51
|
Nemet I, Ropelewski P, Imanishi Y. Applications of phototransformable fluorescent proteins for tracking the dynamics of cellular components. Photochem Photobiol Sci 2016; 14:1787-806. [PMID: 26345171 DOI: 10.1039/c5pp00174a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In the past few decades, fluorescent proteins have revolutionized the field of cell biology. Phototransformable fluorescent proteins are capable of changing their excitation and emission spectra after being exposed to specific wavelength(s) of light. The majority of phototransformable fluorescent proteins have originated from marine organisms. Genetic engineering of these proteins has made available many choices for different colors, modes of conversion, and other biophysical properties. Their phototransformative property has allowed the highlighting and tracking of subpopulations of cells, organelles, and proteins in living systems. Furthermore, phototransformable fluorescent proteins have offered new methods for superresolution fluorescence microscopy and optogenetics manipulation of proteins. One of the major advantages of phototransformable fluorescent proteins is their applicability for visualizing newly synthesized proteins that are en route to their final destinations. In this paper, we will discuss the biological applications of phototransformable fluorescent proteins with special emphasis on the application of tracking membrane proteins in vertebrate photoreceptor cells.
Collapse
Affiliation(s)
- Ina Nemet
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA.
| | | | | |
Collapse
|
52
|
Chen X, Zeng Z, Li R, Xue B, Xi P, Sun Y. Superior performance with sCMOS over EMCCD in super-resolution optical fluctuation imaging. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:66007. [PMID: 27281064 DOI: 10.1117/1.jbo.21.6.066007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/10/2016] [Indexed: 06/06/2023]
Abstract
Super-resolution optical fluctuation imaging (SOFI) is a fast and low-cost live-cell optical nanoscopy for extracting subdiffraction information from the statistics of fluorescence intensity fluctuation. As SOFI is based on the fluctuation statistics, rather than the detection of single molecules, it poses unique requirements for imaging detectors, which still lack a systematic evaluation. Here, we analyze the influences of pixel sizes, frame rates, noise levels, and different gains in SOFI with simulations and experimental tests. Our analysis shows that the smaller pixel size and faster readout speed of scientific-grade complementary metal oxide semiconductor (sCMOS) enables SOFI to achieve high spatiotemporal resolution with a large field-of-view, which is especially beneficial for live-cell super-resolution imaging. Overall, as the performance of SOFI is relatively insensitive to the signal-to-noise ratio (SNR), the gain in pixel size and readout speed exceeds the loss in SNR, indicating sCMOS is superior to electron multiplying charge coupled device in context to SOFI in many cases. Super-resolution imaging of cellular microtubule structures with high-order SOFI is experimentally demonstrated at large field-of-view, taking advantage of the large pixel number and fast frame rate of sCMOS cameras.
Collapse
Affiliation(s)
- Xuanze Chen
- Peking University, College of Engineering, Department of Biomedical Engineering, No. 5 Yiheyuan Road Haidian District, Beijing 100871, ChinabPeking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of
| | - Zhiping Zeng
- Peking University, College of Engineering, Department of Biomedical Engineering, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Rongqin Li
- Peking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Boxin Xue
- Peking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Peng Xi
- Peking University, College of Engineering, Department of Biomedical Engineering, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Yujie Sun
- Peking University, State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, No. 5 Yiheyuan Road Haidian District, Beijing 100871, China
| |
Collapse
|
53
|
Hugelier S, de Rooi JJ, Bernex R, Duwé S, Devos O, Sliwa M, Dedecker P, Eilers PHC, Ruckebusch C. Sparse deconvolution of high-density super-resolution images. Sci Rep 2016; 6:21413. [PMID: 26912448 PMCID: PMC4766479 DOI: 10.1038/srep21413] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/22/2016] [Indexed: 11/09/2022] Open
Abstract
In wide-field super-resolution microscopy, investigating the nanoscale structure of cellular processes, and resolving fast dynamics and morphological changes in cells requires algorithms capable of working with a high-density of emissive fluorophores. Current deconvolution algorithms estimate fluorophore density by using representations of the signal that promote sparsity of the super-resolution images via an L1-norm penalty. This penalty imposes a restriction on the sum of absolute values of the estimates of emitter brightness. By implementing an L0-norm penalty--on the number of fluorophores rather than on their overall brightness--we present a penalized regression approach that can work at high-density and allows fast super-resolution imaging. We validated our approach on simulated images with densities up to 15 emitters per μm(-2) and investigated total internal reflection fluorescence (TIRF) data of mitochondria in a HEK293-T cell labeled with DAKAP-Dronpa. We demonstrated super-resolution imaging of the dynamics with a resolution down to 55 nm and a 0.5 s time sampling.
