Cysteine-mediated mechanism disrupts energy transfer to prevent photooxidation

A D-π-A-based near-infrared fluorescent probe with large Stokes shift for the detection of cysteine in vivo

D-π-A dyes are an ideal strategy for building near-infrared fluorescent probes that have a large Stokes shift due to their excellent properties of adjustable emission wavelength and Stokes shift. Developing a near-infrared (NIR) fluorescent probe (JTPQ-Cys) capable of detecting cysteine (Cys) was the aim of this study. In JTPQ-Cys, julolidine served as the electron donor (D) and quinoline as the electron acceptor (A), with 3,4-ethylenedioxythiophene as the π-bridge. The π-conjugation and vibrational/rotational activity of the molecule were increased by the introduction of 3,4-ethylenedioxythiophene, causing the molecule to exhibit NIR emission and a large Stokes shift. When JTPQ-Cys was used to detect Cys, a clear fluorescence turn-on signal was observed at 741 nm, together with a Stokes shift of 268 nm. The limit of detection of JTPQ-Cys for Cys is 24 nM. Moreover, JTPQ-Cys has been utilized successfully for imaging studies of Cys in cells and zebrafish because it has good photostability, low cytotoxicity, and a high signal-to-noise ratio. Overall, our findings demonstrate the potential of JTPQ-Cys to be one of the best choices for detecting Cys in biological systems, and JTPQ is an ideal fluorophore to construct fluorescence dyes for bioimaging.

Investigating the dissipation of heat and quantum information from DNA-scaffolded chromophore networks

Scaffolded molecular networks are important building blocks in biological pigment-protein complexes, and DNA nanotechnology allows analogous systems to be designed and synthesized. System-environment interactions in these systems are responsible for important processes, such as the dissipation of heat and quantum information. This study investigates the role of nanoscale molecular parameters in tuning these vibronic system-environment dynamics. Here, genetic algorithm methods are used to obtain nanoscale parameters for a DNA-scaffolded chromophore network based on comparisons between its calculated and measured optical spectra. These parameters include the positions, orientations, and energy level characteristics within the network. This information is then used to compute the dynamics, including the vibronic population dynamics and system-environment heat currents, using the hierarchical equations of motion. The dissipation of quantum information is identified by the system's transient change in entropy, which is proportional to the heat currents according to the second law of thermodynamics. These results indicate that the dissipation of quantum information is highly dependent on the particular nanoscale characteristics of the molecular network, which is a necessary first step before gleaning the systematic optimization rules. Subsequently, the I-concurrence dynamics are calculated to understand the evolution of the vibronic system's quantum entanglement, which are found to be long-lived compared to these system-bath dissipation processes.

A red-emitting ultrasensitive fluorescent probe for specific detection and biological visualization of cysteine in vitro and in vivo

Developing efficient strategies for specific detection of cysteine (Cys) is of great importance for identifying complicated biological roles in physiological and pathological processes. Herein, an ultrasensitive red-emission fluorescent probe (termed 1) is constructed for specific detection and biological visualization of Cys. The linked-anthocyanin fluorophore modified with a twisted N, N-diethylamino moiety shows improved red-shifted emission (642 nm) and absolute quantum yield (0.224 in dimethyl sulfoxide), as well as minimal fluorescence background signal and good water solubility. Meanwhile, utilizing acryloyl chloride as recognition group endows the probe 1 with excellent sensitivity and selectivity towards Cys (limit of detection: 2.93 nM). More importantly, the in vitro and in vivo results confirm that the probe 1 has the capacity of fluorescence imaging of Cys and good biological safety, which holds great promise for bioanalysis and biosensing of Cys.

Determining interchromophore effects for energy transport in molecular networks using machine-learning algorithms

Nature uses chromophore networks, with highly optimized structural and energetic characteristics, to perform important chemical functions. Due to its modularity, predictable aggregation characteristics, and established synthetic protocols, structural DNA nanotechnology is a promising medium for arranging chromophore networks with analogous structural and energetic controls. However, this high level of control creates a greater need to know how to optimize the systems precisely. This study uses the system's modularity to produce variations of a coupled 14-Site chromophore network. It uses machine-learning algorithms and spectroscopy measurements to reveal the energy-transport roles of these Sites, paying particular attention to the cooperative and inhibitive effects they impose on each other for transport across the network. The physical significance of these patterns is contextualized, using molecular dynamics simulations and energy-transport modeling. This analysis yields insights about how energy transfers across the Donor-Relay and Relay-Acceptor interfaces, as well as the energy-transport pathways through the homogeneous Relay segment. Overall, this report establishes an approach that uses machine-learning methods to understand, in fine detail, the role that each Site plays in an optoelectronic molecular network.

