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59 results for “Fluorescent protein”
Data From: Near-infrared co-illumination of fluorescent proteins reduces photobleaching and phototoxicity
<p>Data From: Near-infrared co-illumination of fluorescent proteins reduces photobleaching and phototoxicity</p>
Absorption and Emission spectra of fluorescent proteins
<p>Table with absorption spectra and emission spectra of a set of purified fluorescent proteins</p> <p> </p>
Supplementary Data for "Steric and electronic origins of fluorescence in GFP and GFP-like proteins"
<p>Data accompanying "<strong>Steric and electronic origins of fluorescence in GFP and GFP-like proteins</strong>" under consideration at JACS.</p> <p> </p>
Seven Fluorescent proteins profile in Chlamydomonas reinhardtii and R code statistic for analysis
<p><strong>Overview</strong></p> <p>Data points present in this dataset were obtained following the protocol described in dx.doi.org/10.17504/protocols.io.kfnctme. We picked transformed colonies and cultured in 400 μL TAP medium for 7 days in Deep-well plates (Corning Axygen®, No.: PDW500CS, Thermo Fisher Scientific Inc., Waltham, MA), covered with Breathe-Easy® (Sigma-Aldrich®). Cultivation was performed on a rotary shaker, set to 150 rpm, under constant illumination (50 μmol photons/m<sup>2</sup>s). Then 100 μL sample were transferred clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA) and fluorescence was measured using an Infinite® M200 PRO plate reader (Tecan, Männedorf, Switzerland). Supernatant samples were obtained by spinning Deep-well plates at 3000 × <em>g</em> for 10 min and transferring 100 μL from each well to the clear bottom 96-well plate (Corning Costar, Tewksbury, MA, USA), followed by fluorescence measurement. To compare the constructs, R Statistic version 3.3.3 was used to perform one-way ANOVA (with Tukey's test), and to test statistical hypotheses, the significance level was set at 0.05. Graphs were generated in RStudio v1.0.136. The codes are deposit herein.</p> <p><strong>Info</strong></p> <p>ANOVA_Turkey_Sub.R -> code for ANOVA analysis in R statistic 3.3.3</p> <p>Anova_Output_Summary_Guide.pdf -> Explain the ANOVA files content</p> <p>Analysis_Raw_FP.xlsx -> File with raw values organized in a spreadsheet </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.csv -> relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii </em></p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.csv -> whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>pRFU_<strong>FLUORESCENT PROTEIN</strong>_+_bk.doc -> ANOVA of relative supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>sup_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of supernatant mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p>who_RFU_<strong>FLUORESCENT PROTEIN_</strong>+_bk.doc -> ANOVA of whole culture mCherry fluorescence dataset of positive colonies, blanked with parental wild-type cc1690 cell of <em>Chlamydomonas reinhardtii</em> </p> <p> </p> <p><strong>Consider citing our work. </strong></p> <p>1. Molino JVD, de Carvalho JCM, Mayfield S. Evaluation of secretion reporters to microalgae biotechnology: blue to red fluorescent proteins. Algal Res. 2018;31: 252–261. doi:10.1016/j.algal.2018.02.018</p>
In vivo characterisation of fluorescent proteins in budding yeast.