Collapse
Affiliation(s)
| | - Johan J. de Rooi
- Erasmus MC, Department of Biostatistics, Rotterdam, the Netherlands
- Swammerdam Institute for Life Sciences (Universiteit van Amsterdam), 1098 XH Amsterdam, The Netherlands
| | - Romain Bernex
- Université de Lille, LASIR CNRS UMR 8516, F-59000 Lille, France
| | - Sam Duwé
- Department of Chemistry, KU Leuven, Belgium
| | - Olivier Devos
- Université de Lille, LASIR CNRS UMR 8516, F-59000 Lille, France
| | - Michel Sliwa
- Université de Lille, LASIR CNRS UMR 8516, F-59000 Lille, France
| | | | | | | |
Collapse
|
54
|
Vandenberg W, Duwé S, Leutenegger M, Moeyaert B, Krajnik B, Lasser T, Dedecker P. Model-free uncertainty estimation in stochastical optical fluctuation imaging (SOFI) leads to a doubled temporal resolution. BIOMEDICAL OPTICS EXPRESS 2016; 7:467-80. [PMID: 26977356 PMCID: PMC4771465 DOI: 10.1364/boe.7.000467] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 05/21/2023]
Abstract
Stochastic optical fluctuation imaging (SOFI) is a super-resolution fluorescence imaging technique that makes use of stochastic fluctuations in the emission of the fluorophores. During a SOFI measurement multiple fluorescence images are acquired from the sample, followed by the calculation of the spatiotemporal cumulants of the intensities observed at each position. Compared to other techniques, SOFI works well under conditions of low signal-to-noise, high background, or high emitter densities. However, it can be difficult to unambiguously determine the reliability of images produced by any superresolution imaging technique. In this work we present a strategy that enables the estimation of the variance or uncertainty associated with each pixel in the SOFI image. In addition to estimating the image quality or reliability, we show that this can be used to optimize the signal-to-noise ratio (SNR) of SOFI images by including multiple pixel combinations in the cumulant calculation. We present an algorithm to perform this optimization, which automatically takes all relevant instrumental, sample, and probe parameters into account. Depending on the optical magnification of the system, this strategy can be used to improve the SNR of a SOFI image by 40% to 90%. This gain in information is entirely free, in the sense that it does not require additional efforts or complications. Alternatively our approach can be applied to reduce the number of fluorescence images to meet a particular quality level by about 30% to 50%, strongly improving the temporal resolution of SOFI imaging.
Collapse
Affiliation(s)
- Wim Vandenberg
- Department of Chemistry, KULeuven, Celestijnenlaan 200G, 3001 Heverlee,
Belgium
| | - Sam Duwé
- Department of Chemistry, KULeuven, Celestijnenlaan 200G, 3001 Heverlee,
Belgium
| | - Marcel Leutenegger
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen,
Germany
- École Polytechnique Fédérale de Lausanne, Laboratoire d’Optique Biomédicale, 1015 Lausanne,
Switzerland
| | - Benjamien Moeyaert
- Department of Chemistry, KULeuven, Celestijnenlaan 200G, 3001 Heverlee,
Belgium
| | - Bartosz Krajnik
- Department of Chemistry, KULeuven, Celestijnenlaan 200G, 3001 Heverlee,
Belgium
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Torun,
Poland
| | - Theo Lasser
- École Polytechnique Fédérale de Lausanne, Laboratoire d’Optique Biomédicale, 1015 Lausanne,
Switzerland
| | - Peter Dedecker
- Department of Chemistry, KULeuven, Celestijnenlaan 200G, 3001 Heverlee,
Belgium
| |
Collapse
|
55
|
Grimm JB, Klein T, Kopek BG, Shtengel G, Hess HF, Sauer M, Lavis LD. Synthesis of a Far-Red Photoactivatable Silicon-Containing Rhodamine for Super-Resolution Microscopy. Angew Chem Int Ed Engl 2016; 55:1723-7. [PMID: 26661345 PMCID: PMC4736676 DOI: 10.1002/anie.201509649] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 11/20/2022]
Abstract
The rhodamine system is a flexible framework for building small-molecule fluorescent probes. Changing N-substitution patterns and replacing the xanthene oxygen with a dimethylsilicon moiety can shift the absorption and fluorescence emission maxima of rhodamine dyes to longer wavelengths. Acylation of the rhodamine nitrogen atoms forces the molecule to adopt a nonfluorescent lactone form, providing a convenient method to make fluorogenic compounds. Herein, we take advantage of all of these structural manipulations and describe a novel photoactivatable fluorophore based on a Si-containing analogue of Q-rhodamine. This probe is the first example of a "caged" Si-rhodamine, exhibits higher photon counts compared to established localization microscopy dyes, and is sufficiently red-shifted to allow multicolor imaging. The dye is a useful label for super-resolution imaging and constitutes a new scaffold for far-red fluorogenic molecules.
