Chair of Biological Imaging, Technische Universität München, D-80333 München, Germany
- Center for Translational Cancer Research, Technische Universität München, D-81675 München, Germany
| | - Andre C. Stiel
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
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57
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Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I. Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 2018; 15:601-604. [PMID: 29988095 DOI: 10.1038/s41592-018-0052-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/18/2018] [Indexed: 11/09/2022]
Abstract
Reversibly photoswitchable fluorescent proteins (rsFPs) are gaining popularity as tags for optical nanoscopy because they make it possible to image with lower light doses. However, green rsFPs need violet-blue light for photoswitching, which is potentially phototoxic and highly scattering. We developed new rsFPs based on FusionRed that are reversibly photoswitchable with green-orange light. The rsFusionReds are bright and exhibit rapid photoswitching, thereby enabling nanoscale imaging of living cells.
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Affiliation(s)
- Francesca Pennacchietti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Aline R Faro
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Irina I Shemyakina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey A Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Andreas Bodén
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jes Dreier
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation.
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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58
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Stockmar I, Feddersen H, Cramer K, Gruber S, Jung K, Bramkamp M, Shin JY. Optimization of sample preparation and green color imaging using the mNeonGreen fluorescent protein in bacterial cells for photoactivated localization microscopy. Sci Rep 2018; 8:10137. [PMID: 29973667 PMCID: PMC6031688 DOI: 10.1038/s41598-018-28472-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/19/2018] [Indexed: 11/08/2022] Open
Abstract
mNeonGreen fluorescent protein is capable of photo-switching, hence in principle applicable for super-resolution imaging. However, difficult-to-control blinking kinetics that lead to simultaneous emission of multiple nearby mNeonGreen molecules impedes its use for PALM. Here, we determined the on- and off- switching rate and the influence of illumination power on the simultaneous emission. Increasing illumination power reduces the probability of simultaneous emission, but not enough to generate high quality PALM images. Therefore, we introduce a simple data post-processing step that uses temporal and spatial information of molecule localizations to further reduce artifacts arising from simultaneous emission of nearby emitters. We also systematically evaluated various sample preparation steps to establish an optimized protocol to preserve cellular morphology and fluorescence signal. In summary, we propose a workflow for super-resolution imaging with mNeonGreen based on optimization of sample preparation, data acquisition and simple post-acquisition data processing. Application of our protocol enabled us to resolve the expected double band of bacterial cell division protein DivIVA, and to visualize that the chromosome organization protein ParB organized into sub-clusters instead of the typically observed diffraction-limited foci. We expect that our workflow allows a broad use of mNeonGreen for super-resolution microscopy, which is so far difficult to achieve.
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Affiliation(s)
- Iris Stockmar
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Max Plank Institute for Biochemistry, Martinsried, Germany
| | - Helge Feddersen
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Kimberly Cramer
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
- Max Plank Institute for Biochemistry, Martinsried, Germany
| | - Stephan Gruber
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Jung
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
| | - Jae Yen Shin
- Munich Center for Integrated Protein Science (CIPSM) at the Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany.
- Max Plank Institute for Biochemistry, Martinsried, Germany.
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59
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Gp41 dynamically interacts with the TCR in the immune synapse and promotes early T cell activation. Sci Rep 2018; 8:9747. [PMID: 29950577 PMCID: PMC6021400 DOI: 10.1038/s41598-018-28114-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/14/2018] [Indexed: 12/21/2022] Open
Abstract
The HIV-1 glycoprotein gp41 critically mediates CD4+ T-cell infection by HIV-1 during viral entry, assembly, and release. Although multiple immune-regulatory activities of gp41 have been reported, the underlying mechanisms of these activities remain poorly understood. Here we employed multi-colour single molecule localization microscopy (SMLM) to resolve interactions of gp41 proteins with cellular proteins at the plasma membrane (PM) of fixed and live CD4+ T-cells with resolution of ~20–30 nm. We observed that gp41 clusters dynamically associated with the T cell antigen receptor (TCR) at the immune synapse upon TCR stimulation. This interaction, confirmed by FRET, depended on the virus clone, was reduced by the gp41 ectodomain in tight contacts, and was completely abrogated by mutation of the gp41 transmembrane domain. Strikingly, gp41 preferentially colocalized with phosphorylated TCRs at the PM of activated T-cells and promoted TCR phosphorylation. Gp41 expression also resulted in enhanced CD69 upregulation, and in massive cell death after 24–48 hrs. Our results shed new light on HIV-1 assembly mechanisms at the PM of host T-cells and its impact on TCR stimulation.
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60
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Excitation wavelength optimization improves photostability of ASAP-family GEVIs. Mol Brain 2018; 11:32. [PMID: 29866136 PMCID: PMC5987426 DOI: 10.1186/s13041-018-0374-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/21/2018] [Indexed: 01/22/2023] Open
Abstract
Recent interest in high-throughput recording of neuronal activity has motivated rapid improvements in genetically encoded calcium or voltage indicators (GECIs or GEVIs) for all-optical electrophysiology. Among these probes, the ASAPs, a series of voltage indicators based on a variant of circularly permuted green fluorescent protein (cpGFP) and a conjugated voltage sensitive domain (VSD), are capable of detecting both action potentials and subthreshold neuronal activities. Here we show that the ASAPs, when excited by blue light, undergo reversible photobleaching. We find that this fluorescence loss induced by excitation with 470-nm light can be substantially reversed by low-intensity 405-nm light. We demonstrate that 405-nm and 470-nm co-illumination significantly improved brightness and thereby signal-to-noise ratios during voltage imaging compared to 470-nm illumination alone. Illumination with a single wavelength of 440-nm light also produced similar improvements. We hypothesize that reversible photobleaching is related to cis-trans isomerization and protonation of the GFP chromophore of ASAP proteins. Amino acids that influence chromophore isomerization are potential targets of point mutations for future improvements.
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61
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Smyrnova D, Marín MDC, Olivucci M, Ceulemans A. Systematic Excited State Studies of Reversibly Switchable Fluorescent Proteins. J Chem Theory Comput 2018; 14:3163-3172. [PMID: 29772175 DOI: 10.1021/acs.jctc.8b00050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The reversibly switchable fluorescent proteins Dronpa, rsFastLime, rsKame, Padron, and bsDronpa feature the same chromophore but display a 40 nm variation in absorption maxima and an only 18 nm variation in emission maxima. In the present contribution, we employ QM/MM models to investigate the mechanism of such remarkably different spectral variations, which are caused by just a few amino acid replacements. We show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed trends in absorption maxima, with only a 3.5 kcal/mol blue-shift, and in emission maxima, with an even smaller 1.5 kcal/mol blue-shift with respect to the observed quantities. In order to explain the variations across the series, we look at the chromophore's electronic structure change during absorption and emission. Such analysis indicates that a change in charge-transfer character, which is more pronounced during absorption, triggers a cascade of hydrogen-bond-network rearrangements, suggesting preparation to an isomerization event. We also show how the contribution of Arg 89 and Arg 64 residues to the chromophore conformational changes correlate with the spectral variations in absorption and emission. Furthermore, we describe how the conical intersection stability is related to the protein's photophysical properties. While for the Dronpa, rsFastLime, and rsKame triad, the stability correlates with the photoswitching speed, this does not happen for bsDronpa and Padron, suggesting a less obvious photoisomerization mechanism.