<p>Raw results of data of the paper 'In vivo characterisation of fluorescent proteins in budding yeast', including scripts to analyze and plot the data.</p>
Structures for "Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2"
<p>Files with atomic coordinates of the structures obtained in geometry optimization of molecular systems within the protein and cluster models. Supplementary materials for the paper "Protonation States of Molecular Groups in the Chromophore-Binding Site Modulate Properties of the Reversibly Switchable Fluorescent Protein rsEGFP2"</p>
QM/MM models of 11 red fluorescent proteins
<p>Geometry configurations on the ground state potential energy surface are obtained at the QM(PBE0-D3/cc-pvdz)/MM(AMBER) level. The list of fluorescent proteins is as follows:</p> <ol> <li>mRojoA</li> <li>mRojo-THSL</li> <li>mRojo-VFAV</li> <li>mRojo-TFAL</li> <li>mRojo-VYGV</li> <li>mRojo-VYGL</li> <li>mRojo-TYGV</li> <li>RDSmCherry0.2</li> <li>RDSmCherry0.5</li> <li>mKeima</li> <li>eqFP670</li> </ol>
Fluorescence complementation enables quantitative imaging of cell penetrating peptide-mediated protein delivery in plants including WUSCHEL transcription factor
<p>These are data related to the manuscript titled "Fluorescence complementation enables quantitative imaging of cell penetrating peptide-mediated protein delivery in plants including WUSCHEL transcription factor" whose preprint can be found here: https://doi.org/10.1101/2022.05.03.490515</p>
Optimized structures for Optical control of ultrafast structural motion in a fluorescent protein
<p>QM-MM Optimized structures of the<strong> </strong>hydrogen bonding configuration in states A1, A2 and Transition State (TS) between them for rsKiiro protein on ground (s0) and first excited (s1) states. Structures were optimized at PBE0-D3/cc-pVDZ//Amber03 level.</p>
Quantitative determination of the full switching cycle of photochromic fluorescent proteins
<p>Acquired data for the paper by Bourges et al., "Quantitative determination of the full switching cycle of photochromic fluorescent proteins" currently in press in Chemical Communications.</p>
Magnetic control of GFP-like fluorescent proteins - Raw data 1
<p>We've discovered a simple, nontoxic, biocompatible way to control the brightness of <a href="https://www.fpbase.org/protein/avgfp/">GFP</a>-like fluorescent proteins via modest magnetic fields (~10 mT). Fluorescent proteins which seem magnetically inert (e.g. <a href="https://www.fpbase.org/protein/egfp/">EGFP</a>, <a href="https://www.fpbase.org/protein/mscarlet/">mScarlet</a>) become magnetoresponsive in the presence of an appropriate cofactor (e.g. EGFP-<a href="https://doi.org/10.1021/acs.bioconjchem.1c00306">FlavinTag</a>, or an mScarlet/<a href="https://pubchem.ncbi.nlm.nih.gov/compound/Flavin-mononucleotide">FMN</a> solution). This method works at room-temperature and body-temperature, in vitro, in <i>E. coli</i> and in cultured mammalian cells.</p><p>The GFP-family magnetoresponse is weak (ΔF/F≈1%), but shows the hallmarks of evolvability. This suggests exciting technological possibilities, both short-term (e.g. lock-in detection, multiplexing) and long-term (e.g. optically-detected MRI, magnetogenetics).</p><p>We've also discovered weak magnetoresponse from a member of the LOV-domain family. This suggests the possibility that magnetoresponse is a general feature of fluorescent proteins, and not unique to the cryptochrome/photolyase family.</p><p> </p><p>This repository holds some of the raw data for the main text figures. For the contents of the paper, please see: <a href="https://doi.org/10.5281/zenodo.8137174">doi.org/10.5281/zenodo.8137174</a></p>
Magnetic control of GFP-like fluorescent proteins - Raw data 2
<p>We've discovered a simple, nontoxic, biocompatible way to control the brightness of <a href="https://www.fpbase.org/protein/avgfp/">GFP</a>-like fluorescent proteins via modest magnetic fields (~10 mT). Fluorescent proteins which seem magnetically inert (e.g. <a href="https://www.fpbase.org/protein/egfp/">EGFP</a>, <a href="https://www.fpbase.org/protein/mscarlet/">mScarlet</a>) become magnetoresponsive in the presence of an appropriate cofactor (e.g. EGFP-<a href="https://doi.org/10.1021/acs.bioconjchem.1c00306">FlavinTag</a>, or an mScarlet/<a href="https://pubchem.ncbi.nlm.nih.gov/compound/Flavin-mononucleotide">FMN</a> solution). This method works at room-temperature and body-temperature, in vitro, in <i>E. coli</i> and in cultured mammalian cells.</p><p>The GFP-family magnetoresponse is weak (ΔF/F≈1%), but shows the hallmarks of evolvability. This suggests exciting technological possibilities, both short-term (e.g. lock-in detection, multiplexing) and long-term (e.g. optically-detected MRI, magnetogenetics).</p><p>We've also discovered weak magnetoresponse from a member of the LOV-domain family. This suggests the possibility that magnetoresponse is a general feature of fluorescent proteins, and not unique to the cryptochrome/photolyase family.</p><p> </p><p>This repository holds some of the raw data for the main text figures. For the contents of the paper, please see: <a href="https://doi.org/10.5281/zenodo.8137174">doi.org/10.5281/zenodo.8137174</a></p>
Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching
<p>Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.</p>
