Adenosine Triphosphate Molecules Research Articles

Atomistic Insights into the Stabilization of TDP-43 Protofibrils by ATP.

The aberrant accumulation of the transactive response deoxyribonucleic acid (DNA)-binding protein of 43 kDa (TDP-43) aggregates in the cytoplasm of motor neurons is the main pathological hallmark of amyotrophic lateral sclerosis (ALS). Previous experiments reported that adenosine triphosphate (ATP), the universal energy currency for all living cells, could induce aggregation and enhance the folding of TDP-43 fibrillar aggregates. However, the significance of ATP on TDP-43 fibrillation and the mechanism behind it remain elusive. In this work, we conducted multiple atomistic molecular dynamics (MD) simulations totaling 20 μs to search the critical nucleus size of TDP-43282-360 and investigate the impact of ATP molecules on preformed protofibrils. The results reveal that the trimer is the critical nucleus for TDP-43282-360 fibril formation and the tetramer is the minimal stable nucleus. When ATP molecules bind to the TDP-43282-360 trimer and tetramer, they can consolidate the TDP-43282-360 protofibrils by increasing the content of the β-sheet structure and promoting the formation of hydrogen bonds (H-bonds). Binding site analyses show that the N-terminus of TDP-43282-360 protofibrils is the main binding site of ATP, and R293 dominates the direct binding of ATP. Further analyses reveal that the π-π, cation-π, salt bridge, and H-bonding interactions together contribute to the binding of ATP to TDP-43282-360 protofibrils. This study decoded the detailed stabilization mechanism of protofibrillar TDP-43282-360 oligomers by ATP, and may provide new avenues for the development of drug design against ALS.

Aptamer-Loop DNA Nanoflower Recognition and Multicolor Fluorescent Carbon Quantum Dots Labeling System for Multitarget Living Cell Imaging.

Visualization of multiple targets in living cells is important for understanding complex biological processes, but it still faces difficulties, such as complex operation, difficulty in multiplexing, and expensive equipment. Here, we developed a nanoplatform integrating a nucleic acid aptamer and DNA nanotechnology for living cell imaging. Aptamer-based recognition probes (RPs) were synthesized through rolling circle amplification, which were further self-assembled into DNA nanoflowers encapsulated by an aptamer loop. The signal probes (SPs) were obtained by conjugation of multicolor emission carbon quantum dots with oligonucleotides complementary to RPs. Through base pairing, RPs and SPs were hybridized to generate aptamer sgc8-, AS1411-, and Apt-based imaging systems. They were used for individual/simultaneous imaging of cellular membrane protein PTK7, nucleolin, and adenosine triphosphate (ATP) molecules. Fluorescence imaging and intensity analysis showed that the living cell imaging system can not only specifically recognize and efficiently bind their respective targets but also provide a 5-10-fold signal amplification. Cell-cycle-dependent distribution of nucleolin and concentration-dependent fluorescence intensity of ATP demonstrated the utility of the system for tracking changes in cellular status. Overall, this system shows the potential to be a simple, low-cost, highly selective, and sensitive living cell imaging platform.

Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding.

A small, nucleotide-binding domain, the ATP-cone, is found at the N-terminus of most ribonucleotide reductase (RNR) catalytic subunits. By binding adenosine triphosphate (ATP) or deoxyadenosine triphosphate (dATP) it regulates the enzyme activity of all classes of RNR. Functional and structural work on aerobic RNRs has revealed a plethora of ways in which dATP inhibits activity by inducing oligomerisation and preventing a productive radical transfer from one subunit to the active site in the other. Anaerobic RNRs, on the other hand, store a stable glycyl radical next to the active site and the basis for their dATP-dependent inhibition is completely unknown. We present biochemical, biophysical, and structural information on the effects of ATP and dATP binding to the anaerobic RNR from Prevotella copri. The enzyme exists in a dimer-tetramer equilibrium biased towards dimers when two ATP molecules are bound to the ATP-cone and tetramers when two dATP molecules are bound. In the presence of ATP, P. copri NrdD is active and has a fully ordered glycyl radical domain (GRD) in one monomer of the dimer. Binding of dATP to the ATP-cone results in loss of activity and increased dynamics of the GRD, such that it cannot be detected in the cryo-EM structures. The glycyl radical is formed even in the dATP-bound form, but the substrate does not bind. The structures implicate a complex network of interactions in activity regulation that involve the GRD more than 30 Å away from the dATP molecules, the allosteric substrate specificity site and a conserved but previously unseen flap over the active site. Taken together, the results suggest that dATP inhibition in anaerobic RNRs acts by increasing the flexibility of the flap and GRD, thereby preventing both substrate binding and radical mobilisation.