Collapse
Affiliation(s)
- Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Teresa Klein
- Department of Biotechnology and Biophysics, Julius Maximilian University Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Benjamin G Kopek
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
- Hope College, Department of Biology, 35 E. 12th Street, Holland, MI, 49423, USA
| | - Gleb Shtengel
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Julius Maximilian University Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA, 20147, USA.
| |
Collapse
|
56
|
Berardozzi R, Adam V, Martins A, Bourgeois D. Arginine 66 Controls Dark-State Formation in Green-to-Red Photoconvertible Fluorescent Proteins. J Am Chem Soc 2016; 138:558-65. [PMID: 26675944 DOI: 10.1021/jacs.5b09923] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoactivated localization microscopy (PALM) is a powerful technique to investigate cellular nanostructures quantitatively and dynamically. However, the use of PALM for molecular counting or single-particle tracking remains limited by the propensity of photoconvertible fluorescent protein markers (PCFPs) to repeatedly enter dark states. By designing the single mutants mEos2-A69T and Dendra2-T69A, we completely swapped the blinking behaviors of mEos2 and Dendra2, two popular PCFPs. We combined X-ray crystallography and single-molecule microscopy to show that blinking in mEos2 and Dendra2 is largely controlled by the orientation of arginine 66, a highly conserved residue in Anthozoan PCFPs. The Arg66 side-chain conformation affects the bleaching and the on-to-off transition quantum yields, as well as the fraction of molecules entering long-lived dark states, resulting in widely different apparent blinking behaviors that largely modulate the efficiency of current blinking correction procedures. The present work provides mechanistic insight into the complex photophysics of Anthozoan PCFPs and will facilitate future engineering of bright and low-blinking variants suitable for PALM.
Collapse
Affiliation(s)
- Romain Berardozzi
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Alexandre Martins
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes , CEA, CNRS, 38044 Grenoble, France
| |
Collapse
|
57
|
Hertel F, Mo GCH, Duwé S, Dedecker P, Zhang J. RefSOFI for Mapping Nanoscale Organization of Protein-Protein Interactions in Living Cells. Cell Rep 2015; 14:390-400. [PMID: 26748717 DOI: 10.1016/j.celrep.2015.12.036] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/04/2015] [Accepted: 12/06/2015] [Indexed: 11/27/2022] Open
Abstract
It has become increasingly clear that protein-protein interactions (PPIs) are compartmentalized in nanoscale domains that define the biochemical architecture of the cell. Despite tremendous advances in super-resolution imaging, strategies to observe PPIs at sufficient resolution to discern their organization are just emerging. Here we describe a strategy in which PPIs induce reconstitution of fluorescent proteins (FPs) that are capable of exhibiting single-molecule fluctuations suitable for stochastic optical fluctuation imaging (SOFI). Subsequently, spatial maps of these interactions can be resolved in super-resolution in living cells. Using this strategy, termed reconstituted fluorescence-based SOFI (refSOFI), we investigated the interaction between the endoplasmic reticulum (ER) Ca(2+) sensor STIM1 and the pore-forming channel subunit ORAI1, a crucial process in store-operated Ca(2+) entry (SOCE). Stimulating SOCE does not appear to change the size of existing STIM1/ORAI1 interaction puncta at the ER-plasma membrane junctions, but results in an apparent increase in the number of interaction puncta.