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Affiliation(s)
- Daryna Smyrnova
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Heverlee , Belgium
| | - María Del Carmen Marín
- Department of Biotechnology, Chemistry, and Pharmacy , Universitá di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry, and Pharmacy , Universitá di Siena , via A. Moro 2 , I-53100 Siena , Italy.,Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Arnout Ceulemans
- Quantum Chemistry and Physical Chemistry Division, Department of Chemistry , KU Leuven , Celestijnenlaan 200F , B-3001 Heverlee , Belgium
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62
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Carrascosa E, Bull JN, Scholz MS, Coughlan NJA, Olsen S, Wille U, Bieske EJ. Reversible Photoisomerization of the Isolated Green Fluorescent Protein Chromophore. J Phys Chem Lett 2018; 9:2647-2651. [PMID: 29724104 DOI: 10.1021/acs.jpclett.8b01201] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fluorescent proteins have revolutionized the visualization of biological processes, prompting efforts to understand and control their intrinsic photophysics. Here we investigate the photoisomerization of deprotonated p-hydroxybenzylidene-2,3-dimethylimidazolinone anion (HBDI-), the chromophore in green fluorescent protein and in Dronpa protein, where it plays a role in switching between fluorescent and nonfluorescent states. In the present work, isolated HBDI- molecules are switched between the Z and E forms in the gas phase in a tandem ion mobility mass spectrometer outfitted for selecting the initial and final isomers. Excitation of the S1 ← S0 transition provokes both Z → E and E → Z photoisomerization, with a maximum response for both processes at 480 nm. Photodetachment is a minor channel at low light intensity. At higher light intensities, absorption of several photons in the drift region drives photofragmentation, through channels involving CH3 loss and concerted CO and CH3CN loss, although isomerization remains the dominant process.
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Affiliation(s)
- Eduardo Carrascosa
- School of Chemistry , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - James N Bull
- School of Chemistry , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Michael S Scholz
- School of Chemistry , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Neville J A Coughlan
- School of Chemistry , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Seth Olsen
- School of Chemistry , Monash University , Clayton , Victoria 3800 , Australia
| | - Uta Wille
- School of Chemistry , The University of Melbourne , Parkville , Victoria 3010 , Australia
| | - Evan J Bieske
- School of Chemistry , The University of Melbourne , Parkville , Victoria 3010 , Australia
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63
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Chen YH, Sung R, Sung K. Synthesis and Properties of the p-Sulfonamide Analogue of the Green Fluorescent Protein (GFP) Chromophore: The Mimic of GFP Chromophore with Very Strong N-H Photoacid Strength. Org Lett 2018. [PMID: 29527893 DOI: 10.1021/acs.orglett.8b00257] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The para-sulfonamide analogue ( p-TsABDI) of a green fluorescent protein (GFP) chromophore was synthesized to mimic the GFP chromophore. Its S1 excited-state p Ka* value in dimethylsulfoxide (DMSO) is -1.5, which is strong enough to partially protonate dipolar aprotic solvents and causes excited-state proton transfer (ESPT), so it can partially mimic the GFP chromophore to further study the ESPT-related photophysics and the blinking phenomenon of GFP. In comparison with 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) (p Ka = 7.4, p Ka* = 1.3 in water), p-TsABDI (p Ka = 6.7, p Ka* = -1.5 in DMSO) is a better photoacid for pH-jump studies.
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Affiliation(s)
- Yi-Hui Chen
- Department of Chemistry , National Cheng Kung University , Tainan , Taiwan
| | - Robert Sung
- Department of Chemistry , National Cheng Kung University , Tainan , Taiwan
| | - Kuangsen Sung
- Department of Chemistry , National Cheng Kung University , Tainan , Taiwan
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64
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McDonald AD, Jones BJP, Nygren DR, Adams C, Álvarez V, Azevedo CDR, Benlloch-Rodríguez JM, Borges FIGM, Botas A, Cárcel S, Carrión JV, Cebrián S, Conde CAN, Díaz J, Diesburg M, Escada J, Esteve R, Felkai R, Fernandes LMP, Ferrario P, Ferreira AL, Freitas EDC, Goldschmidt A, Gómez-Cadenas JJ, González-Díaz D, Gutiérrez RM, Guenette R, Hafidi K, Hauptman J, Henriques CAO, Hernandez AI, Hernando Morata JA, Herrero V, Johnston S, Labarga L, Laing A, Lebrun P, Liubarsky I, López-March N, Losada M, Martín-Albo J, Martínez-Lema G, Martínez A, Monrabal F, Monteiro CMB, Mora FJ, Moutinho LM, Muñoz Vidal J, Musti M, Nebot-Guinot M, Novella P, Palmeiro B, Para A, Pérez J, Querol M, Repond J, Renner J, Riordan S, Ripoll L, Rodríguez J, Rogers L, Santos FP, Dos Santos JMF, Simón A, Sofka C, Sorel M, Stiegler T, Toledo JF, Torrent J, Tsamalaidze Z, Veloso JFCA, Webb R, White JT, Yahlali N. Demonstration of Single-Barium-Ion Sensitivity for Neutrinoless Double-Beta Decay Using Single-Molecule Fluorescence Imaging. PHYSICAL REVIEW LETTERS 2018; 120:132504. [PMID: 29694208 DOI: 10.1103/physrevlett.120.132504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/02/2018] [Indexed: 06/08/2023]
Abstract
A new method to tag the barium daughter in the double-beta decay of ^{136}Xe is reported. Using the technique of single molecule fluorescent imaging (SMFI), individual barium dication (Ba^{++}) resolution at a transparent scanning surface is demonstrated. A single-step photobleach confirms the single ion interpretation. Individual ions are localized with superresolution (∼2 nm), and detected with a statistical significance of 12.9σ over backgrounds. This lays the foundation for a new and potentially background-free neutrinoless double-beta decay technology, based on SMFI coupled to high pressure xenon gas time projection chambers.