Effects of Time-Dependent Adenosine Triphosphate Consumption Caused by Neuron Firing on Adenosine Triphosphate Concentrations in Synaptic Boutons Containing and Lacking a Stationary Mitochondrion.

The precise mechanism behind the supply of adenosine triphosphate (ATP) to approximately half of the presynaptic release sites in axons that lack a stationary mitochondrion is not fully understood. This paper presents a mathematical model designed to simulate the transient ATP concentration in presynaptic en passant boutons. The model is utilized to investigate how the ATP concentration responds to increased ATP demand during neuronal firing in boutons with a stationary mitochondrion and those without one. The analysis suggests that neuron firing may cause oscillations in the ATP concentrations, with peak-to-peak amplitudes ranging from 0.06% to 5% of their average values. However, this does not deplete boutons lacking a mitochondrion of ATP; for physiologically relevant values of model parameters, their concentration remains approximately 3.75 times higher than the minimum concentration required for synaptic activity. The variance in average ATP concentrations between boutons containing a stationary mitochondrion and those lacking one ranges from 0.3% to 0.8%, contingent on the distance between the boutons. The model indicates that diffusion-driven ATP transport is rapid enough to adequately supply ATP molecules to boutons lacking a stationary mitochondrion.

Endothelial calcium dynamics elicited by ATP release from red blood cells

Red blood cells (RBCs) exhibit an interesting response to hydrodynamic flow, releasing adenosine triphosphate (ATP). Subsequently, these liberated ATP molecules initiate a crucial interaction with endothelial cells (ECs), thereby setting off a cascade involving the release of calcium ions (Ca2+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{2+}$$\\end{document}). Ca2+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{2+}$$\\end{document} exerts control over a plethora of cellular functions, and acts as a mediator for dilation and contraction of blood vessel walls. This study focuses on the relationship between RBC dynamics and Ca2+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{2+}$$\\end{document} dynamics, based on numerical simulations under Poiseuille flow within a linear two-dimensional channel. It is found that the concentration of ATP depends upon a variety of factors, including RBC density, channel width, and the vigor of the flow. The results of our investigation reveals several features. Firstly, the peak amplitude of Ca2+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{2+}$$\\end{document} per EC escalates in direct proportion to the augmentation of RBC concentration. Secondly, increasing the flow strength induces a reduction in the time taken to reach the peak of Ca2+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{2+}$$\\end{document} concentration, under the condition of a constant channel width. Additionally, when flow strength remains constant, an increase in channel width corresponds to an elevation in calcium peak amplitude, coupled with a decrease in peak time. This implies that Ca2+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{2+}$$\\end{document} signals should transition from relatively unconstrained channels to more confined pathways within real vascular networks. This notion gains support from our examination of calcium propagation in a linear channel. In this scenario, the localized Ca2+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{2+}$$\\end{document} release initiates a propagating wave that gradually encompasses the entire channel. Notably, our computed propagation speed agrees with observations.

Engineering smart thioflavin T binders with switchable DNA topologies for constructing multiple label-free biosensors

