Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch

An innovative dual-organelle targeting NIR fluorescence probe for detecting hydroxyl radicals in biosystem and inflammation models

The hydroxyl radical (OH) is highly reactive and plays a significant role in a number of physiological and pathological processes within biosystems. Aberrant changes in the level of hydroxyl radical are associated with many disorders including tumor, inflammatory and cardiovascular diseases. Thus, detecting reactive oxygen species (ROS) in biological systems and imaging them is highly significant. In this work, a novel fluorescent probe (HR-DL) has been developed, targeting two organelles simultaneously. The probe is based on a coumarin-quinoline structure and exhibits high selectivity and sensitivity towards hydroxyl radicals (OH). When reacting with OH, the hydrogen abstraction process released its long-range π-conjugation and ICT processes, leading to a substantial red-shift in wavelength. This probe has the benefits of good water solubility (in its oxidative state), short response time (within 10 s), and unique dual lysosome/mitochondria targeting capabilities. It has been applied for sensing OH in biosystem and inflammation mice models.

A water-soluble red-emitting fluorescence probe for detecting hazardous hydrazine in environmental waters and biosystems

Hydrazine (N2H4), a crucial chemical raw material, enhances people's lives and fosters human progress. Hydrazine usage or leakage has caused environmental contamination, affecting water, soil, and living beings. Hydrazine simultaneously presents a possible risk to human health due to its carcinogenic properties. Thus, quick and precise detection of hydrazine is crucial in environmental studies and biological contexts. We prepared a red-emitting fluorescence turn-on probe (XT-HZ) to detect hydrazine specifically. The probe has a low detecting limit for hydrazine (63 nM) with excitation wavelength at 570 nm and emission wavelength at 625 nm. Besides, the probe XT-HZ had excellent water solubility, high selectivity, and good sensitivity for detecting hydrazine. Finally, probe XT-HZ was applied in the imaging of N2H4 in living cells, zebrafish and environmental water samples.

A dual-functional NIR fluorescence probe for detecting hypochlorous acid and bisulfite in biosystem

BACKGROUND

Bisulfite (HSO3-) serves as a bleaching agent, antioxidant, antimicrobial, and regulator of enzymatic reactions in biosystem. However, abnormal levels of bisulfite can be detrimental to health. Hypochlorous acid (HOCl), which acts as bioactive small molecules, is crucial for maintaining normal biological functions in living organisms. Disruption of its equilibrium can lead to oxidative stress and various diseases. Therefore, it's essential to monitor the fluctuations of HOCl and HSO3- at cellular and in vivo levels to study their physiological and pathological functions.

RESULTS

This study constructed a novel NIR bifunctional colorimetric fluorescent probe using thienocoumarin-indanedione structures to identify hypochlorite (ClO-) and bisulfite (HSO3-). By using CSO-IO to recognize HSO3- and HOCl, two distinct products were generated, displaying green and blue fluorescence, respectively. This property effectively allows for the simultaneous dual-functional detection of HSO3- (LOD: 113 nM) and HOCl (LOD: 43 nM).

SIGNIFICANCE

In this work, the biocompatible molecule CSO-IO has been effectively designed to detect HOCl/HSO3- in living cells and zebrafish. As a result, the dual-functional fluorescent probe has the potential to be utilized as a molecular tool to detect HSO3- derived compounds and HOCl simultaneously within the complex biological system.

Probing the toxic hypochlorous acid in natural waters and biosystem by a coumarin-based fluorescence probe

Since the onset of the SARS-CoV-2 pandemic in early 2020, there has been a notable rise in sodium hypochlorite disinfectants. Sodium hypochlorite undergoes hydrolysis to generate hypochlorous acid for virus eradication. This chlorine-based disinfectant is widely utilized for public disinfection due to its effectiveness. Although sodium hypochlorite disinfection is convenient, its excessive and indiscriminate use can harm the water environment and pose a risk to human health. Hypochlorous acid, a reactive oxygen species, plays a crucial role in the troposphere, stratospheric chemistry, and oxidizing capacity. Additionally, hypochlorous acid is vital as a reactive oxygen species in biological systems, and its irregular metabolism and level is associated with several illnesses. Thus, it is crucial to identify hypochlorous acid to comprehend its environmental and biological functions precisely. Here, we constructed a new fluorescent probe, utilizing the twisted intramolecular charge transfer mechanism to quickly and accurately detect hypochlorous acid in environmental water and biosystems. The probe showed a notable increase in fluorescence when exposed to hypochlorous acid, demonstrating its excellent selectivity, fast response time (less than 10 seconds), a large Stokes shift (∼ 102 nm), and a low detection limit of 15.5 nM.