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Affiliation(s)
- A D McDonald
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - B J P Jones
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - D R Nygren
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - C Adams
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - V Álvarez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - C D R Azevedo
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - J M Benlloch-Rodríguez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - F I G M Borges
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - A Botas
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - S Cárcel
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - J V Carrión
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - S Cebrián
- Laboratorio de Física Nuclear y Astropartículas, Universidad de Zaragoza, Calle Pedro Cerbuna, 12, 50009 Zaragoza, Spain
| | - C A N Conde
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - J Díaz
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Diesburg
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - J Escada
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - R Esteve
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - R Felkai
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - L M P Fernandes
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - P Ferrario
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - A L Ferreira
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - E D C Freitas
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - A Goldschmidt
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, California 94720, USA
| | - J J Gómez-Cadenas
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - D González-Díaz
- Instituto Gallego de Física de Altas Energías, Univ. de Santiago de Compostela, Campus sur, Rúa Xosé María Suárez Núñez, s/n, 15782 Santiago de Compostela, Spain
| | - R M Gutiérrez
- Centro de Investigación en Ciencias Básicas y Aplicadas, Universidad Antonio Nariño, Sede Circunvalar, Carretera 3 Este No. 47 A-15, Bogotá, Colombia
| | - R Guenette
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - K Hafidi
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - J Hauptman
- Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011-3160, USA
| | - C A O Henriques
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - A I Hernandez
- Centro de Investigación en Ciencias Básicas y Aplicadas, Universidad Antonio Nariño, Sede Circunvalar, Carretera 3 Este No. 47 A-15, Bogotá, Colombia
| | - J A Hernando Morata
- Instituto Gallego de Física de Altas Energías, Univ. de Santiago de Compostela, Campus sur, Rúa Xosé María Suárez Núñez, s/n, 15782 Santiago de Compostela, Spain
| | - V Herrero
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - S Johnston
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - L Labarga
- Departamento de Física Teórica, Universidad Autónoma de Madrid, Campus de Cantoblanco, 28049 Madrid, Spain
| | - A Laing
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - P Lebrun
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - I Liubarsky
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - N López-March
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Losada
- Centro de Investigación en Ciencias Básicas y Aplicadas, Universidad Antonio Nariño, Sede Circunvalar, Carretera 3 Este No. 47 A-15, Bogotá, Colombia
| | - J Martín-Albo
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - G Martínez-Lema
- Instituto Gallego de Física de Altas Energías, Univ. de Santiago de Compostela, Campus sur, Rúa Xosé María Suárez Núñez, s/n, 15782 Santiago de Compostela, Spain
| | - A Martínez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - F Monrabal
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - C M B Monteiro
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - F J Mora
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - L M Moutinho
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - J Muñoz Vidal
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Musti
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Nebot-Guinot
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - P Novella
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - B Palmeiro
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - A Para
- Fermi National Accelerator Laboratory, Batavia, Illinois 60510, USA
| | - J Pérez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Querol
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - J Repond
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - J Renner
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - S Riordan
- Argonne National Laboratory, Argonne Illinois 60439, USA
| | - L Ripoll
- Escola Politècnica Superior, Universitat de Girona, Av. Montilivi, s/n, 17071 Girona, Spain
| | - J Rodríguez
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - L Rogers
- Department of Physics, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - F P Santos
- LIP, Department of Physics, University of Coimbra, P-3004 516 Coimbra, Portugal
| | - J M F Dos Santos
- LIBPhys, Physics Department, University of Coimbra, Rua Larga, 3004-516 Coimbra, Portugal
| | - A Simón
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - C Sofka
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - M Sorel
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - T Stiegler
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843-4242, USA
| | - J F Toledo
- Instituto de Instrumentación para Imagen Molecular (I3M), Centro Mixto CSIC-Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - J Torrent
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
| | - Z Tsamalaidze
- Joint Institute for Nuclear Research (JINR), Joliot-Curie 6, 141980 Dubna, Russia
| | - J F C A Veloso
- Institute of Nanostructures, Nanomodelling and Nanofabrication (i3N), Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - R Webb
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843-4242, USA
| | - J T White
- Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843-4242, USA
| | - N Yahlali
- Instituto de Física Corpuscular (IFIC), CSIC & Universitat de València, Calle Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
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65
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Shitashima Y, Shimozawa T, Kumagai A, Miyawaki A, Asahi T. Two Distinct Fluorescence States of the Ligand-Induced Green Fluorescent Protein UnaG. Biophys J 2018; 113:2805-2814. [PMID: 29262373 DOI: 10.1016/j.bpj.2017.10.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 09/27/2017] [Accepted: 10/13/2017] [Indexed: 11/29/2022] Open
Abstract
UnaG is a recently discovered ligand-induced fluorescent protein that utilizes bound bilirubin (BR) as its fluorophore. The fluorescence of the UnaG-BR complex (holoUnaG) compares in quantum efficiency to that of enhanced green fluorescent protein, but it is superior in that the fluorophore formation is instantaneous and not dependent on oxygen; hence, much attention has been paid to UnaG as a new fluorescent probe. However, many important molecular properties of fluorescent probes remain unknown, such as the association/dissociation rates of BR, which determine the stability thereof, and the dispersibility of UnaG in aqueous solutions, which influence the functions of labeled proteins. In this study, we found, in the process of investigating the association rate, that the holoUnaG takes two distinct fluorescence states, which we named holoUnaG1 and holoUnaG2. The holoUnaG1 initially forms after binding BR and then changes to the brighter holoUnaG2 by a reversible intra-molecular reaction, thereby finally reaching an equilibrium between the two states. Spectroscopic analysis indicated that the intra-molecular reaction was associated not with a chemical change of BR but with a change in the environmental conditions surrounding BR. We also revealed that the molecular brightness ratio and equilibrium population ratio of the two states (holoUnaG1/holoUnaG2) were 1:3.9 and 6:4, respectively, using photon number counting analysis. From these results, we have suggested a novel schema, to our knowledge, for the formation of the UnaG and BR complex system and have determined the various rate constants associated therein. Additionally, using analytical ultracentrifugation, we established that UnaG in the apo-state (apoUnaG) and the holoUnaG are monomeric in aqueous solution. These findings provide not only key information for the practical use of UnaG as a fluorescent probe, but also the possibility for development of a brighter UnaG mutant by genetic engineering to constitutive holoUnaG2.
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Affiliation(s)
- Yoh Shitashima
- Department of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan; Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Togo Shimozawa
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku, Tokyo, Japan.
| | - Akiko Kumagai
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Atsushi Miyawaki
- Laboratory for Cell Function Dynamics, Brain Science Institute, RIKEN, Wako, Saitama, Japan
| | - Toru Asahi
- Department of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, Japan; Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku, Tokyo, Japan
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66
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Gozem S, Luk HL, Schapiro I, Olivucci M. Theory and Simulation of the Ultrafast Double-Bond Isomerization of Biological Chromophores. Chem Rev 2017; 117:13502-13565. [DOI: 10.1021/acs.chemrev.7b00177] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Samer Gozem
- Department
of Chemistry, Georgia State University, Atlanta, Georgia 30302, United States
| | - Hoi Ling Luk
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Igor Schapiro
- Fritz
Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Massimo Olivucci
- Chemistry
Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro
2, 53100 Siena, Italy
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67
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Super-resolution microscopy reveals functional organization of dopamine transporters into cholesterol and neuronal activity-dependent nanodomains. Nat Commun 2017; 8:740. [PMID: 28963530 PMCID: PMC5622129 DOI: 10.1038/s41467-017-00790-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/27/2017] [Indexed: 01/13/2023] Open
Abstract
Dopamine regulates reward, cognition, and locomotor functions. By mediating rapid reuptake of extracellular dopamine, the dopamine transporter is critical for spatiotemporal control of dopaminergic neurotransmission. Here, we use super-resolution imaging to show that the dopamine transporter is dynamically sequestrated into cholesterol-dependent nanodomains in the plasma membrane of presynaptic varicosities and neuronal projections of dopaminergic neurons. Stochastic optical reconstruction microscopy reveals irregular dopamine transporter nanodomains (∼70 nm mean diameter) that were highly sensitive to cholesterol depletion. Live photoactivated localization microscopy shows a similar dopamine transporter membrane organization in live heterologous cells. In neurons, dual-color dSTORM shows that tyrosine hydroxylase and vesicular monoamine transporter-2 are distinctively localized adjacent to, but not overlapping with, the dopamine transporter nanodomains. The molecular organization of the dopamine transporter in nanodomains is reversibly reduced by short-term activation of NMDA-type ionotropic glutamate receptors, implicating dopamine transporter nanodomain distribution as a potential mechanism to modulate dopaminergic neurotransmission in response to excitatory input.The dopamine transporter (DAT) has a crucial role in the regulation of neurotransmission. Here, the authors use super-resolution imaging to show that DAT clusters into cholesterol-dependent membrane regions that are reversibly regulated by ionotropic glutamate receptors activation.