Thioflavin T (ThT) has been used as a sensitive fluorescence probe for lighting up nucleic acids. The binding of ThT is dependent on the structural topologies of DNA sequences. To date, most oligonucleotides interact with ThT through only a single topology, and this limits the applications of ThT as a sensing agent. Here, we modulated an HIV-1 integrase aptamer, 93del, to have switchable topologies by optimizing its 3′ flanking residues to enhance its ThT-binding capacity. Our data revealed that the sequences formed stem-loop hairpins and I-motif/G-quadruplex (G4) hybrids in Na+ buffer under alkaline and acidic conditions, respectively. Both topologies could bind ThT with high affinity (Kd ∼ 0.5 μM) and dramatically enhance the fluorescent signal of ThT. However, in the presence of K+, the sequences could be assembled into interlocked G4s, which had a low affinity for ThT but a high affinity for N-methyl mesoporphyrin IX (NMM). This allowed us to build highly sensitive fluorescent K+ sensors that were insusceptible to interference from Na+. Additionally, we found that the stacking of homologous base pairs in the hairpin loops was essential for ThT recognition and could be used as an indicator in the construction of label-free molecular beacons, allowing monitoring of microRNAs effectively in human serum spiked test. By employing external stimuli to induce the transformation of these topologies, we were able to sensitively detect adenosine triphosphate (ATP) molecules or Hg2+in vitro under specific acidic conditions. Our study provides a strategy for exploiting undiscovered functions of existing aptamers.

Nanopore single molecule ATP detection based on the dual effects of specific capturing and signal amplification

Adenosine triphosphate (ATP) plays a crucial role in energy metabolism. Some serious diseases such as Alzheimer’s disease are related to abnormal ATP concentrations. Fast, sensitive, and specific ATP detection is important and challenging in disease diagnosis and biomedical research. In present study, conical nanopore was designed and employed to detect ATP at single molecule level. For overcoming the inherent defects such as non-selectivity and low sensitivity of nanopore in sensing small target molecule, two collaborative improvements of specific identification and signal amplification were proposed. We first used split aptamer capture probes (H1 and S1) to anchor ATP molecule, and then used auxiliary probes (H2 and H3) to form a long-nicked duplex ATP-DNA concatemer by hybridization chain reaction (HCR). Referring ATP-DNA concatemer rather than native ATP to nanopore sensor, characteristic current signals with high signal-to-noise ratio were obtained. By such indirect way, specific and sensitive ATP detection was realized with a linear range from 20 pM to 5 nM and a detection limit of 3.9 pM (S/N = 3). Additionally, the sensor exhibited many merits such as simplify, anti-interference, and especially allowing ATP detection in real sample. So, we believe that the nanopore sensor has good application prospects in screening and management of ATP-related diseases.

Inhibition of microtubule function prevents hypoxia-induced glycolysis

In normoxic conditions where oxygen supply exceeds demand, mammalian cells produce 38 molecules of adenosine triphosphate (ATP) per molecule of glucose through cellular respiration which is primarily oxygen-dependent. In hypoxia where oxygen demand exceeds supply, the cell enters a bioenergetic crisis due to the decrease in oxygen-dependent ATP synthesis. The cell relies on overcoming this deficiency in ATP through upregulation of glycolytic gene expression via the hypoxia inducible factor 1-a (HIF-1a). However, it is highly unlikely, if not impossible, that the bioenergetic requirements of the hypoxic cell depend solely on the increased expression of glycolytic enzymes distributed randomly in the cytoplasm. We have recently shown that in response to hypoxia, glycolytic enzymes coalesce to form a glycolytic metabolon to effciently increase ATP production in response to this metabolic challenge (Kierans SJ, et al., 2023). While the function of this metabolon has been characterised, the mechanisms underpinning formation, scaffolding, and intracellular distribution remains poorly understood. Here we investigate the possible role of the cytoskeleton as a scaffold or transport system. Microtubules are a primary method of intracellular transport and may alter the energy distribution strategies of cells in bioenergetic crisis. It is hypothesized that the microtubular network transports glycolytic enzymes and/or facilitates increased glycolytic ATP production by promoting metabolon formation to induce glycolysis in hypoxia. Through western blots, it was successfully shown that upon exposure to 1% oxygen, caco2 intestinal epithelial cells induce a robust hypoxic response by stabilising HIF-1a. To investigate the role of the microtubules, two microtubule inhibitors were used: nocodazole, a microtubule assembly and disassembly inhibitor and dynarrestin, a dynein-1 motor transport protein inhibitor. Non-toxic concentrations of nocodazole and dynarrestin were determined using cell viability assays (trypan blue and resazurin assays). Upon exposure to 24 hours of hypoxia, caco2 cells elicit a statistically significant increase in intracellular lactate (185.9% ± 7.5% SEM, n = 3), which was then supressed when treated with nocodazole or dynarrestin (20.6% ± 10.2% SEM and 74.9% ± 8.87 SEM respectively, n = 3). These results thus implicate a role for the transport and structural capabilities of the microtubules in hypoxia-induced glycolysis. Kierans, S. J., Fagundes, R. R., Malkov, M. I., Sparkes, R., Dillon, E. T., Smolenski, A.,... & Taylor, C. T. (2023). Hypoxia induces a glycolytic complex in intestinal epithelial cells independent of HIF-1-driven glycolytic gene expression. Proceedings of the National Academy of Sciences, 120(35), e2208117120. University College Dublin, School of Medicine. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Probing actin-activated ATP turnover kinetics of human cardiac myosin II by single molecule fluorescence.