Understanding Disorder, Vibronic Structure, and Delocalization in Electronically Coupled Dimers on DNA Duplexes

Structural DNA nanotechnology is a promising approach to create chromophore networks with modular structures and Hamiltonians to control the material's functions. The functional behaviors of these systems depend on the interactions of the chromophores' vibronic states, as well as interactions with their environment. To optimize their functions, it is necessary to characterize the chromophore network's structural and energetic properties, including the electronic delocalization in some cases. In this study, parameters of interest are deduced in DNA-scaffolded Cyanine 3 and Cyanine 5 dimers. The methods include steady-state optical measurements, physical modeling, and a genetic algorithm approach. The parameters include the chromophore network's vibronic Hamiltonian, molecular positions, transition dipole orientations, and environmentally induced energy broadening. Additionally, the study uses temperature-dependent optical measurements to characterize the spectral broadening further. These combined results reveal the quantum mechanical delocalization, which is important for functions like coherent energy transport and quantum information applications.

Roles of Exogenous α-Lipoic Acid and Cysteine in Mitigation of Drought Stress and Restoration of Grain Quality in Wheat

Cysteine (Cys) and α-lipoic acid (ALA) are naturally occurring antioxidants (sulfur-containing compounds) that can protect plants against a wide spectrum of environmental stresses. However, up to now, there are no conclusive data on their integrative roles in mitigation of drought stress in wheat plants. Here, we studied the influence of ALA at 0.02 mM (grain dipping pre-cultivation treatment) and Cys (25 and 50 ppm as a foliar application) under well watered and deficit irrigation (100% and 70% of recommended dose). The results showed that deficit irrigation markedly caused obvious cellular oxidative damage as indicated by elevating the malondialdehyde (MDA) and hydrogen peroxide content (H₂O₂). Moreover, water stressed plants exhibited multiple changes in physiological metabolism, which affected the quantitative and qualitative variables of grain yield. The enzymatic antioxidants, including superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT) and peroxidase (POX) were improved by Cys application. SOD and APX had the same response when treated with ALA, but CAT and POX did not. Moreover, both studied molecules stimulated chlorophyll (Chl) and osmolytes' biosynthesis. In contrast, the Chl a/b ratio was decreased, while flavonoids were not affected by either of the examined molecules. Interestingly, all above-mentioned changes were associated with an improvement in the scavenging capacity of reactive oxygen species (ROS), leaf relative water content (RWC), grain number, total grain yield, weight of 1000 kernels, gluten index, falling number, and alveographic parameters (P, W, and P/L values). Furthermore, heatmap plot analysis revealed several significant correlations between different studied parameters, which may explore the importance of applied Cys and ALA as effective compounds in wheat cultivation under water deficit conditions.

Photosynthesis tunes quantum-mechanical mixing of electronic and vibrational states to steer exciton energy transfer

Photosynthetic species evolved to protect their light-harvesting apparatus from photoxidative damage driven by intracellular redox conditions or environmental conditions. The Fenna-Matthews-Olson (FMO) pigment-protein complex from green sulfur bacteria exhibits redox-dependent quenching behavior partially due to two internal cysteine residues. Here, we show evidence that a photosynthetic complex exploits the quantum mechanics of vibronic mixing to activate an oxidative photoprotective mechanism. We use two-dimensional electronic spectroscopy (2DES) to capture energy transfer dynamics in wild-type and cysteine-deficient FMO mutant proteins under both reducing and oxidizing conditions. Under reducing conditions, we find equal energy transfer through the exciton 4-1 and 4-2-1 pathways because the exciton 4-1 energy gap is vibronically coupled with a bacteriochlorophyll-a vibrational mode. Under oxidizing conditions, however, the resonance of the exciton 4-1 energy gap is detuned from the vibrational mode, causing excitons to preferentially steer through the indirect 4-2-1 pathway to increase the likelihood of exciton quenching. We use a Redfield model to show that the complex achieves this effect by tuning the site III energy via the redox state of its internal cysteine residues. This result shows how pigment-protein complexes exploit the quantum mechanics of vibronic coupling to steer energy transfer.