Experimental and computational investigation of the effect of Hsc70 structural variants on inhibiting amylin aggregation

The misfolding and aggregation of human islet amyloid polypeptide (hIAPP), also known as amylin, have been implicated in the pathogenesis of type 2 diabetes (T2D). Heat shock proteins, specifically, heat shock cognate 70 (Hsc70), are molecular chaperones that protect against hIAPP misfolding and inhibits its aggregation. Nevertheless, there is an incomplete understanding of the mechanistic interactions between Hsc70 domains and hIAPP, thus limiting their potential therapeutic role in diabetes. This study investigates the inhibitory capacities of different Hsc70 variants, aiming to identify the structural determinants that strike a balance between efficacy and cytotoxicity. Our experimental findings demonstrate that the ATPase activity of Hsc70 is not a pivotal factor for inhibiting hIAPP misfolding. We underscore the significance of the C-terminal substrate-binding domain of Hsc70 in inhibiting hIAPP aggregation, emphasizing that the removal of the lid subdomain diminishes the inhibitory effect of Hsc70. Additionally, we employed atomistic discrete molecular dynamics simulations to gain deeper insights into the interaction between Hsc70 variants and hIAPP. Integrating both experimental and computational findings, we propose a mechanism by which Hsc70's interaction with hIAPP monomers disrupts protein-protein connections, primarily by shielding the β-sheet edges of the Hsc70-β-sandwich. The distinctive conformational dynamics of the alpha helices of Hsc70 potentially enhance hIAPP binding by obstructing the exposed edges of the β-sandwich, particularly at the β5-β8 region along the alpha helix interface. This, in turn, inhibits fibril growth, and similar results were observed following hIAPP dimerization. Overall, this study elucidates the structural intricacies of Hsc70 crucial for impeding hIAPP aggregation, improving our understanding of the potential anti-aggregative properties of molecular chaperones in diabetes treatment.

A precise method to monitor hydroxyl radical in natural waters based on a fluoride-containing fluorescence probe

In natural waters, hydroxyl radical (OH) can initiate many free radical-induced reactions, oxidizing various inorganic and organic compounds through electron transfer reactions, dehydrogenation reactions, addition reactions, and self-quenching reactions. However, due to its extremely low concentration and short lifetime in natural waters, studies on the quantitative measurement of OH levels are insufficient. In this work, we developed the first quinolinium-based fluorescence probe containing fluoride substituted donor that could detect hydroxyl radicals in the water system. This probe exhibits excellent selectivity towards OH with a large Stokes shift (114 nm) and 23-fold enhancement in fluorescence. Additionally, this probe has been proven to be low toxicity and applied to detect OH in living cells, zebrafish, and natural water samples with good recovery (over 92 %).

Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch

Riboswitches sense various ions in bacteria and activate gene expression to synthesize proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain (AD) of the fluoride riboswitch shows that the F- ion is encapsulated by three Mg2+ ions bound to the ligand-binding domain (LBD) located at the core of the AD. The assembly mechanism of this intricate structure is unknown. To this end, we performed computer simulations using coarse-grained and all-atom RNA models to bridge multiple time scales involved in riboswitch folding and ion binding. We show that F- encapsulation by the Mg2+ ions bound to the riboswitch involves multiple sequential steps. Broadly, two Mg2+ ions initially interact with the phosphate groups of the LBD using water-mediated outer-shell coordination and transition to a direct inner-shell interaction through dehydration to strengthen their interaction with the LBD. We propose that the efficient binding mode of the third Mg2+ and F- is that they form a water-mediated ion pair and bind to the LBD simultaneously to minimize the electrostatic repulsion between three Mg2+ bound to the LBD. The tertiary stacking interactions among the LBD nucleobases alone are insufficient to stabilize the alignment of the phosphate groups to facilitate Mg2+ binding. We show that the stability of the whole assembly is an intricate balance of the interactions among the five phosphate groups, three Mg2+, and the encapsulated F- ion aided by the Mg2+ solvated water. These insights are helpful in the rational design of RNA-based ion sensors and fast-switching logic gates.

Fluorescence probe for selectively monitoring biothiols within cells and mouse depression diagnosis

As a global mental disorder, depression is associated with oxidative stress in the brain. Cysteine, a reductive biothiols, regulates the oxidative situation in many biological events including the stress that occurs in the tissues. Exploring the pathology and physiology of depression is still a challenge and always in an urgent need. Thus, developing a new method that could track Cys level without the interferes from other competing substances is of great importance. Herein, we developed a fluorescence probe that could selectively sensing Cys over other biothiols. Besides, we have demonstrated its desirable performance in cellular applications and mouse brain. This work provides a new method for Cys imaging and understanding pathogenesis of depression. We hope the work described here could be used as a potential chemical approach for the diagnosis of Cys associated diseases in clinical applications.