Mechanistic insights into myosin II energy transduction in striated muscle in health and disease would benefit fromfunctional studies of a wide range of point-mutants. This approach is, however, hampered by the slow turnaround of myosin II expression that usually relies on adenoviruses for gene transfer. A recently developed virus-free method is more time effective but would yield too small amounts of myosin for standard biochemical analyses. However, if the fluorescent adenosine triphosphate (ATP) and single molecule (sm) total internal reflection fluorescence microscopy previously used to analyze basal ATP turnover by myosin alone, can be expanded to actin-activated ATP turnover, it would appreciably reduce the required amount of myosin. To that end, we here describe zero-length cross-linking of human cardiac myosin II motor fragments (sub-fragment 1 long [S1L]) to surface-immobilized actin filaments in a configuration with maintained actin-activated ATP turnover. After optimizing the analysis of sm fluorescence events, we show that the amount of myosin produced from C2C12 cells in one 60 mm cell culture plate is sufficient to obtain both the basal myosin ATP turnover rate and the maximum actin-activated rate constant (kcat). Our analysis of many single binding events of fluorescent ATP to many S1L motor fragments revealed processes reflecting basal and actin-activated ATPase, but also a third exponential process consistent with non-specific ATP-binding outside the active site.

Modulation by Co (II) Ion of Optical Activities of L/D-glutathione (GSH)-modified Chiral Copper Nanoclusters for Sensitive Adenosine Triphosphate Detection.

Chiral nanoscale enantiomers exhibit different biological effects in living systems. However, their chirality effect on the detection sensitivity for chiral biological targets still needs to be explored. Here, we discovered that Co2+ can modulate the luminescence performance of L/D-glutathione (GSH)-modified copper nanoclusters (L/D-Cu NCs) and induce strong chiroptical activities as the asymmetric factor was enhanced 223-fold with their distribution regulating from the ultraviolet to visible region. One Co2+ coordinated with two GSH molecules that modified on the surface of Cu NCs in the way of CoN2O2. On this basis, dual-modal chiral and luminescent signals of Co2+ coordinated L/D-Cu NCs (L/D-Co-Cu NCs) were used to detect the chiral adenosine triphosphate (ATP) based on the competitive interaction between surficial GSH and ATP molecules with Co2+. The limits of detection of ATP obtained with fluorescence and circular dichroism intensity were 9.15 μM and 15.75 nM for L-Co-Cu NCs, and 5.35 μM and 4.69 nM for D-Co-Cu NCs. This demonstrated that selecting suitable chiral configurations of nanoprobes effectively enhances detection sensitivity. This study presents not only a novel method to modulate and enhance the chiroptical activity of nanomaterials but also a unique perspective of chirality effects on the detection performances for bio-targets.

Modulation by Co (II) Ion of Optical Activities of L/D‐glutathione (GSH)‐modified Chiral Copper Nanoclusters for Sensitive Adenosine Triphosphate Detection

AbstractChiral nanoscale enantiomers exhibit different biological effects in living systems. However, their chirality effect on the detection sensitivity for chiral biological targets still needs to be explored. Here, we discovered that Co2+ can modulate the luminescence performance of L/D‐glutathione (GSH)‐modified copper nanoclusters (L/D−Cu NCs) and induce strong chiroptical activities as the asymmetric factor was enhanced 223‐fold with their distribution regulating from the ultraviolet to visible region. One Co2+ coordinated with two GSH molecules that modified on the surface of Cu NCs in the way of CoN2O2. On this basis, dual‐modal chiral and luminescent signals of Co2+ coordinated L/D−Cu NCs (L/D−Co−Cu NCs) were used to detect the chiral adenosine triphosphate (ATP) based on the competitive interaction between surficial GSH and ATP molecules with Co2+. The limits of detection of ATP obtained with fluorescence and circular dichroism intensity were 9.15 μM and 15.75 nM for L−Co−Cu NCs, and 5.35 μM and 4.69 nM for D−Co−Cu NCs. This demonstrated that selecting suitable chiral configurations of nanoprobes effectively enhances detection sensitivity. This study presents not only a novel method to modulate and enhance the chiroptical activity of nanomaterials but also a unique perspective of chirality effects on the detection performances for bio‐targets.