Collapse
Affiliation(s)
- Fabian Hertel
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Gary C H Mo
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sam Duwé
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| |
Collapse
|
58
|
Grimm JB, Klein T, Kopek BG, Shtengel G, Hess HF, Sauer M, Lavis LD. Synthesis of a Far-Red Photoactivatable Silicon-Containing Rhodamine for Super-Resolution Microscopy. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509649] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jonathan B. Grimm
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
| | - Teresa Klein
- Department of Biotechnology and Biophysics; Julius Maximilian University Wuerzburg; Am Hubland 97074 Wuerzburg Germany
| | - Benjamin G. Kopek
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
- Hope College; Department of Biology; 35 E. 12th Street Holland MI 49423 USA
| | - Gleb Shtengel
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
| | - Harald F. Hess
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
| | - Markus Sauer
- Department of Biotechnology and Biophysics; Julius Maximilian University Wuerzburg; Am Hubland 97074 Wuerzburg Germany
| | - Luke D. Lavis
- Janelia Research Campus; Howard Hughes Medical Institute; 19700 Helix Drive Ashburn VA 20147 USA
| |
Collapse
|
59
|
Duwé S, De Zitter E, Gielen V, Moeyaert B, Vandenberg W, Grotjohann T, Clays K, Jakobs S, Van Meervelt L, Dedecker P. Expression-Enhanced Fluorescent Proteins Based on Enhanced Green Fluorescent Protein for Super-resolution Microscopy. ACS NANO 2015; 9:9528-41. [PMID: 26308583 DOI: 10.1021/acsnano.5b04129] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
"Smart fluorophores", such as reversibly switchable fluorescent proteins, are crucial for advanced fluorescence imaging. However, only a limited number of such labels is available, and many display reduced biological performance compared to more classical variants. We present the development of robustly photoswitchable variants of enhanced green fluorescent protein (EGFP), named rsGreens, that display up to 30-fold higher fluorescence in E. coli colonies grown at 37 °C and more than 4-fold higher fluorescence when expressed in HEK293T cells compared to their ancestor protein rsEGFP. This enhancement is not due to an intrinsic increase in the fluorescence brightness of the probes, but rather due to enhanced expression levels that allow many more probe molecules to be functional at any given time. We developed rsGreens displaying a range of photoswitching kinetics and show how these can be used for multimodal diffraction-unlimited fluorescence imaging such as pcSOFI and RESOLFT, achieving a spatial resolution of ∼70 nm. By determining the first ever crystal structures of a negative reversibly switchable FP derived from Aequorea victoria in both the "on"- and "off"-conformation we were able to confirm the presence of a cis-trans isomerization and provide further insights into the mechanisms underlying the photochromism. Our work demonstrates that genetically encoded "smart fluorophores" can be readily optimized for biological performance and provides a practical strategy for developing maturation- and stability-enhanced photochromic fluorescent proteins.
Collapse
Affiliation(s)
| | | | | | | | | | - Tim Grotjohann
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Goettingen, Germany
| | | | - Stefan Jakobs
- Department of Neurology, University of Goettingen Medical School , Robert-Koch-Str. 40, 37075 Goettingen, Germany
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Goettingen, Germany
| | | | | |
Collapse
|
60
|
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
| |
Collapse
|
61
|
Mishin AS, Belousov VV, Solntsev KM, Lukyanov KA. Novel uses of fluorescent proteins. Curr Opin Chem Biol 2015; 27:1-9. [PMID: 26022943 DOI: 10.1016/j.cbpa.2015.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/07/2015] [Indexed: 11/28/2022]
Abstract
The field of genetically encoded fluorescent probes is developing rapidly. New chromophore structures were characterized in proteins of green fluorescent protein (GFP) family. A number of red fluorescent sensors, for example, for pH, Ca(2+) and H2O2, were engineered for multiparameter imaging. Progress in development of microscopy hardware and software together with specially designed FPs pushed superresolution fluorescence microscopy towards fast live-cell imaging. Deeper understanding of FPs structure and photophysics led to further development of imaging techniques. In addition to commonly used GFP-like proteins, unrelated types of FPs on the base of flavin-binding domains, bilirubin-binding domains or biliverdin-binding domains were designed. Their distinct biochemical and photophysical properties opened previously unexplored niches of FP uses such as labeling under anaerobic conditions, deep tissue imaging and even patients' blood analysis.