Data from: Regulation of green fluorescent proteins by Sea Anemones (Anthopleura spp.) in response to light
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Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching
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Quantitative comparison of fluorescent proteins using protein nanocages in live cells
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Data for 'Ranking Single Fluorescent Protein Based Calcium Biosensor Performance by Molecular Dynamics Simulations'
<h2>Melike Berksoz, Canan Atilgan* </h2> <h3>Faculty of Engineering and Natural Sciences, Sabanci University </h3> <p><strong>*Correspondance:</strong> Canan Atilgan, Faculty of Natural Sciences and Engineering, Sabancı University, Tuzla 34956 Istanbul, Türkiye, E-mail: canan@sabanciuniv.edu</p> <p>Genetically Encoded Fluorescent Biosensors (GEFBs) have become indispensable tools for visualizing biological processes <em>in</em> <em>vivo.</em> A typical GEFB is composed of a sensory domain (SD) which undergoes a conformational change upon ligand binding and a genetically fused fluorescent protein (FP). Ligand binding in the SD allosterically modulates the chromophore environment and changes its spectral properties. Single fluorescent (FP)-based biosensors, a subclass of GEFBs, offer a simple experimental setup; they are easy to produce in living cells, structurally stable and simple due to their single-wavelength operation. However, they pose a significant challenge for structure optimization, especially concerning the length and residue content of linkers between the FP and SD which effect how well the chromophore responds to conformational change in the SD. In this work, we use classical all-atom molecular dynamics simulations to analyze the dynamic properties of a series of calmodulin-based calcium biosensors, all with different FP-SD interaction interfaces and varying degrees of calcium binding dependent fluorescence change. Our results indicate that biosensor performance can be predicted based on distribution of water molecules around the chromophore and shifts in hydrogen bond occupancies between the ligand-bound and ligand-free sensor structures.</p> <p>Hydrogen bond occupancies were calculated with merging_bonds.py script. Double counted hydrogen bonds where a residue acts both as acceptor and donor are merged into a single entry with merge_files.py. To run sasa.tcl, you need VMD software. Trajectories were created with NAMD2 with a dcdfrequency of 5000 timesteps (every 10 ps) and strided in a 1:100 ratio (every 1 ns=1 frame in dcd). </p>
Arabidopsis SAUR63 seedling phenotypes and fluorescent fusion protein localization
<p>In plants, regulated cell expansion determines organ size and shape. Several members of the family of redundantly acting Small Auxin Up RNA (SAUR) proteins can stimulate plasma membrane (PM) H+-ATPase proton pumping activity by inhibiting PM-associated PP2C.D phosphatases, thereby increasing the PM electrochemical potential, acidifying the apoplast, and stimulating cell expansion. Similarly, Arabidopsis thaliana SAUR63 was able to increase growth of various organs, antagonize PP2C.D5 phosphatase, and increase H+-ATPase activity. This dataset includes i) measurements of seedling growth in plants with altered activity of SAUR63 and PP2C.D5; ii) data from fluorescent images to measure extracellular pH; iii) analyses of subcellular localization of SAUR63:YFP fusion protein variants in roots; and iv) SAUR63:YFP localization after transient expression in Nicotiana benthamiana leaves with perturbed plasma membrane lipid composition. These data underlie figures presented in the linked manuscript. Using a gain-of-function approach to bypass genetic redundancy, we dissected structural requirements for SAUR63 growth-promoting activity. The divergent N-terminal domain of SAUR63 has a predicted basic amphipathic α-helix, and was able to drive partial PM association. Deletion of the N-terminal domain decreased PM association of a SAUR63 fusion protein, as well as decreasing protein level and eliminating growth-promoting activity. Conversely, forced PM association restored ability to promote H+-ATPase activity and cell expansion, indicating that SAUR63 is active when PM-associated. Lipid binding assays and perturbations of PM lipid composition indicate that the N-terminal domain can interact with PM anionic lipids. Mutations in the conserved SAUR domain also reduced PM association in root cells. Thus, both the N-terminal domain and the SAUR domain may cooperatively mediate the SAUR63 PM association required to promote growth. Data is licensed by the authors for use and distribution subject to citation of the original source in accordance with the Creative Commons Attribution (CC BY) license.</p>
MD trajectories of lipidated fluorescent proteins constructs cleGFP and dleGFP
<p>MD trajectories of lipidated fluorescent proteins.</p> <p>Force field: Martini2.2p</p> <p>File formats: Gromacs 2018</p> <p>cleGFP 200µs, c-terminal lipidation</p> <p>dleGFP 85.46µs, c-terminal and internal lipidation (i.e. "d" doubly-lipidated)</p>
Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry
<p>Source data for figure 1, figure 3a, and supplementary figure 1.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.