FPredX : interpretable models for the prediction of spectral maxima, brightness and oligomeric states of fluorescent proteins

2021 ◽  
Author(s):  
Chunlai Tam ◽  
Kam Y. J. Zhang
Keyword(s):  
Fluorescent Proteins ◽  
Interpretable Models

Fluorescent proteins for in vivo imaging, where's the biliverdin?

2020 ◽  
Vol 48 (6) ◽  
pp. 2657-2667
Author(s):  
Felipe Montecinos-Franjola ◽  
John Y. Lin ◽  
Erik A. Rodriguez
Keyword(s):  
Hydrogen Peroxide ◽  
In Vivo Imaging ◽  
Near Infrared ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Fluorescent Imaging ◽  
Infrared Light ◽  
Red Fluorescent Protein ◽  
Color Palette

Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10−18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.

1019: Visualization of the Neurovascular Bundles and Major Pelvic Ganglion with Fluorescent Proteins after Penile Injection

2006 ◽  
Vol 175 (4S) ◽  
pp. 328-328 ◽  
Author(s):  
Hugo H. Davila ◽  
Maggie Mamcarz ◽  
Irving Nadelhaft ◽  
Raoul Salup ◽  
Jorge Lockhart ◽  
...  
Keyword(s):  
Fluorescent Proteins ◽  
Pelvic Ganglion ◽  
Major Pelvic Ganglion ◽  
Neurovascular Bundles

Semiconductor Quantum Dots for Multicolor Fluorescence Imaging and Spectroscopy of Single Cancer Cells

2003 ◽  
Vol 773 ◽  
Author(s):  
Xiaohu Gao ◽  
Shuming Nie ◽  
Wallace H. Coulter
Keyword(s):  
Quantum Dots ◽  
Cancer Cells ◽  
Fluorescence Imaging ◽  
Organic Dyes ◽  
Fluorescent Proteins ◽  
Single Cells ◽  
Quantitative Imaging ◽  
Semiconductor Quantum Dots ◽  
Single Cancer ◽  
Imaging And Spectroscopy

AbstractLuminescent quantum dots (QDs) are emerging as a new class of biological labels with unique properties and applications that are not available from traditional organic dyes and fluorescent proteins. Here we report new developments in using semiconductor quantum dots for quantitative imaging and spectroscopy of single cancer cells. We show that both live and fixed cells can be labeled with multicolor QDs, and that single cells can be analyzed by fluorescence imaging and wavelength-resolved spectroscopy. These results raise new possibilities in cancer imaging, molecular profiling, and disease staging.

Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins

2019 ◽  
Author(s):  
Jeffrey Chang ◽  
Matthew Romei ◽  
Steven Boxer
Keyword(s):  
Rational Design ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Super Resolution ◽  
Unit Cell Size ◽  
Chlorine Substituent ◽  
Gfp Chromophore ◽  
The One ◽  
Green Fluorescent ◽  
Super Resolution Microscopy

<p>Double-bond photoisomerization in molecules such as the green fluorescent protein (GFP) chromophore can occur either via a volume-demanding one-bond-flip pathway or via a volume-conserving hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization would inform the rational design of photoswitchable GFPs as improved tools for super-resolution microscopy. In this communication, we reveal the photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving crystal structures of <i>cis</i> and <i>trans</i> rsEGFP2 containing a monochlorinated chromophore. The position of the chlorine substituent in the <i>trans</i> state breaks the symmetry of the phenolate ring of the chromophore and allows us to distinguish the two pathways. Surprisingly, we find that the pathway depends on the arrangement of protein monomers within the crystal lattice: in a looser packing, the one-bond-flip occurs, whereas in a tighter packing (7% smaller unit cell size), the hula-twist occurs.</p><p> </p><p> </p><p> </p><p> </p><p> </p><p> </p> <p> </p>

POSSIBLE APPLICATION OF METAL SENSITIVE RED FLUORESCENT PROTEINS IN ENVIRONMENTAL MONITORING

2012 ◽  
Vol 11 (1) ◽  
pp. 193-198 ◽  
Author(s):  
Laszlo Szilagyi ◽  
Maria Szabo (Palfi) ◽  
Judit Petres ◽  
Ildiko Miklossy ◽  
Beata Abraham ◽  
...  
Keyword(s):  
Environmental Monitoring ◽  
Fluorescent Proteins ◽  
Red Fluorescent Proteins
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