Collapse
Affiliation(s)
- Alexander S Mishin
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia
| | - Vsevolod V Belousov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, GA 30332-0400, United States
| | - Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
| |
Collapse
|
62
|
Zhang X, Chen X, Zeng Z, Zhang M, Sun Y, Xi P, Peng J, Xu P. Development of a reversibly switchable fluorescent protein for super-resolution optical fluctuation imaging (SOFI). ACS NANO 2015; 9:2659-67. [PMID: 25695314 DOI: 10.1021/nn5064387] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Reversibly switchable fluorescent proteins (RSFPs) can be effectively used for super-resolution optical fluctuation imaging (SOFI) based on the switching and fluctuation of single molecules. Several properties of RSFPs strongly influence the quality of SOFI images. These properties include (i) the averaged fluorescence intensity in the fluctuation state, (ii) the on/off contrast ratio, (iii) the photostability, and (iv) the oligomerization tendency. The first three properties determine the fluctuation range of the imaged pixels and the SOFI signal, which are of essential importance to the spatial resolution, and the last may lead to artificial aggregation of target proteins. The RSFPs that are currently used for SOFI are low in averaged fluorescence intensity in the fluctuation state, photostability, and on/off contrast ratio, thereby limiting the range of application of SOFI in biological super-resolution imaging. In this study, we developed a novel monomeric green RSFP termed Skylan-S, which features very high photostability, contrast ratio, and averaged fluorescence intensity in the fluctuation state. Taking advantage of the excellent optical properties of Skylan-S, a 4-fold improvement in the fluctuation range of the imaged pixels and higher SOFI resolution can be obtained compared with Dronpa. Furthermore, super-resolution imaging of the actin or tubulin structures and clathrin-coated pits (CCPs) in living U2OS cells labeled with Skylan-S was demonstrated using the SOFI technique. Overall, Skylan-S developed with outstanding photochemical properties is promising for long-time SOFI imaging with high spatial-temporal resolution.
Collapse
Affiliation(s)
- Xi Zhang
- †Institute of Entomology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
- ‡Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuanze Chen
- §Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
- ∥State Key Laboratory of Biomembrane and Membrane Biotechnology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiping Zeng
- §Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Mingshu Zhang
- ‡Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yujie Sun
- ∥State Key Laboratory of Biomembrane and Membrane Biotechnology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Peng Xi
- §Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Jianxin Peng
- †Institute of Entomology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Pingyong Xu
- ‡Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
63
|
Duwé S, Moeyaert B, Dedecker P. Diffraction-unlimited fluorescence microscopy of living biological samples using pcSOFI. ACTA ACUST UNITED AC 2015; 7:27-41. [PMID: 25727061 DOI: 10.1002/9780470559277.ch140025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The complex microscopic nature of many live biological processes is often obscured by the diffraction limit of light, requiring diffraction-unlimited fluorescence microscopy to resolve them. Because of the vast range of different processes that can be studied, sub-diffraction imaging should work efficiently under many different conditions. Photochromic stochastic optical fluctuation imaging (pcSOFI) is a recent addition to the field of diffraction-unlimited fluorescence microscopy. This robust and versatile method employs a statistical analysis of random fluctuations in the emission of single labels, in this case reversibly switchable fluorescent proteins (RSFPs), to retrieve super-resolution information. Added to the resolution enhancement, pcSOFI also offers contrast enhancement and background reduction in a practical and convenient way. Here, we describe the necessary steps to obtain diffraction-unlimited images, including multicolor and three-dimensional imaging, and highlight the advantages of pcSOFI together with the circumstances under which pcSOFI can be favorably applied.
Collapse
Affiliation(s)
- Sam Duwé
- Department of Chemistry, University of Leuven, Heverlee, Belgium
| | | | | |
Collapse
|
64
|
Diffraction-unlimited imaging: from pretty pictures to hard numbers. Cell Tissue Res 2015; 360:151-78. [DOI: 10.1007/s00441-014-2109-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/22/2014] [Indexed: 10/23/2022]
|
65
|
Fast super-resolution imaging with ultra-high labeling density achieved by joint tagging super-resolution optical fluctuation imaging. Sci Rep 2015; 5:8359. [PMID: 25665878 PMCID: PMC4322366 DOI: 10.1038/srep08359] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 01/19/2015] [Indexed: 12/23/2022] Open
Abstract
Previous stochastic localization-based super-resolution techniques are largely limited by the labeling density and the fidelity to the morphology of specimen. We report on an optical super-resolution imaging scheme implementing joint tagging using multiple fluorescent blinking dyes associated with super-resolution optical fluctuation imaging (JT-SOFI), achieving ultra-high labeling density super-resolution imaging. To demonstrate the feasibility of JT-SOFI, quantum dots with different emission spectra were jointly labeled to the tubulin in COS7 cells, creating ultra-high density labeling. After analyzing and combining the fluorescence intermittency images emanating from spectrally resolved quantum dots, the microtubule networks are capable of being investigated with high fidelity and remarkably enhanced contrast at sub-diffraction resolution. The spectral separation also significantly decreased the frame number required for SOFI, enabling fast super-resolution microscopy through simultaneous data acquisition. As the joint-tagging scheme can decrease the labeling density in each spectral channel, thereby bring it closer to single-molecule state, we can faithfully reconstruct the continuous microtubule structure with high resolution through collection of only 100 frames per channel. The improved continuity of the microtubule structure is quantitatively validated with image skeletonization, thus demonstrating the advantage of JT-SOFI over other localization-based super-resolution methods.
