Dual Illumination Enhances Transformation of an Engineered Green-to-Red Photoconvertible Fluorescent Protein

The molecular mechanisms for the photoconversion of fluorescent proteins remain elusive owing to the challenges of monitoring chromophore structural dynamics during the light-induced processes. We implemented time-resolved electronic and stimulated Raman spectroscopies to reveal two hidden species of an engineered ancestral GFP-like protein LEA, involving semi-trapped protonated and trapped deprotonated chromophores en route to photoconversion in pH 7.9 buffer. A new dual-illumination approach was examined, using 400 and 505 nm light simultaneously to achieve faster conversion and higher color contrast. Substitution of UV irradiation with visible light benefits bioimaging, while the spectral benchmark of a trapped chromophore with characteristic ring twisting and bridge-H bending motions enables rational design of functional proteins. With the improved H-bonding network and structural motions, the photoexcited chromophore could increase the photoswitching-aided photoconversion while reducing trapped species.     

A General Mechanism of Photoconversion of Green‐to‐Red Fluorescent Proteins Based on Blue and Infrared Light Reduces Phototoxicity in Live‐Cell Single‐Molecule Imaging

Photoconversion of fluorescent proteins by blue and complementary near‐infrared light, termed primed conversion (PC), is a mechanism recently discovered for Dendra2. We demonstrate that controlling the conformation of arginine at residue 66 by threonine at residue 69 of fluorescent proteins from Anthozoan families (Dendra2, mMaple, Eos, mKikGR, pcDronpa protein families) represents a general route to facilitate PC. Mutations of alanine 159 or serine 173, which are known to influence chromophore flexibility and allow for reversible photoswitching, prevent PC. In addition, we report enhanced photoconversion for pcDronpa variants with asparagine 116. We demonstrate live‐cell single‐molecule imaging with reduced phototoxicity using PC and record trajectories of RNA polymerase in Escherichia coli cells.     

Dual Gold‐Catalyzed Head‐to‐Tail Coupling of Iodoalkynes

Various haloalkynes are converted in the presence of a dual activation gold catalyst. Via a dual activation process a completely atom economic head‐to‐tail coupling delivers gem‐dihalogenated conjugated enynes as valuable building blocks for organic synthesis.     

Quenching of pH‐Responsive Luminescence of a Benzoindolizine Sensor by an Ultrafast Hydrogen Shift

Fluorescent‐sensor design requires consideration of how photochemical dynamics control properties of a sensing state. Transient absorption (TA) spectroscopy reveals an ultrafast net [1,3]‐hydrogen shift following excitation of a protonated methoxy benzoindolizine (bzi) sensor in solution. These photochemical dynamics explain a quenched pH‐responsive fluorescence shift and dramatically reduced fluorescence quantum yield relative to other (e. g. methyl) bzi compounds that do not tautomerize. Calculations predict the energetic and structural feasibility for rearrangement in protonated bzi compounds, such that interaction between the pi‐network and strongly electron‐donating methoxyl must lower the barrier for suprafacial H or H⁺ shift across an allylic moiety. As bzi compounds broadly exhibit pH‐responsive emission shifts, chemical interactions that modulate this electronic interaction and suppress tautomerization could be used to facilitate binding‐ or surface‐specific acid‐responsive sensing.     

Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo‐Switchable Fluorescent Protein

Reversibly switchable fluorescent proteins (RSFPs) are essential for high‐resolution microscopy of biological samples, but the reason why these proteins are photochromic is still poorly understood. To address this problem, we performed molecular dynamics simulations of the fast switching Met159Thr mutant of the RSFP Dronpa. Our simulations revealed a ground state structural heterogeneity in the chromophore pocket that consists of three populations with one, two, or three hydrogen bonds to the phenolate moiety of the chromophore. By means of non‐adiabatic quantum mechanics/molecular dynamics simulations, we demonstrated that the subpopulation with a single hydrogen bond is responsible for off‐switching through photo‐isomerization of the chromophore, whereas two or more hydrogen bonds inhibit the isomerization and promote fluorescence instead. While rational design of new RSFPs has so far focused on structure alone, our results suggest that structural heterogeneity must be considered as well.     