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68
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Thédié D, Berardozzi R, Adam V, Bourgeois D. Photoswitching of Green mEos2 by Intense 561 nm Light Perturbs Efficient Green-to-Red Photoconversion in Localization Microscopy. J Phys Chem Lett 2017; 8:4424-4430. [PMID: 28850784 DOI: 10.1021/acs.jpclett.7b01701] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Green-to-red photoconvertible fluorescent proteins (PCFPs) such as mEos2 and its derivatives are widely used in PhotoActivated Localization Microscopy (PALM). However, the complex photophysics of these genetically encoded markers complicates the quantitative analysis of PALM data. Here, we show that intense 561 nm light (∼1 kW/cm2) typically used to localize single red molecules considerably affects the green-state photophysics of mEos2 by populating at least two reversible dark states. These dark states retard green-to-red photoconversion through a shelving effect, although one of them is rapidly depopulated by 405 nm light illumination. Multiple mEos2 switching and irreversible photobleaching is thus induced by yellow/green and violet photons before green-to-red photoconversion occurs, contributing to explain the apparent limited signaling efficiency of this PCFP. Our data reveals that the photophysics of PCFPs of anthozoan origin is substantially more complex than previously thought, and suggests that intense 561 nm laser light should be used with care, notably for quantitative or fast PALM approaches.
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Affiliation(s)
- Daniel Thédié
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Romain Berardozzi
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Virgile Adam
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, CNRS, Université Grenoble Alpes, CEA, IBS, 38044 Grenoble, France
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69
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Abstract
The zebrafish (Danio rerio) possesses a vertebrate-type retina that is extraordinarily conserved in evolution. This well-organized and anatomically easily accessible part of the central nervous system has been widely investigated in zebrafish, promoting general understanding of retinal development, morphology, function and associated diseases. Over the recent years, genome and protein engineering as well as imaging techniques have experienced revolutionary advances and innovations, creating new possibilities and methods to study zebrafish development and function. In this review, we focus on some of these emerging technologies and how they may impact retinal research in the future. We place an emphasis on genetic techniques, such as transgenic approaches and the revolutionizing new possibilities in genome editing.
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Affiliation(s)
- Stephanie Niklaus
- a Institute of Molecular Life Sciences , University of Zurich , Zurich , Switzerland.,b Life Science Zurich Graduate Program - Neuroscience , Zurich , Switzerland
| | - Stephan C F Neuhauss
- a Institute of Molecular Life Sciences , University of Zurich , Zurich , Switzerland
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70
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Brunker J, Yao J, Laufer J, Bohndiek SE. Photoacoustic imaging using genetically encoded reporters: a review. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:2645343. [PMID: 28717818 DOI: 10.1117/1.jbo.22.7.070901] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
Genetically encoded contrast in photoacoustic imaging (PAI) is complementary to the intrinsic contrast provided by endogenous absorbing chromophores such as hemoglobin. The use of reporter genes expressing absorbing proteins opens the possibility of visualizing dynamic cellular and molecular processes. This is an enticing prospect but brings with it challenges and limitations associated with generating and detecting different types of reporters. The purpose of this review is to compare existing PAI reporters and signal detection strategies, thereby offering a practical guide, particularly for the nonbiologist, to choosing the most appropriate reporter for maximum sensitivity in the biological and technological system of interest.
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Affiliation(s)
- Joanna Brunker
- University of Cambridge, Cancer Research UK Cambridge Institute and Department of Physics, Cambridge, United Kingdom
| | - Junjie Yao
- Duke University, Photoacoustic Imaging Lab, Department of Biomedical Engineering, Durham, North Carolina, United States
| | - Jan Laufer
- Martin-Luther-Universität Halle-Wittenberg, Institut für Physik, Halle (Saale), Germany
| | - Sarah E Bohndiek
- University of Cambridge, Cancer Research UK Cambridge Institute and Department of Physics, Cambridge, United Kingdom
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71
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Lum W, Bruzas I, Gorunmez Z, Unser S, Beck T, Sagle L. Novel Liposome-Based Surface-Enhanced Raman Spectroscopy (SERS) Substrate. J Phys Chem Lett 2017; 8:2639-2646. [PMID: 28535675 DOI: 10.1021/acs.jpclett.7b00694] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Although great strides have been made in recent years toward making highly enhancing surface-enhanced Raman spectroscopy (SERS) substrates, the biological compatibility of such substrates remains a crucial problem. To address this issue, liposome-based SERS substrates have been constructed in which the biological probe molecule is encapsulated inside the aqueous liposome compartment, and metallic elements are assembled using the liposome as a scaffold. Therefore, the probe molecule is not in contact with the metallic surfaces. Herein we report our initial characterization of these novel nanoparticle-on-mirror substrates, both experimentally and theoretically, using finite-difference time-domain calculations. The substrates are shown to be structurally stable to laser irradiation, the liposome compartment does not rise above 45 °C, and they exhibit an analytical enhancement factor of 8 × 106 for crystal violet encapsulated in 38 liposomes sandwiched between a 40 nm planar gold mirror and 80 nm gold colloid.
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Affiliation(s)
- William Lum
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| | - Ian Bruzas
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| | - Zohre Gorunmez
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| | - Sarah Unser
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| | - Thomas Beck
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
| | - Laura Sagle
- Department of Chemistry, College of Arts and Sciences, University of Cincinnati , 301 West Clifton Court, Cincinnati, Ohio 45221-0172, United States
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72
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Jiang Y, Novoa M, Nongnual T, Powell R, Bruce T, McNeill J. Improved Superresolution Imaging Using Telegraph Noise in Organic Semiconductor Nanoparticles. NANO LETTERS 2017; 17:3896-3901. [PMID: 28537735 DOI: 10.1021/acs.nanolett.7b01440] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Small semiconductor structures often exhibit "telegraph noise". If the number of charge carriers is small, then spontaneous changes in the number of carriers can lead to abrupt switching between two or more discrete levels, leading to burst noise or popcorn noise in transistors. We have observed similar behavior in the fluorescence of organic semiconductor nanoparticles, where typical carrier populations are often less than ∼10 carriers per nanoparticle. Spontaneous changes in the number of charges results in abrupt switching between 2 or more fluorescence intensity levels, because the charges act as highly efficient fluorescence quenchers. The equilibrium number of charges is determined by competition between a photodriven ionization process and spontaneous recombination. Doping with redox-active molecules also affects the balance. Nanoparticles of the conjugated polymer PFBT doped with the fullerene derivative PCBM, rapidly establish a fluctuating steady-state population of tens of hole polaron charge carriers, sufficient to nearly completely suppress nanoparticle fluorescence. However, fluctuations in the number of charges lead to occasional bursts of fluorescence. This spontaneous photoswitching phenomenon can be exploited for superresolution imaging. The repeated, spontaneous generation of short, intense bursts of fluorescence photons results in a localization precision of ∼0.6 nm, about 4 times better than typical resolution obtained by localization of dye molecules.
