Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes

AbstractWe developed genetically encoded voltage indicators (GEVIs) using bright near-infrared (NIR) fluorescent proteins from bacterial phytochromes. These new NIR GEVIs are optimized for combination of voltage imaging with simultaneous blue light optogenetic actuator activation. Iterative optimizations led to a GEVI here termed nirButterfly, which reliably reports neuronal activities including subthreshold membrane potential depolarization and hyperpolarization, as well as spontaneous spiking, or electrically- and optogenetically-evoked action potentials. This enables largely improved all-optical causal interrogations of physiology.

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Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging

Biophysical Journal ◽

10.1016/j.bpj.2017.09.007 ◽

2017 ◽

Vol 113 (10) ◽

pp. 2299-2309 ◽

Cited By ~ 24

Author(s):

Kiryl D. Piatkevich ◽

Ho-Jun Suk ◽

Suhasa B. Kodandaramaiah ◽

Fumiaki Yoshida ◽

Ellen M. DeGennaro ◽

...

Keyword(s):

Near Infrared ◽

Fluorescent Proteins ◽

Bacterial Phytochromes

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

Biochemical Society Transactions ◽

10.1042/bst20200444 ◽

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.

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Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome

Communications Chemistry ◽

10.1038/s42004-020-00437-3 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Yusaku Hontani ◽

Mikhail Baloban ◽

Francisco Velazquez Escobar ◽

Swetta A. Jansen ◽

Daria M. Shcherbakova ◽

...

Keyword(s):

Real Time ◽

Rational Design ◽

Near Infrared ◽

Fluorescent Proteins ◽

Covalent Bond ◽

Binding Pocket ◽

Tissue Imaging ◽

Covalent Attachment ◽

Time Resolved

AbstractNear-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C–S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins.

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Using Scuba for In Situ Determination of Chlorophyll Distributions in Corals by Underwater Near Infrared Fluorescence Imaging

Journal of Marine Science and Engineering ◽

10.3390/jmse8010053 ◽

2020 ◽

Vol 8 (1) ◽

pp. 53

Author(s):

Thomas Oh ◽

Jittiwat Sermsripong ◽

Barry W. Hicks

Keyword(s):

Fluorescence Imaging ◽

Large Scale ◽

Near Infrared ◽

Fluorescent Proteins ◽

Fluorescence Emission ◽

Florida Keys ◽

Nir Fluorescence ◽

Novel Method ◽

Near Infrared Fluorescence Imaging

Studies reporting quantitation and imaging of chlorophyll in corals using visible fluorescent emission in the red near 680 nm can suffer from competing emission from other red-emitting pigments. Here, we report a novel method of selectively imaging chlorophyll distributions in coral in situ using only the near infrared (NIR) fluorescence emission from chlorophyll. Commercially available equipment was assembled that allowed the sequential imaging of visible, visible-fluorescent, and NIR-fluorescent pigments on the same corals. The relative distributions of chlorophyll and fluorescent proteins (GFPs) were examined in numerous corals in the Caribbean Sea, the Egyptian Red Sea, the Indonesian Dampier Strait, and the Florida Keys. Below 2 m depth, solar induced NIR chlorophyll fluorescence can be imaged in daylight without external lighting, thus, it is much easier to do than visible fluorescence imaging done at night. The distributions of chlorophyll and GFPs are unique in every species examined, and while there are some tissues where both fluorophores are co-resident, often tissues are selectively enriched in only one of these fluorescent pigments. Although laboratory studies have clearly shown that GFPs can be photo-protective, their inability to prevent large scale bleaching events in situ may be due to their limited tissue distribution.

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Tracing Reversible Light-Induced Binding with Near-infrared Fluorescent Proteins

Methods in Molecular Biology - Photoswitching Proteins ◽

10.1007/978-1-0716-0755-8_12 ◽

2020 ◽

pp. 171-188

Author(s):

Anne Rademacher ◽

Fabian Erdel ◽

Jorge Trojanowski ◽

Karsten Rippe

Keyword(s):

Near Infrared ◽

Fluorescent Proteins

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ChemInform Abstract: Engineering of Bacterial Phytochromes for Near-Infrared Imaging, Sensing, and Light-Control in Mammals

ChemInform ◽

10.1002/chin.201326242 ◽

2013 ◽

Vol 44 (26) ◽

pp. no-no ◽

Cited By ~ 1

Author(s):

Kiryl D. Piatkevich ◽

Fedor V. Subach ◽

Vladislav V. Verkhusha

Keyword(s):

Near Infrared ◽

Infrared Imaging ◽

Light Control ◽

Near Infrared Imaging ◽

Bacterial Phytochromes

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Comparative Analysis of Bacteriophytochrome Agp2 and Its Engineered Photoactivatable NIR Fluorescent Proteins PAiRFP1 and PAiRFP2

Biomolecules ◽

10.3390/biom10091286 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1286 ◽

Cited By ~ 1

Author(s):

Faez Iqbal Khan ◽

Fakhrul Hassan ◽

Razique Anwer ◽

Feng Juan ◽

Dakun Lai

Keyword(s):

Comparative Analysis ◽

Structural Changes ◽

Near Infrared ◽

Fluorescent Proteins ◽

Irradiation Time ◽

Fluorescence Emission ◽

Emission Spectra ◽

Md Simulations ◽

Fluorescence Emission Spectra ◽

Molecular Stability

Two photoactivatable near infrared fluorescent proteins (NIR FPs) named “PAiRFP1” and “PAiRFP2” are formed by directed molecular evolution from Agp2, a bathy bacteriophytochrome of Agrobacterium tumefaciens C58. There are 15 and 24 amino acid substitutions in the structure of PAiRFP1 and PAiRFP2, respectively. A comprehensive molecular exploration of these bacteriophytochrome photoreceptors (BphPs) are required to understand the structure dynamics. In this study, the NIR fluorescence emission spectra for PAiRFP1 were recorded upon repeated excitation and the fluorescence intensity of PAiRFP1 tends to increase as the irradiation time was prolonged. We also predicted that mutations Q168L, V244F, and A480V in Agp2 will enhance the molecular stability and flexibility. During molecular dynamics (MD) simulations, the average root mean square deviations of Agp2, PAiRFP1, and PAiRFP2 were found to be 0.40, 0.49, and 0.48 nm, respectively. The structure of PAiRFP1 and PAiRFP2 were more deviated than Agp2 from its native conformation and the hydrophobic regions that were buried in PAiRFP1 and PAiRFP2 core exposed to solvent molecules. The eigenvalues and the trace of covariance matrix were found to be high for PAiRFP1 (597.90 nm2) and PAiRFP2 (726.74 nm2) when compared with Agp2 (535.79 nm2). It was also found that PAiRFP1 has more sharp Gibbs free energy global minima than Agp2 and PAiRFP2. This comparative analysis will help to gain deeper understanding on the structural changes during the evolution of photoactivatable NIR FPs. Further work can be carried out by combining PCR-based directed mutagenesis and spectroscopic methods to provide strategies for the rational designing of these PAiRFPs.

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