Collapse
|
66
|
Duan C, Byrdin M, El Khatib M, Henry X, Adam V, Bourgeois D. Rational design of enhanced photoresistance in a photoswitchable fluorescent protein. Methods Appl Fluoresc 2015; 3:014004. [DOI: 10.1088/2050-6120/3/1/014004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
67
|
Kim H, Zou T, Modi C, Dörner K, Grunkemeyer TJ, Chen L, Fromme R, Matz MV, Ozkan SB, Wachter RM. A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins. Structure 2015; 23:34-43. [PMID: 25565105 PMCID: PMC4370283 DOI: 10.1016/j.str.2014.11.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/20/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022]
Abstract
In proteins, functional divergence involves mutations that modify structure and dynamics. Here we provide experimental evidence for an evolutionary mechanism driven solely by long-range dynamic motions without significant backbone adjustments, catalytic group rearrangements, or changes in subunit assembly. Crystallographic structures were determined for several reconstructed ancestral proteins belonging to a GFP class frequently employed in superresolution microscopy. Their chain flexibility was analyzed using molecular dynamics and perturbation response scanning. The green-to-red photoconvertible phenotype appears to have arisen from a common green ancestor by migration of a knob-like anchoring region away from the active site diagonally across the β barrel fold. The allosterically coupled mutational sites provide active site conformational mobility via epistasis. We propose that light-induced chromophore twisting is enhanced in a reverse-protonated subpopulation, activating internal acid-base chemistry and backbone cleavage to enlarge the chromophore. Dynamics-driven hinge migration may represent a more general platform for the evolution of novel enzyme activities.
Collapse
Affiliation(s)
- Hanseong Kim
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Taisong Zou
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Chintan Modi
- Institute for Cellular and Molecular Biology, The University of Texas, Austin, TX 78712, USA
| | - Katerina Dörner
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Timothy J Grunkemeyer
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Liqing Chen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
| | - Mikhail V Matz
- Section of Integrative Biology, The University of Texas, Austin, TX 78712, USA
| | - S Banu Ozkan
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
| | - Rebekka M Wachter
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA; Center for Bioenergy and Photosynthesis, Arizona State University, Tempe, AZ 85287, USA.
| |
Collapse
|
68
|
Wang Y, Tang L, Liu W, Zhao Y, Oscar BG, Campbell RE, Fang C. Excited state structural events of a dual-emission fluorescent protein biosensor for Ca²⁺ imaging studied by femtosecond stimulated Raman spectroscopy. J Phys Chem B 2014; 119:2204-18. [PMID: 25226022 DOI: 10.1021/jp505698z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fluorescent proteins (FPs) are luminescent biomolecules that emit characteristic hues upon irradiation. A group of calmodulin (CaM)-green FP (GFP) chimeras have been previously engineered to enable the optical detection of calcium ions (Ca(2+)). We investigate one of these genetically encoded Ca(2+) biosensors for optical imaging (GECOs), GEM-GECO1, which fluoresces green without Ca(2+) but blue with Ca(2+), using femtosecond stimulated Raman spectroscopy (FSRS). The time-resolved FSRS data (<800 cm(-1)) reveal that initial structural evolution following 400 nm photoexcitation involves small-scale coherent proton motions on both ends of the chromophore two-ring system with a <250 fs time constant. Upon Ca(2+) binding, the chromophore adopts a more twisted conformation in the protein pocket with increased hydrophobicity, which inhibits excited-state proton transfer (ESPT) by effectively trapping the protonated chromophore in S1. Both the chromophore photoacidity and local environment form the ultrafast structural dynamics basis for the dual-emission properties of GEM-GECO1. Its photochemical transformations along multidimensional reaction coordinates are evinced by distinct stages of FSRS spectral evolution, particularly related to the ∼460 and 504 cm(-1) modes. The direct observation of lower frequency modes provides crucial information about the nuclear motions preceding ESPT, which enriches our understanding of photochemistry and enables the rational design of new biosensors.