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Affiliation(s)
- Yifei Jiang
- Department of Chemistry and ‡Clemson Light Imaging Facility, Clemson University , Clemson, South Carolina 29634, United States
| | - Muskendol Novoa
- Department of Chemistry and ‡Clemson Light Imaging Facility, Clemson University , Clemson, South Carolina 29634, United States
| | - Teeranan Nongnual
- Department of Chemistry and ‡Clemson Light Imaging Facility, Clemson University , Clemson, South Carolina 29634, United States
| | - Rhonda Powell
- Department of Chemistry and ‡Clemson Light Imaging Facility, Clemson University , Clemson, South Carolina 29634, United States
| | - Terri Bruce
- Department of Chemistry and ‡Clemson Light Imaging Facility, Clemson University , Clemson, South Carolina 29634, United States
| | - Jason McNeill
- Department of Chemistry and ‡Clemson Light Imaging Facility, Clemson University , Clemson, South Carolina 29634, United States
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73
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Pakhomov AA, Chertkova RV, Deyev IE, Petrenko AG, Martynov VI. Generation of photoactivatable fluorescent protein from photoconvertible ancestor. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s106816201703013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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74
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Chow RWY, Vermot J. The rise of photoresponsive protein technologies applications in vivo: a spotlight on zebrafish developmental and cell biology. F1000Res 2017; 6. [PMID: 28413613 PMCID: PMC5389412 DOI: 10.12688/f1000research.10617.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/06/2017] [Indexed: 12/24/2022] Open
Abstract
The zebrafish ( Danio rerio) is a powerful vertebrate model to study cellular and developmental processes in vivo. The optical clarity and their amenability to genetic manipulation make zebrafish a model of choice when it comes to applying optical techniques involving genetically encoded photoresponsive protein technologies. In recent years, a number of fluorescent protein and optogenetic technologies have emerged that allow new ways to visualize, quantify, and perturb developmental dynamics. Here, we explain the principles of these new tools and describe some of their representative applications in zebrafish.
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Affiliation(s)
- Renee Wei-Yan Chow
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique UMR8104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julien Vermot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique UMR8104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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75
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Lin CY, Both J, Do K, Boxer SG. Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs). Proc Natl Acad Sci U S A 2017; 114:E2146-E2155. [PMID: 28242710 PMCID: PMC5358378 DOI: 10.1073/pnas.1618087114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Split GFPs have been widely applied for monitoring protein-protein interactions by expressing GFPs as two or more constituent parts linked to separate proteins that only fluoresce on complementing with one another. Although this complementation is typically irreversible, it has been shown previously that light accelerates dissociation of a noncovalently attached β-strand from a circularly permuted split GFP, allowing the interaction to be reversible. Reversible complementation is desirable, but photodissociation has too low of an efficiency (quantum yield <1%) to be useful as an optogenetic tool. Understanding the physical origins of this low efficiency can provide strategies to improve it. We elucidated the mechanism of strand photodissociation by measuring the dependence of its rate on light intensity and point mutations. The results show that strand photodissociation is a two-step process involving light-activated cis-trans isomerization of the chromophore followed by light-independent strand dissociation. The dependence of the rate on temperature was then used to establish a potential energy surface (PES) diagram along the photodissociation reaction coordinate. The resulting energetics-function model reveals the rate-limiting process to be the transition from the electronic excited-state to the ground-state PES accompanying cis-trans isomerization. Comparisons between split GFPs and other photosensory proteins, like photoactive yellow protein and rhodopsin, provide potential strategies for improving the photodissociation quantum yield.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Johan Both
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Keunbong Do
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5012
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76
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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77
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Chen YC, Dickson RM. Improved Fluorescent Protein Contrast and Discrimination by Optically Controlling Dark State Lifetimes. J Phys Chem Lett 2017; 8:733-736. [PMID: 28125231 PMCID: PMC5313373 DOI: 10.1021/acs.jpclett.6b02816] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Modulation and optical control of photoswitchable fluorescent protein (PS-FP) dark state lifetimes drastically improves sensitivity and selectivity in fluorescence imaging. The dark state population of PS-FPs generates an out-of-phase fluorescence component relative to the sinusoidally modulated 488 nm laser excitation. Because this apparent phase advanced emission results from slow recovery to the fluorescent manifold, we hasten recovery and, therefore, modulation frequency by varying coillumination intensity at 405 nm. As 405 nm illumination regenerates the fluorescent ground state more rapidly than via thermal recovery, we experimentally demonstrate that secondary illumination can control PS-FPs dark state lifetime to act as an additional dimension for discriminating spatially and spectrally overlapping emitters. This experimental combination of out of phase imaging after optical modulation (OPIOM) and synchronously amplified fluorescence image recovery (SAFIRe) optically controls the fluorescent protein dark state lifetimes for improved time resolution, with the resulting modulation-based selective signal recovery being quantitatively modeled. The combined experimental results and quantitative numerical simulations further demonstrate the potential of SAFIRe-OPIOM for wide-field biological imaging with improved speed, sensitivity, and optical resolution over other modulation-based fluorescence microscopies.
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78
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Ni M, Zhuo S, So PTC, Yu H. Fluorescent probes for nanoscopy: four categories and multiple possibilities. JOURNAL OF BIOPHOTONICS 2017; 10:11-23. [PMID: 27221311 PMCID: PMC5775479 DOI: 10.1002/jbio.201600042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/08/2016] [Accepted: 05/03/2016] [Indexed: 05/08/2023]
Abstract
Nanoscopy enables breaking down the light diffraction limit and reveals the nanostructures of objects being studied using light. In 2014, three scientists pioneered the development of nanoscopy and won the Nobel Prize in Chemistry. This recognized the achievement of the past twenty years in the field of nanoscopy. However, fluorescent probes used in the field of nanoscopy are still numbered. Here, we review the currently available four categories of probes and existing methods to improve the performance of probes.
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Affiliation(s)
- Ming Ni
- Fujian Provincial Key Laboratory for Photonics Technology & Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou 350007, China
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
- Corresponding authors: ; ;
| | - Shuangmu Zhuo
- Fujian Provincial Key Laboratory for Photonics Technology & Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Normal University, Fuzhou 350007, China
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #10-01 CREATE Tower, Singapore 138602, Singapore
- Corresponding authors: ; ;
| | - Peter T. C. So
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #10-01 CREATE Tower, Singapore 138602, Singapore
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Hanry Yu
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, Singapore 138669, Singapore
- Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #10-01 CREATE Tower, Singapore 138602, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, MD9-04-11, 2 Medical Drive, Singapore 117597, Singapore
- Mechanobiology Institute, National University of Singapore, T-Lab, #05-01, 5A Engineering Drive 1, Singapore 117411, Singapore
- Corresponding authors: ; ;
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79
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Lyu S, Fang J, Duan T, Fu L, Liu J, Li H. Optically controlled reversible protein hydrogels based on photoswitchable fluorescent protein Dronpa. Chem Commun (Camb) 2017; 53:13375-13378. [DOI: 10.1039/c7cc06991j] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Exploiting the optically controlled association and dissociation behavior of a photoswitchable fluorescent protein, Dronpa145N, here we demonstrate the engineering of an optically switchable reversible protein hydrogel using Dronpa145N-based protein building blocks.