Peculiarities of the Fluorescence Quenching in the ATP – Calix[4]arene C-107 Aqueous Solutions

The nature of fluorescence (FL) quenching for the aqueous solutions of adenosine triphosphate (ATP) with calix[4]arenes C-107 in the presence of silver nitrate AgNO3 is studied. It is shown that, for the water solutions of ATP and calix[4]arenes C-107 at a constant concentration of ATP molecules with an increase in the content of C-107, a complex nature of the PL quenching is observed, while maintaining the position of the PL band near 395 nm (λex = 285 nm). Its complexity is based, on the one hand, in the wide range of concentrations of C-107, at which it occurs, and, on the other hand, there are gaps in the quenching values for individual concentrations of calix[4]arene, near which it changes slightly. The indicated nature of the PL quenching significantly depends on the wavelength of excitation and the temperature. Similar quenching behavior is preserved, when AgNO3s alts are added to the ATP–C-107 mixtures, (CATP = CC-107 = 1 × 10−4M) in the concentration range from 1 × 10−4M to 1 × 10−3M. The computer modeling shows that the system ATP–C-107 can form energetically stable complexes, when ATP is located on the top of the calix[4]arene and along the wall of it due to π-π-stacking interaction, and the complexes are characterized by a shrinking of the energy bands.

Femtomolar endogenous adenosine triphosphate-responded photoelectrochemical biosensor based on Au@Cu2O core-shell nanocubes for the ultrasensitive determination of Escherichia coli O157:H7 in foods

Sensitive and precise determination of virulent foodborne pathogens is significant for food safety. Herein, an ultrasensitive photoelectrochemical (PEC) bioanalysis was developed using the endogenous adenosine triphosphate (ATP)-responded Au@Cu2O core-shell nanocubes (Au@Cu2O NCs) to measure Escherichia coli O157: H7 (E. coli O157:H7) in food. Briefly, the phage-functionalized gold wire was used to specifically recognize the target pathogen. With the bacteriolysis of lysozyme, the endogenous ATP molecules were emitted from the captured target bacteria and enriched by another ATP aptamer-modified gold wire. Following the exchange with complementary DNA (cDNA) chains, the bonded ATP would be released. It could simultaneously etch the Au@Cu2O NCs and compete with external circuit electrons to combine photogenerated holes on the Au@Cu2O NCs-modified screen-printed electrode. With the synergy of the two signal amplification mechanisms, a significant attenuation of photocurrent signal appeared even with femtomolar ATP. Therefore, the purpose of ultrasensitive determination of E. coli O157:H7 was realized, which depended on the endogenous ATP rather than exogenous signal probes. The proposed biosensor presented a good analysis performance within 10–106 CFU/mL with a detection limit of 5 CFU/mL. Besides, its specificity, repeatability, and stability were also investigated and acceptable. The detection results for food samples matched well with the results detected by the plate counting method. This work gives an innovative and sensitive signal amplification strategy for PEC bioassays in foodborne pathogens detection.

Black Phosphorus/MnO2 Nanocomposite Disrupting Bacterial Thermotolerance for Efficient Mild-Temperature Photothermal Therapy.