Collapse
Affiliation(s)
- Yanli Wang
- Department of Chemistry, Oregon State University , Corvallis, Oregon 97331-4003, United States
| | | | | | | | | | | | | |
Collapse
|
69
|
Chozinski TJ, Gagnon LA, Vaughan JC. Twinkle, twinkle little star: photoswitchable fluorophores for super-resolution imaging. FEBS Lett 2014; 588:3603-12. [PMID: 25010263 DOI: 10.1016/j.febslet.2014.06.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 01/01/2023]
Abstract
Photoswitchable fluorescent probes are key elements of newly developed super-resolution fluorescence microscopy techniques that enable far-field interrogation of biological systems with a resolution of 50 nm or better. In contrast to most conventional fluorescence imaging techniques, the performance achievable by most super-resolution techniques is critically impacted by the photoswitching properties of the fluorophores. Here we review photoswitchable fluorophores for super-resolution imaging with discussion of the fundamental principles involved, a focus on practical implementation with available tools, and an outlook on future directions.
Collapse
Affiliation(s)
| | - Lauren A Gagnon
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA; Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA.
| |
Collapse
|
70
|
Habuchi S. Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science. Front Bioeng Biotechnol 2014; 2:20. [PMID: 25152893 PMCID: PMC4126472 DOI: 10.3389/fbioe.2014.00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.
Collapse
Affiliation(s)
- Satoshi Habuchi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Jeddah , Saudi Arabia
| |
Collapse
|
71
|
In cellulo evaluation of phototransformation quantum yields in fluorescent proteins used as markers for single-molecule localization microscopy. PLoS One 2014; 9:e98362. [PMID: 24915511 PMCID: PMC4051587 DOI: 10.1371/journal.pone.0098362] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule localization microscopy of biological samples requires a precise knowledge of the employed fluorescent labels. Photoactivation, photoblinking and photobleaching of phototransformable fluorescent proteins influence the data acquisition and data processing strategies to be used in (Fluorescence) Photoactivation Localization Microscopy ((F)-PALM), notably for reliable molecular counting. As these parameters might depend on the local environment, they should be measured in cellulo in biologically relevant experimental conditions. Here, we measured phototransformation quantum yields for Dendra2 fused to actin in fixed mammalian cells in typical (F)-PALM experiments. To this aim, we developed a data processing strategy based on the clustering optimization procedure proposed by Lee et al (PNAS 109, 17436–17441, 2012). Using simulations, we estimated the range of experimental parameters (molecular density, molecular orientation, background level, laser power, frametime) adequate for an accurate determination of the phototransformation yields. Under illumination at 561 nm in PBS buffer at pH 7.4, the photobleaching yield of Dendra2 fused to actin was measured to be (2.5±0.4)×10−5, whereas the blinking-off yield and thermally-activated blinking-on rate were measured to be (2.3±0.2)×10−5 and 11.7±0.5 s−1, respectively. These phototransformation yields differed from those measured in poly-vinyl alcohol (PVA) and were strongly affected by addition of the antifading agent 1,4-diazabicyclo[2.2.2]octane (DABCO). In the presence of DABCO, the photobleaching yield was reduced 2-fold, the blinking-off yield was decreased more than 3-fold, and the blinking-on rate was increased 2-fold. Therefore, DABCO largely improved Dendra2 photostability in fixed mammalian cells. These findings are consistent with redox-based bleaching and blinking mechanisms under (F)-PALM experimental conditions. Finally, the green-to-red photoconversion quantum yield of Dendra2 was estimated to be (1.4±0.6)×10−5in cellulo under 405 nm illumination.
Collapse
|
72
|
Adam V, Berardozzi R, Byrdin M, Bourgeois D. Phototransformable fluorescent proteins: Future challenges. Curr Opin Chem Biol 2014; 20:92-102. [DOI: 10.1016/j.cbpa.2014.05.016] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 05/19/2014] [Accepted: 05/22/2014] [Indexed: 01/28/2023]
|