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Affiliation(s)
- Shanshan Lyu
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
- State Key Laboratory of Organic–Inorganic Composite Materials
| | - Jing Fang
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Tianyu Duan
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Linglan Fu
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Junqiu Liu
- State Key Lab for Supramolecular Structure and Materials
- Jilin University Changchun
- Jilin
- P. R. China
| | - Hongbin Li
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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80
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Kennes K, Dedecker P, Hutchison JA, Fron E, Uji-i H, Hofkens J, Van der Auweraer M. Field-Controlled Charge Separation in a Conductive Matrix at the Single-Molecule Level: Toward Controlling Single-Molecule Fluorescence Intermittency. ACS OMEGA 2016; 1:1383-1392. [PMID: 30023508 PMCID: PMC6044678 DOI: 10.1021/acsomega.6b00207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/09/2016] [Indexed: 06/07/2023]
Abstract
The fluorescence intermittency or "blinking" of single molecules of ATTO647N (ATTO) in the conductive matrix polyvinylcarbazole (PVK) is described in the presence of an external applied electric field. It is shown that due to the energy distribution of the highest occupied molecular orbital (HOMO) level of PVK, which is energetically close to the HOMO of ATTO, sporadic electron transfer occurs. As a result, the on/off dynamics of blinking can be influenced by the electric field. This field will, depending on the respective position and orientation of the dye/polymer system with respect to those of the electrodes, either enhance or suppress electron transfer from PVK to ATTO as well as the back electron transfer from reduced ATTO to PVK. After the charge-transfer step, the applied field will pull the hole in PVK away from the dye, increasing the overall time the dye resides in a dark state.
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Affiliation(s)
- Koen Kennes
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - Peter Dedecker
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - James A. Hutchison
- ISIS
& icFRC, University of Strasbourg and
CNRS UMR 7006, 8 allée
Gaspard Monge, Strasbourg 67000, France
- School
of Chemistry and Bio21 Institute, University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Eduard Fron
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
| | - Hiroshi Uji-i
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
- RIES, Hokkaido
University, N20W10, Kita-Ward, Sapporo 001-0020, Japan
| | - Johan Hofkens
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
- RIES, Hokkaido
University, N20W10, Kita-Ward, Sapporo 001-0020, Japan
| | - Mark Van der Auweraer
- Molecular
Imaging and Photonics, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium
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81
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Brinks D, Adam Y, Kheifets S, Cohen AE. Painting with Rainbows: Patterning Light in Space, Time, and Wavelength for Multiphoton Optogenetic Sensing and Control. Acc Chem Res 2016; 49:2518-2526. [PMID: 27786461 DOI: 10.1021/acs.accounts.6b00415] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Photons are a fascinating reagent, flowing and reacting quite differently compared to more massive and less ephemeral particles of matter. The optogenetic palette comprises an ever growing set of light-responsive proteins, which open the possibility of using light to perturb and to measure biological processes with great precision in space and time. Yet there are limits on what light can achieve. Diffraction limits the smallest features, and scattering in tissue limits the largest. Photobleaching, diffusion of photogenerated products, and optical crosstalk between overlapping absorption spectra further muddy the optogenetic picture, particularly when one wants to use multiple optogenetic tools simultaneously. But these obstacles are surmountable. Most light-responsive proteins and small molecules undergo more than one light-driven transition, often with different action spectra and kinetics. By overlapping multiple laser beams, carefully patterned in space, time, and wavelength, one can steer molecules into fluorescent or nonfluorescent, active or inactive conformations. By doing so, one can often circumvent the limitations of simple one-photon excitation and achieve new imaging and stimulation capabilities. These include subdiffraction spatial resolution, optical sectioning, robustness to light scattering, and multiplexing of more channels than can be achieved with simple one-photon excitation. The microbial rhodopsins are a particularly rich substrate for this type of multiphoton optical control. The natural diversity of these proteins presents a huge range of starting materials. The spectroscopy and photocycles of microbial rhodopsins are relatively well understood, providing states with absorption maxima across the visible spectrum, which can be accessed on experimentally convenient time scales. A long history of mutational studies in microbial rhodopsins allows semirational protein engineering. Mutants of Archaerhodopsin 3 (Arch) come in all the colors of the rainbow. In a solution of purified Arch-eGFP, a focused green laser excites eGFP fluorescence throughout the laser path, while a focused red laser excites fluorescence of Arch only near the focus, indicative of multiphoton fluorescence. This nonlinearity occurs at a laser intensity ∼1010-fold lower than in conventional two-photon microscopy! The mutant Arch(D95H) shows photoswitchable optical bistability. In a lawn of E. coli expressing this mutant, illumination with patterned blue light converts the molecule into a state that is fluorescent. Illumination with red light excites this fluorescence, and gradually resets the molecules back to the non-fluorescent state. This review describes the new types of molecular logic that can be implemented with multi-photon control of microbial rhodopsins, from whole-brain activity mapping to measurements of absolute membrane voltage. Part of our goal in this Account is to describe recent work in nonlinear optogenetics, but we also present a variety of interesting things one could do if only the right optogenetic molecules were available. This latter component is intended to inspire future spectroscopic, protein discovery, and protein engineering work.
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Affiliation(s)
- Daan Brinks
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yoav Adam
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Simon Kheifets
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Adam E. Cohen
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- Howard
Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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82
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Nienhaus K, Nienhaus GU. Chromophore photophysics and dynamics in fluorescent proteins of the GFP family. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:443001. [PMID: 27604321 DOI: 10.1088/0953-8984/28/44/443001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins of the green fluorescent protein (GFP) family are indispensable for fluorescence imaging experiments in the life sciences, particularly of living specimens. Their essential role as genetically encoded fluorescence markers has motivated many researchers over the last 20 years to further advance and optimize these proteins by using protein engineering. Amino acids can be exchanged by site-specific mutagenesis, starting with naturally occurring proteins as templates. Optical properties of the fluorescent chromophore are strongly tuned by the surrounding protein environment, and a targeted modification of chromophore-protein interactions requires a profound knowledge of the underlying photophysics and photochemistry, which has by now been well established from a large number of structural and spectroscopic experiments and molecular-mechanical and quantum-mechanical computations on many variants of fluorescent proteins. Nevertheless, such rational engineering often does not meet with success and thus is complemented by random mutagenesis and selection based on the optical properties. In this topical review, we present an overview of the key structural and spectroscopic properties of fluorescent proteins. We address protein-chromophore interactions that govern ground state optical properties as well as processes occurring in the electronically excited state. Special emphasis is placed on photoactivation of fluorescent proteins. These light-induced reactions result in large structural changes that drastically alter the fluorescence properties of the protein, which enables some of the most exciting applications, including single particle tracking, pulse chase imaging and super-resolution imaging. We also present a few examples of fluorescent protein application in live-cell imaging experiments.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang Gaede-Straße 1, 76131 Karlsruhe, Germany
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83
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84
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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85
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Niu J, Ben Johny M, Dick IE, Inoue T. Following Optogenetic Dimerizers and Quantitative Prospects. Biophys J 2016; 111:1132-1140. [PMID: 27542508 DOI: 10.1016/j.bpj.2016.07.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 07/22/2016] [Accepted: 07/22/2016] [Indexed: 01/06/2023] Open
Abstract
Optogenetics describes the use of genetically encoded photosensitive proteins to direct intended biological processes with light in recombinant and native systems. While most of these light-responsive proteins were originally discovered in photosynthetic organisms, the past few decades have been punctuated by experiments that not only commandeer but also engineer and enhance these natural tools to explore a wide variety of physiological questions. In addition, the ability to tune dynamic range and kinetic rates of optogenetic actuators is a challenging question that is heavily explored with computational methods devised to facilitate optimization of these systems. Here, we explain the basic mechanisms of a few popular photodimerizing optogenetic systems, discuss applications, compare optogenetic tools against more traditional chemical methods, and propose a simple quantitative understanding of how actuators exert their influence on targeted processes.