The emergence of multi-drug resistant (MDR) pathogens is a major public health concern, posing a substantial global economic burden. Photothermal therapy (PTT) at mild temperature presents a promising alternative to traditional antibiotics due to its biological safety and ability to circumvent drug resistance. However, the efficacy of mild PTT is limited by bacterial thermotolerance. Herein, a nanocomposite, BP@Mn-NC, comprising black phosphorus nanosheets and a manganese-based nanozyme (Mn-NZ) is developed, which possesses both photothermal and catalytic properties. Mn-NZ imparts glucose oxidase- and peroxidase-like properties to BP@Mn-NC, generating reactive oxygen species (ROS) that induce lipid peroxidation and malondialdehyde accumulation across the bacterial cell membrane. This process disrupts unprotected respiratory chain complexes exposed on the bacterial cell membrane, leading to a reduction in the intracellular adenosine triphosphate (ATP) content. Consequently, mild PTT mediated by BP@Mn-NC effectively eliminates MDR infections by specifically impairing bacterial thermotolerance because of the dependence of bacterial heat shock proteins (HSPs) on ATP molecules for their proper functioning. This study paves the way for the development of a novel photothermal strategy to eradicate MDR pathogens, which targets bacterial HSPs through ROS-mediated inhibition of bacterial respiratory chain activity.

ATP and ssDNA aptamer-mediated peroxidase-like activity of rGO@PDA@CeO2 nanozyme: Exosomal proteins profiling and detection at physiological pH for colorimetric sensor

Exosomes are extracellular vesicles that inherit molecular markers from their parent cells for the transfer and delivery of membrane and cytosolic molecules between cells. Exosome detection and protein profiling provide noninvasive access to disease diagnosis and treatment. The nanozyme designed in this paper contains polydopamine-functionalization of graphene oxide (rGO@PDA) units that can adsorb ssDNA aptamers and CeO2 metal oxide nanosheet units with peroxidase activity. As auxiliary regulator, adenosine triphosphate (ATP) enhances peroxidase activity of rGO@PDA@CeO2 under a wide range of pH (4–7.4), which breaks through the limitation that traditional nanozymes can only exhibit peroxidase activity under acidic conditions. The ssDNA aptamers, which are recognition probes of exosome, can be adsorbed on the surface of rGO@PDA by aromatic stacking, competing with ATP molecules. Thus, the ssDNA aptamer acts as the switch for colorimetric sensor to flexibly regulate the peroxidase activity of the rGO@PDA@CeO2 under physiological conditions, and realizes sensitive detection of exosomes. This assay achieves a detection linear range of 0.46 × 107–108 particle/mL and a limit down to 3.81 × 105 particles/mL. In addition, this aptasensor sensitively profiles six exosomal protein across five cell types and clinical samples, suggesting their potential in clinic diagnosis.

Mitochondrial epigenetics in aging and cardiovascular diseases.

Mitochondria are cellular organelles which generate adenosine triphosphate (ATP) molecules for the maintenance of cellular energy through the oxidative phosphorylation. They also regulate a variety of cellular processes including apoptosis and metabolism. Of interest, the inner part of mitochondria-the mitochondrial matrix-contains a circular molecule of DNA (mtDNA) characterised by its own transcriptional machinery. As with genomic DNA, mtDNA may also undergo nucleotide mutations that have been shown to be responsible for mitochondrial dysfunction. During physiological aging, the mitochondrial membrane potential declines and associates with enhanced mitophagy to avoid the accumulation of damaged organelles. Moreover, if the dysfunctional mitochondria are not properly cleared, this could lead to cellular dysfunction and subsequent development of several comorbidities such as cardiovascular diseases (CVDs), diabetes, respiratory and cardiovascular diseases as well as inflammatory disorders and psychiatric diseases. As reported for genomic DNA, mtDNA is also amenable to chemical modifications, namely DNA methylation. Changes in mtDNA methylation have shown to be associated with altered transcriptional programs and mitochondrial dysfunction during aging. In addition, other epigenetic signals have been observed in mitochondria, in particular the interaction between mtDNA methylation and non-coding RNAs. Mitoepigenetic modifications are also involved in the pathogenesis of CVDs where oxygen chain disruption, mitochondrial fission, and ROS formation alter cardiac energy metabolism leading to hypertrophy, hypertension, heart failure and ischemia/reperfusion injury. In the present review, we summarize current evidence on the growing importance of epigenetic changes as modulator of mitochondrial function in aging. A better understanding of the mitochondrial epigenetic landscape may pave the way for personalized therapies to prevent age-related diseases.

Fluorescence Imaging of Nanoparticle Uptake into Liquid-Liquid Phase-Separated Droplets.