A curcumin-analogous fluorescent sensor for cysteine detection with a bilateral-response click-like mechanism

A novel curcumin-analogous fluorescent sensor, DNP, was developed for cysteine detection with a bilateral-response click-like mechanism. DNP indicated high selectivity and practical sensitivity. It could recognize Cys from other biologically relevant molecules, especially, from GSH and Hcy. The most interesting point was that, with typical azide groups for sensing, DNP indicated a covalent binding procedure with Cys instead of a presupposed simple reduction for reductive sulfide. Moreover, the recognition occurred at both sides of the sensor. DNP could be utilized into the detection of endogenous and exogenous Cys in living cells. Though the specific optical performances of DNP still need optimization, this work supplied novel information for broadening the vision on fluorophores and mechanisms, for the monitoring of Cys and even other sulfur-containing species.

Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models

In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formulations and computational modeling of some of the light harvesting complexes including FMO. The most recent research developments in the photosynthetic light harvesting complexes are thoroughly discussed. The theoretical background related to the spectral density, quantum coherence and density functional theory has been elaborated. Furthermore, details about the transfer and excitation of energy in different sites of the FMO complex along with other vital photosynthetic light harvesting complexes have also been provided. Finally, we conclude this review by providing the current and potential applications in environmental science, energy, health and medicine, where such mathematical and computational studies of the photosynthesis and the light harvesting complexes can be readily integrated.

An imidazo[1,5-α]pyridine-derivated fluorescence sensor for rapid and selective detection of sulfite

Sulfur-containing species are essential in the composition and the metabolism of the organisms, thus developing a full set of implements to cover all of them is still a favorable choice. Herein, we chose imidazo [1,5-α]pyridine moiety as the basic fluorophore for the detection of sulfite, and preliminarily completed the toolset since biothiols (GSH, Cys, Hcy), H₂S, and PhSH could be detected by sensors based on the same backbone. The designed sensor, IPD-SFT, with structural novelty and large Stokes shift (130 nm), indicated the most attractive advantages of remarkably rapid response period (within 1 min) and high selectivity for sulfite from all the sulfur-containing species. Other practical properties included high sensitivity (LOD = 50 nM) and wide pH adaptability (5.0-11.0). Furthermore, IPD-SFT could monitor both exogenous and endogenous sulfite. It not only raised a potential tool for sulfite detection, but also preliminarily completed the toolset for all the sulfur-containing species. The development of such toolsets might reveal the sulfur-containing metabolism and corresponding physiology and pathological procedures.

The Unified Theory of Resonance Energy Transfer According to Molecular Quantum Electrodynamics

An overview is given of the molecular quantum electrodynamical (QED) theory of resonance energy transfer (RET). In this quantized radiation field description, RET arises from the exchange of a single virtual photon between excited donor and unexcited acceptor species. Diagrammatic time-dependent perturbation theory is employed to calculate the transfer matrix element, from which the migration rate is obtained via the Fermi golden rule. Rate formulae for oriented and isotropic systems hold for all pair separation distances, R, beyond wave function overlap. The two well-known mechanisms associated with migration of energy, namely the R−6 radiationless transfer rate due to Förster and the R−2 radiative exchange, correspond to near- and far-zone asymptotes of the general result. Discriminatory pair transfer rates are also presented. The influence of an environment is accounted for by invoking the polariton, which mediates exchange and by introducing a complex refractive index to describe local field and screening effects. This macroscopic treatment is compared and contrasted with a microscopic analysis in which the role of a neutral, polarizable and passive third-particle in mediating transfer of energy is considered. Three possible coupling mechanisms arise, each requiring summation over 24 time-ordered diagrams at fourth-order of perturbation theory with the total rate being a sum of two- and various three-body terms.

Changes in aggregation states of light-harvesting complexes as a mechanism for modulating energy transfer in desert crust cyanobacteria

In this paper we propose an energy dissipation mechanism that is completely reliant on changes in the aggregation state of the phycobilisome light-harvesting antenna components. All photosynthetic organisms regulate the efficiency of excitation energy transfer (EET) to fit light energy supply to biochemical demands. Not many do this to the extent required of desert crust cyanobacteria. Following predawn dew deposition, they harvest light energy with maximum efficiency until desiccating in the early morning hours. In the desiccated state, absorbed energy is completely quenched. Time and spectrally resolved fluorescence emission measurements of the desiccated desert crust Leptolyngbya ohadii strain identified (i) reduced EET between phycobilisome components, (ii) shorter fluorescence lifetimes, and (iii) red shift in the emission spectra, compared with the hydrated state. These changes coincide with a loss of the ordered phycobilisome structure, evident from small-angle neutron and X-ray scattering and cryo-transmission electron microscopy data. Based on these observations we propose a model where in the hydrated state the organized rod structure of the phycobilisome supports directional EET to reaction centers with minimal losses due to thermal dissipation. In the desiccated state this structure is lost, giving way to more random aggregates. The resulting EET path will exhibit increased coupling to the environment and enhanced quenching.