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Affiliation(s)
- Jacqueline Niu
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland.
| | - Manu Ben Johny
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland
| | - Ivy E Dick
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland; Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Takanari Inoue
- Department of Biomedical Engineering, School of Medicine, The Johns Hopkins University, Baltimore, Maryland; Department of Cell Biology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland; The Center for Cell Dynamics, Institute for Basic Biomedical Sciences, The Johns Hopkins University, Baltimore, Maryland; Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan.
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86
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Evolution and characterization of a new reversibly photoswitching chromogenic protein, Dathail. J Mol Biol 2016; 428:1776-89. [DOI: 10.1016/j.jmb.2016.02.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/27/2016] [Accepted: 02/29/2016] [Indexed: 12/11/2022]
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87
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Higashino A, Mizuno M, Mizutani Y. Chromophore Structure of Photochromic Fluorescent Protein Dronpa: Acid-Base Equilibrium of Two Cis Configurations. J Phys Chem B 2016; 120:3353-9. [PMID: 26991398 DOI: 10.1021/acs.jpcb.6b01752] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Dronpa is a novel photochromic fluorescent protein that exhibits fast response to light. The present article is the first report of the resonance and preresonance Raman spectra of Dronpa. We used the intensity and frequency of Raman bands to determine the structure of the Dronpa chromophore in two thermally stable photochromic states. The acid-base equilibrium in one photochromic state was observed by spectroscopic pH titration. The Raman spectra revealed that the chromophore in this state shows a protonation/deprotonation transition with a pKa of 5.2 ± 0.3 and maintains the cis configuration. The observed resonance Raman bands showed that the other photochromic state of the chromophore is in a trans configuration. The results demonstrate that Raman bands selectively enhanced for the chromophore yield valuable information on the molecular structure of the chromophore in photochromic fluorescent proteins after careful elimination of the fluorescence background.
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Affiliation(s)
- Asuka Higashino
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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88
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Colletier JP, Sliwa M, Gallat FX, Sugahara M, Guillon V, Schirò G, Coquelle N, Woodhouse J, Roux L, Gotthard G, Royant A, Uriarte LM, Ruckebusch C, Joti Y, Byrdin M, Mizohata E, Nango E, Tanaka T, Tono K, Yabashi M, Adam V, Cammarata M, Schlichting I, Bourgeois D, Weik M. Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP. J Phys Chem Lett 2016; 7:882-887. [PMID: 26866390 DOI: 10.1021/acs.jpclett.5b02789] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.
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Affiliation(s)
| | - Michel Sliwa
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - François-Xavier Gallat
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Michihiro Sugahara
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Virginia Guillon
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Giorgio Schirò
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Nicolas Coquelle
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Joyce Woodhouse
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Laure Roux
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Guillaume Gotthard
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
- The European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
| | - Antoine Royant
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
- The European Synchrotron Radiation Facility (ESRF) , 6 rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
| | - Lucas Martinez Uriarte
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - Cyril Ruckebusch
- Université de Lille , CNRS, UMR 8516, LASIR, Laboratoire de Spectrochimie Infrarouge et Raman, F59 000 Lille, France
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Martin Byrdin
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University , Osaka 565-0871, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Virgile Adam
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1 , Rennes, France
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung , Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Dominique Bourgeois
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale , Université de Grenoble Alpes, CEA, CNRS, F-38044 Grenoble, France
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89
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Lin H, Yuan JM. Stochastic dynamic study of optical transition properties of single GFP-like molecules. J Biol Phys 2016; 42:271-97. [PMID: 26841730 DOI: 10.1007/s10867-015-9407-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/11/2015] [Indexed: 10/22/2022] Open
Abstract
Due to high fluctuations and quantum uncertainty, the processes of single-molecules should be treated by stochastic methods. To study fluorescence time series and their statistical properties, we have applied two stochastic methods, one of which is an analytic method to study the off-time distributions of certain fluorescence transitions and the other is Gillespie's method of stochastic simulations. These methods have been applied to study the optical transition properties of two single-molecule systems, GFPmut2 and a Dronpa-like molecule, to yield results in approximate agreement with experimental observations on these systems. Rigorous oscillatory time series of GFPmut2 before it unfolds in the presence of denaturants have not been obtained based on the stochastic method used, but, on the other hand, the stochastic treatment puts constraints on the conditions under which such oscillatory behavior is possible. Furthermore, a sensitivity analysis is carried out on GFPmut2 to assess the effects of transition rates on the observables, such as fluorescence intensities.
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Affiliation(s)
- Hanbing Lin
- Department of Physics, Drexel University, Philadelphia, PA, 19104, USA
| | - Jian-Min Yuan
- Department of Physics, Drexel University, Philadelphia, PA, 19104, USA.
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90
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GRIFFITHS N, JAIPARGAS EA, WOZNY M, BARTON K, MATHUR N, DELFOSSE K, MATHUR J. Photo-convertible fluorescent proteins as tools for fresh insights on subcellular interactions in plants. J Microsc 2016; 263:148-57. [DOI: 10.1111/jmi.12383] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 12/22/2015] [Indexed: 12/25/2022]
Affiliation(s)
- N. GRIFFITHS
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology; University of Guelph; Guelph ON Canada
| | - E.-A. JAIPARGAS
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology; University of Guelph; Guelph ON Canada
| | - M.R. WOZNY
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology; University of Guelph; Guelph ON Canada
| | - K.A. BARTON
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology; University of Guelph; Guelph ON Canada
| | - N. MATHUR
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology; University of Guelph; Guelph ON Canada
| | - K. DELFOSSE
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology; University of Guelph; Guelph ON Canada
| | - J. MATHUR
- Laboratory of Plant Development and Interactions, Department of Molecular and Cellular Biology; University of Guelph; Guelph ON Canada
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91
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Antoku Y, Dedecker P, Pinheiro PS, Vosch T, Sørensen JB. Spatial distribution and temporal evolution of DRONPA-fused SNAP25 clusters in adrenal chromaffin cells. Photochem Photobiol Sci 2016; 14:1005-12. [PMID: 25837695 DOI: 10.1039/c4pp00423j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Sub-diffraction imaging of plasma membrane localized proteins, such as the SNARE (Soluble NSF Attachment Protein Receptor) proteins involved in exocytosis, in fixed cells have resulted in images with high spatial resolution, at the expense of dynamical information. Here, we have imaged localized fluorescence bursts of DRONPA-fused SNAP-25 molecules in live chromaffin cells by Total Internal Reflection Fluorescence (TIRF) imaging. We find that this method allows tracking protein cluster dynamics over relatively long times (∼20 min.), partly due to the diffusion into the TIRF field of fresh molecules, making possible the simultaneous identification of cluster size, location and temporal evolution. The results indicate that the DRONPA-fused SNAP-25 clusters display rich dynamics, going from staying constant to disappearing and reappearing in specific cluster domains within minutes.