Protein Recognition by an Ensemble of Fluorescent DNA G‐Quadruplexes

Sniffing out proteins : Fluorescent DNA G‐quadruplexes have been used for building versatile signaling receptors for proteins in a single solution. Introducing a protein sample to the ensemble results in a unique emission signature for unambiguous identification (see scheme, R=fluorophore). The self‐assembled, pattern‐based protein detection systems are easily fabricated, have the potential for high‐throughput operations, and have the ability to handle small protein samples.

     

A Cell‐Targeted Non‐Cytotoxic Fluorescent Nanogel Thermometer Created with an Imidazolium‐Containing Cationic Radical Initiator

A cationic fluorescent nanogel thermometer based on thermo‐responsive N‐isopropylacrylamide and environment‐sensitive benzothiadiazole was developed with a new azo compound bearing imidazolium rings as the first cationic radical initiator. This cationic fluorescent nanogel thermometer showed an excellent ability to enter live mammalian cells in a short incubation period (10 min), a high sensitivity to temperature variations in live cells (temperature resolution of 0.02–0.84 °C in the range 20–40 °C), and remarkable non‐cytotoxicity, which permitted ordinary cell proliferation and even differentiation of primary cultured cells.     

Extending Metal‐to‐Polyoxometalate Charge Transfer Lifetimes: The Effect of Heterometal Location

In an effort to develop robust molecular sensitizers for solar fuel production, the electronic structure and photodynamics of transition‐metal‐substituted polyoxometalates (POMs), a novel class of compound in this context, was examined. Experimental and computational techniques including femtosecond (fs) transient absorption spectroscopy have been used to study the cobalt‐containing Keggin POMs, [Co^IIW₁₂O₄₀]^6? ( 1 a ), [Co^IIIW₁₂O₄₀]^5? ( 2 a ), [SiCo^II(H₂O)W₁₁O₃₉]^6? ( 3 a ), and [SiCo^III(H₂O)W₁₁O₃₉]^5? ( 4 a ), finding the longest lived charge transfer excited state so far observed in a POM and elucidating the electronic structures and excited‐state dynamics of these compounds at an unprecedented level. All species exhibit a bi‐exponential decay in which early dynamic processes with time constants in the fs domain yield longer lived excited states which decay with time constants in the ps to ns domain. The initially formed states of 1 a and 3 a are considered to result from metal‐to‐polyoxometalate charge transfer (MPCT) from Co^II to W, while the longer‐lived excited state of 1 a is tentatively assigned to a localized intermediate MPCT state. The excited state formed by the tetrahedral cobalt(II) centered heteropolyanion ( 1 a ) is far longer‐lived (τ=420 ps in H₂O; τ=1700 ps in MeCN) than that of 3 a (τ=1.3 ps), in which the single Co^II atom is located in a pseudo‐octahedral addendum site. Short‐lived states are observed for the two Co^III‐containing heteropolyanions 2 a (τ=4.4 ps) and 4 a (τ=6.3 ps) and assigned solely to O→Co^III charge transfer. The dramatically extended lifetime for 1 a versus 3 a is ascribed to a structural change permitted by the coordinatively flexible central site, weak orbital overlap of the central Co with the polytungstate framework, and putative transient valence trapping of the excited electron on a single W atom, a phenomenon not noted previously in POMs.     

Probing Invisible,Excited Protein States by Non‐Uniformly Sampled Pseudo‐4D CEST Spectroscopy

Chemical exchange saturation transfer (CEST) NMR spectroscopy is a powerful tool for studies of slow timescale protein dynamics. Typical experiments are based on recording a large number of 2D data sets and quantifying peak intensities in each of the resulting planes. A weakness of the method is that peaks must be resolved in 2D spectra, limiting applications to relatively small proteins. Resolution is significantly improved in 3D spectra but recording uniformly sampled data is time‐prohibitive. Here we describe non‐uniformly sampled HNCO‐based pseudo‐4D CEST that provides excellent resolution in reasonable measurement times. Data analysis is done through fitting in the time domain, without the need of reconstructing the frequency dimensions, exploiting previously measured accurate peak positions in reference spectra. The methodology is demonstrated on several protein systems, including a nascent form of superoxide dismutase that is implicated in neurodegenerative disease.     