TPP Riboswitch Populates Holo-Form-like Structure Even in the Absence of Cognate Ligand at High Mg2+ Concentration

Riboswitches are noncoding RNA that regulate gene expression by folding into specific three-dimensional structures (holo-form) upon binding by their cognate ligand in the presence of Mg²⁺. Riboswitch functioning is also hypothesized to be under kinetic control requiring large cognate ligand concentrations. We ask the question under thermodynamic conditions, can the riboswitches populate structures similar to the holo-form only in the presence of Mg²⁺ and absence of cognate ligand binding. We addressed this question using thiamine pyrophosphate (TPP) riboswitch as a model system and computer simulations using a coarse-grained model for RNA. The folding free energy surface (FES) shows that with the initial increase in Mg²⁺ concentration ([Mg²⁺]), the aptamer domain (AD) of TPP riboswitch undergoes a barrierless collapse in its dimensions. On further increase in [Mg²⁺], intermediates separated by barriers appear on the FES, and one of the intermediates has a TPP ligand-binding competent structure. We show that site-specific binding of the Mg²⁺ aids in the formation of tertiary contacts. For [Mg²⁺] greater than physiological concentration, AD folds into a structure similar to the crystal structure of the TPP holo-form even in the absence of the TPP ligand. The folding kinetics shows that TPP AD populates an intermediate due to the misalignment of two arms present in the structure, which acts as a kinetic trap, leading to larger folding timescales. The predictions of the intermediate structures from the simulations are amenable for experimental verification.

Monitoring thiophenols in both environmental water samples and bio-samples: A method based on a fluorescent probe with broad pH adaptation

Thiophenol, which is a highly toxic sulfhydryl compound widely used in chemical industry, is an environmental pollutant that threatens human health significantly. It is of great importance to detect highly toxic thiophenols in both environmental and biological system. Thus, the need to develop rapid response, selective and sensitive probes is urgent. In this study, a novel probe was presented for the detection of thiophenols based on an intramolecular charge transfer (ICT) mechanism. This probe exhibits rapid response, broad pH adaptation (2-10), highly selectivity, a large Stokes shift (131 nm) and 40-fold enhancement in fluorescence. Besides, this probe showed low toxicity towards human cell HEK293 and could be applied to detect thiophenol both in living cells, zebrafish and environmental water samples with good recovery (over 94%). All the results indicated that this probe could be a promising sensor for applications for thiophenol derivatives detection in both environmental and biological sciences.

Integrative structural dynamics probing of the conformational heterogeneity in synaptosomal-associated protein 25

SNAP-25 (synaptosomal-associated protein of 25 kDa) is a prototypical intrinsically disordered protein (IDP) that is unstructured by itself but forms coiled-coil helices in the SNARE complex. With high conformational heterogeneity, detailed structural dynamics of unbound SNAP-25 remain elusive. Here, we report an integrative method to probe the structural dynamics of SNAP-25 by combining replica-exchange discrete molecular dynamics (rxDMD) simulations and label-based experiments at ensemble and single-molecule levels. The rxDMD simulations systematically characterize the coil-to-molten globular transition and reconstruct structural ensemble consistent with prior ensemble experiments. Label-based experiments using Förster resonance energy transfer and double electron-electron resonance further probe the conformational dynamics of SNAP-25. Agreements between simulations and experiments under both ensemble and single-molecule conditions allow us to assign specific helix-coil transitions in SNAP-25 that occur in submillisecond timescales and potentially play a vital role in forming the SNARE complex. We expect that this integrative approach may help further our understanding of IDPs.

Piperazine-Coumarin based fluorescence probe with enhanced brightness and solubility for bio-thiol detection and esophageal carcinoma diagnosis

The development of novel fluorescent dyes for bio-thiol is of great importance in biological, clinical and pharmaceutical sciences. Given the importance of bio-thiol anticipating in numerous physiological processes, there is a great need to construct fluorescent biosensors with high quality to detect them. Fluorophores, especially those used in bio-system, usually require high-quality properties such as high brightness, good water solubility, bio-compatible and photostability. Herein, we reported a novel fluorescent probe based on piperazine-coumarin scaffold with enhanced brightness and solubility. To further demonstrate the potential clinical applications, we performed living cell fluorescence image and human esophageal carcinoma diagnosis. The result indicated that we were able to distinguish pathological tissue from normal tissue by applying this probe. Thus, we hope this design will be helpful to develop high-quality fluorophores for clinical diagnosis.

Out-of-Equilibrium Biophysical Chemistry: The Case for Multidimensional, Integrated Single-Molecule Approaches

Out-of-equilibrium processes are ubiquitous across living organisms and all structural hierarchies of life. At the molecular scale, out-of-equilibrium processes (for example, enzyme catalysis, gene regulation, and motor protein functions) cause biological macromolecules to sample an ensemble of conformations over a wide range of time scales. Quantifying and conceptualizing the structure–dynamics to function relationship is challenging because continuously evolving multidimensional energy landscapes are necessary to describe nonequilibrium biological processes in biological macromolecules. In this perspective, we explore the challenges associated with state-of-the-art experimental techniques to understanding biological macromolecular function. We argue that it is time to revisit how we probe and model functional out-of-equilibrium biomolecular dynamics. We suggest that developing integrated single-molecule multiparametric force–fluorescence instruments and using advanced molecular dynamics simulations to study out-of-equilibrium biomolecules will provide a path towards understanding the principles of and mechanisms behind the structure–dynamics to function paradigm in biological macromolecules.