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Affiliation(s)
- Yasuko Antoku
- Department of Neuroscience and Pharmacology and Center for Biomembranes in Nanomedicine (CBN), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark.
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92
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Park JW, Rhee YM. Emission shaping in fluorescent proteins: role of electrostatics and π-stacking. Phys Chem Chem Phys 2016; 18:3944-55. [DOI: 10.1039/c5cp07535a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We obtained the fluorescence spectrum of the GFP with trajectory simulations, and revealed the role of the protein sidechains in emission shifts.
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Affiliation(s)
- Jae Woo Park
- Center for Self-assembly and Complexity
- Institute for Basic Science (IBS)
- Pohang 37673
- Korea
- Department of Chemistry
| | - Young Min Rhee
- Center for Self-assembly and Complexity
- Institute for Basic Science (IBS)
- Pohang 37673
- Korea
- Department of Chemistry
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93
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Abstract
The field of fluorescent proteins (FPs) is constantly developing. The use of FPs changed the field of life sciences completely, starting a new era of direct observation and quantification of cellular processes. The broad spectrum of FPs (see Fig. 1) with a wide range of characteristics allows their use in many different experiments. This review discusses the use of FPs for imaging in budding yeast (Saccharomyces cerevisiae) and fission yeast Schizosaccharomyces pombe). The information included in this review is relevant for both species unless stated otherwise.
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Affiliation(s)
- Maja Bialecka-Fornal
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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94
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Morozov D, Groenhof G. Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo-Switchable Fluorescent Protein. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508452] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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95
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Morozov D, Groenhof G. Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo-Switchable Fluorescent Protein. Angew Chem Int Ed Engl 2015; 55:576-8. [DOI: 10.1002/anie.201508452] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/04/2015] [Indexed: 11/09/2022]
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96
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Pakhomov AA, Chertkova RV, Martynov VI. pH-sensor properties of a fluorescent protein from Dendronephthya sp. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 41:669-74. [DOI: 10.1134/s1068162015060114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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97
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Yao J, Kaberniuk AA, Li L, Shcherbakova DM, Zhang R, Wang L, Li G, Verkhusha VV, Wang LV. Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe. Nat Methods 2015; 13:67-73. [PMID: 26550774 PMCID: PMC4697872 DOI: 10.1038/nmeth.3656] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/16/2015] [Indexed: 12/24/2022]
Abstract
Photoacoustic tomography (PAT) of genetically encoded probes allows imaging of targeted biological processes with high spatial resolution at depths. Here, we combined multi-scale photoacoustic imaging with, for the first time, a reversibly switchable non-fluorescent bacterial phytochrome BphP1. With a heme-derived biliverdin chromophore, BphP1 has the most red-shifted absorption among reported genetically encoded probes, and is reversibly photoconvertible between its red and near-infrared light absorption states. We combined single-wavelength PAT with efficient BphP1 photoswitching, enabling differential imaging that substantially removed background signals, enhanced detection sensitivity, increased penetration depth, and improved spatial resolution. In doing so, we monitored tumor growth and metastasis with a ~100 µm resolution at depths approaching 10 mm using photoacoustic computed tomography, and imaged individual cancer cells with a sub-optical-diffraction resolution of ~140 nm using photoacoustic microscopy. This technology is promising for biomedical studies at different length scales.
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Affiliation(s)
- Junjie Yao
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Andrii A Kaberniuk
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Lei Li
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Daria M Shcherbakova
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Ruiying Zhang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lidai Wang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Guo Li
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lihong V Wang
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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98
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Liu B, Xue Y, Zhao W, Chen Y, Fan C, Gu L, Zhang Y, Zhang X, Sun L, Huang X, Ding W, Sun F, Ji W, Xu T. Three-dimensional super-resolution protein localization correlated with vitrified cellular context. Sci Rep 2015; 5:13017. [PMID: 26462878 PMCID: PMC4604464 DOI: 10.1038/srep13017] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/14/2015] [Indexed: 11/17/2022] Open
Abstract
We demonstrate the use of cryogenic super-resolution correlative light and electron microscopy (csCLEM) to precisely determine the spatial relationship between proteins and their native cellular structures. Several fluorescent proteins (FPs) were found to be photoswitchable and emitted far more photons under our cryogenic imaging condition, resulting in higher localization precision which is comparable to ambient super-resolution imaging. Vitrified specimens were prepared by high pressure freezing and cryo-sectioning to maintain a near-native state with better fluorescence preservation. A 2-3-fold improvement of resolution over the recent reports was achieved due to the photon budget performance of screening out Dronpa and optimized imaging conditions, even with thin sections which is at a disadvantage when calculate the structure resolution from label density. We extended csCLEM to mammalian cells by introducing cryo-sectioning and observed good correlation of a mitochondrial protein with the mitochondrial outer membrane at nanometer resolution in three dimensions.
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Affiliation(s)
- Bei Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yanhong Xue
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Fan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Lusheng Gu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yongdeng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaojun Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Ji
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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99
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Smyrnova D, Moeyaert B, Michielssens S, Hofkens J, Dedecker P, Ceulemans A. Molecular Dynamic Indicators of the Photoswitching Properties of Green Fluorescent Proteins. J Phys Chem B 2015; 119:12007-16. [DOI: 10.1021/acs.jpcb.5b04826] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Daryna Smyrnova
- Quantum
Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven, Celestijnenenlaan 200F, 3001 Heverlee, Belgium
| | - Benjamien Moeyaert
- Molecular
Imaging and Photonics Division, Department of Chemistry, KU Leuven, Celestijnenenlaan 200F, 3001 Heverlee, Belgium
| | - Servaas Michielssens
- Quantum
Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven, Celestijnenenlaan 200F, 3001 Heverlee, Belgium
| | - Johan Hofkens
- Molecular
Imaging and Photonics Division, Department of Chemistry, KU Leuven, Celestijnenenlaan 200F, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Molecular
Imaging and Photonics Division, Department of Chemistry, KU Leuven, Celestijnenenlaan 200F, 3001 Heverlee, Belgium
| | - Arnout Ceulemans
- Quantum
Chemistry and Physical Chemistry Division, Department of Chemistry, KU Leuven, Celestijnenenlaan 200F, 3001 Heverlee, Belgium
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100
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Abstract
Long-term fluorescence live-cell imaging experiments have long been limited by the effects of excitation-induced phototoxicity. The advent of light-sheet microscopy now allows users to overcome this limitation by restricting excitation to a narrow illumination plane. In addition, light-sheet imaging allows for high-speed image acquisition with uniform illumination of samples composed of multiple cell layers. The majority of studies conducted thus far have used custom-built platforms with specialized hardware and software, along with specific sample handling approaches. The first versatile commercially available light-sheet microscope, Lightsheet Z.1, offers a number of innovative solutions, but it requires specific strategies for sample handling during long-term imaging experiments. There are currently no standard procedures describing the preparation of plant specimens for imaging with the Lightsheet Z.1. Here we describe a detailed protocol to prepare plant specimens for light-sheet microscopy, in which Arabidopsis seeds or seedlings are placed in solid medium within glass capillaries or fluorinated ethylene propylene tubes. Preparation of plant material for imaging may be completed within one working day.
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