Easy‐to‐Attach/Detach Solubilizing‐Tag‐Aided Chemical Synthesis of an Aggregative Capsid Protein

A solubilizing Trt‐K₁₀ tag was developed for the effective chemical preparation of peptides/proteins with low solubility. The Trt‐K₁₀ tag comprises a hydrophilic oligo‐Lys sequence and a trityl anchor, and can be selectively introduced to a side chain thiol of Cys of deprotected peptides/proteins with a trityl alcohol‐type introducing reagent Trt(OH)‐K₁₀ under acidic conditions. Significantly, the ligation product in the reaction mixture of a thiol‐additive‐free native chemical ligation can be modified directly in a one‐pot manner to facilitate the isolation of the product by high‐performance liquid chromatography. Finally, the Trt‐K₁₀ tag can be readily removed with a standard trifluoroacetic acid cocktail. Using this easy‐to‐attach/detach tag‐aided method, a hepatitis B virus capsid protein that is usually difficult to handle was synthesized successfully.     

Mechanism‐Dependent Modulation of Ultrafast Interfacial Water Dynamics in Intrinsically Disordered Protein Complexes

The recognition of intrinsically disordered proteins (IDPs) is highly dependent on dynamics owing to the lack of structure. Here we studied the interplay between dynamics and molecular recognition in IDPs with a combination of time‐resolving tools on timescales ranging from femtoseconds to nanoseconds. We interrogated conformational dynamics and surface water dynamics and its attenuation upon partner binding using two IDPs, IBB and Nup153FG, both of central relevance to the nucleocytoplasmic transport machinery. These proteins bind the same nuclear transport receptor (Importinβ) with drastically different binding mechanisms, coupled folding–binding and fuzzy complex formation, respectively. Solvent fluctuations in the dynamic interface of the Nup153FG‐Importinβ fuzzy complex were largely unperturbed and slightly accelerated relative to the unbound state. In the IBB‐Importinβ complex, on the other hand, substantial relative slowdown of water dynamics was seen in a more rigid interface. These results show a correlation between interfacial water dynamics and the plasticity of IDP complexes, implicating functional relevance for such differential modulation in cellular processes, including nuclear transport.     

Active‐Site‐Matched Fluorescent Probes for Rapid and Direct Detection of Vicinal‐Sulfydryl‐Containing Peptides/Proteins in Living Cells

Vicinal‐sulfydryl‐containing peptides/proteins (VSPPs) play a crucial role in human pathologies. Fluorescent probes that are capable of detecting intracellular VSPPs in vivo would be useful tools to explore the mechanisms of some diseases. In this study, by regulating the spatial separation of two maleimide groups in a fluorescent dye to match that of two active cysteine residues contained in the conserved amino acid sequence (–CGPC–) of human thioredoxin, two active‐site‐matched fluorescent probes, o‐Dm‐Ac and m‐Dm‐Ac, were developed for real‐time imaging of VSPPs in living cells. As a result, the two probes can rapidly respond to small peptide models and reduced proteins, such as WCGPCK (W‐6), WCGGPCK (W‐7), and WCGGGPCK (W‐8), reduced bovine serum albumin (rBSA), and reduced thioredoxin (rTrx). Moreover, o‐Dm‐Ac displays a higher binding sensitivity with the above‐mentioned peptides and proteins, especially with W‐7 and rTrx. Furthermore, o‐Dm‐Ac was successfully used to rapidly and directly detect VSPPs both in vitro and in living cells. Thus, a novel probe‐design strategy was proposed and the synthesized probe applied successfully in imaging of target proteins in situ.     

Measurement of Local Sodium Ion Levels near Micelle Surfaces with Fluorescent Photoinduced‐Electron‐Transfer Sensors

The Na⁺ concentration near membranes controls our nerve signals aside from several other crucial bioprocesses. Fluorescent photoinduced electron transfer (PET) sensor molecules target Na⁺ ions in nanospaces near micellar membranes with excellent selectivity against H⁺. The Na⁺ concentration near anionic micelles was found to be higher than that in bulk water by factors of up to 160. Sensor molecules that are not held tightly to the micelle surface only detected a Na⁺ amplification factor of 8. These results were strengthened by the employment of control compounds whose PET processes are permanently “on” or “off”.