Liquid-liquid phase separation (LLPS) in living cells has received considerable attention in the biomedical research field. This study is the first to report nanoparticle (NP) uptake into LLPS droplets. Fluorescent dye, Nile red loaded polystyrene NPs (NR-PSt NPs) uptake into model LLPS droplets consisting of adenosine triphosphate (ATP) and poly-L-lysine (PLL) was visualized using fluorescence imaging. Fluorescence imaging showed that the LLPS droplets had a quick NP uptake behavior. Furthermore, temperature changes (4-37 °C) significantly affected the NP uptake behavior of the LLPS droplets. Moreover, the NP-incorporated droplets displayed high stability under strong ionic strength conditions (1 M NaCl). ATP measurements displayed that ATP was released from the NP-incorporated droplets, indicating that the weakly negatively charged ATP molecules and strongly negatively charged NPs were exchanged, which resulted in the high stability of the LLPS droplets. These fundamental findings will contribute to the LLPS studies using various NPs.

Molecular Insights on the Conformational Transitions and Activity Regulation of the c-Met Kinase Induced by Ligand Binding.

The tyrosine-protein kinase Met (c-Met) is an important signaling molecule involved in cellular growth and division. The dysregulation of c-Met may induce many fatal diseases, including non-small cell lung cancer, gastrointestinal cancers, hepatocellular carcinoma, etc. The activation of the c-Met kinase is dominant by the structure and dynamics of many important functional motifs, which are regulated by adenosine triphosphate (ATP) binding. c-Met inhibitors bind to the ATP-binding site or the allosteric pocket to compete with ATP molecules or alter the conformation of the function-related domains. Nevertheless, the mechanisms of ligand binding to c-Met are still unclear, especially the regulation of the functional motifs by different inhibitors. These greatly impede the development of novel drugs to overcome the drug tolerance to the currently marketed c-Met inhibitors. In this study, we used enhanced sampling technology to study the binding and regulation of two specific c-Met inhibitors. The results show that the two ligands adopt different binding processes even though with similar binding affinity. More importantly, our results uncovered different protein conformational features and the correlated motions of functional motifs regulated by the inhibitors, providing the structural basis for the functional suppression of the protein kinases.

Enantioselective catalysts based on metal-organic framework-supported nucleotides

Adenosine triphosphate (ATP) and other nucleotides can be irreversibly bound to the metal-organic framework (MOF) MIL-101(Cr). Analysis of X-ray diffraction data suggests that the location of the adsorbed ATP molecule is in proximity of the Cr3 clusters. Solid-state NMR and DFT calculations indicate that ATP is bound to MIL-101(Cr) through linkages of the terminal phosphate group with Cr(III) of the framework. In the presence of Cu(II) ions, the MOF-supported nucleotides can function as stable and reusable enantioselective heterogeneous catalysts for reactions like Diels-Alder and Michael addition. Compared to the corresponding homogeneous nucleotide-based artificial metalloenzymes (ArMs), the MOF-supported nucleotide-based ArMs exhibit significantly enhanced activity and selectivity in certain cases, demonstrating their potential as a new class of enantioselective heterogeneous catalysts.

Application of phytoaccumulation perspective of Monochoria hastate L. on fluoride contaminated water in hydroponic treatment: its statistical design and characterization studies

The present research work approaches the accumulation of fluoride ions from contaminated water using an aquatic plant Monochoria hastate L. in hydroponic culture. A design of experiment (DOE) has been adopted and an analysis of variance has been conducted to establish the statistical significance of various process parameters. The different experimental factors are root and shoot (Factor A), fluoride concentration (Factor B), and experimental days (Factor C) largely influence the output response. Plants treated with 5 mg/L of fluoride solutions accumulated the highest concentration in root biomass 1.23 mg/gm, and shoot biomass 0.820 mg/gm, dry weight after 21 days’ experimentation. The accumulation mechanism and potentiality of treated plants depend on root cells of the plasma membrane and energy-capturing molecules of adenosine triphosphate. Monochoria hastate L. root biomass was characterized to confirm the accumulation of fluoride ions in the experimented plants using scanning electron micrographs-energy dispersive spectrum (SEM-EDS), and Fourier transforms infrared analysis (FTIR) analysis.