Adsorption and covalent coupling of ATP-binding DNA aptamers onto cellulose

With the long-term goal of developing paper surfaces that will detect pathogens, we have investigated physical adsorption and covalent coupling as strategies for treating cellulose surfaces with a DNA aptamer that binds ATP. Physical adsorption was reversible and the isotherms fitted the Langmuir equation with an adsorption maximum of 0.105 mg/m2 at high ionic strength (300 mM NaCl, 25 mM Tris-HCl) and only 0.024 mg/m2 in lower ionic strength buffer (25 mM Tris-HCl). Covalent coupling of amine-terminated aptamer with oxidized cellulose film (Schiff base + reduction) gave 25% coupling efficiency while maintaining the aptamer activity which was illustrated by using a known fluorescent aptamer that is capable of ATP detection. Therefore, covalent coupling, without spacer molecules, is a promising approach for supporting biosensing aptamers on cellulose.     

Controlled interparticle spacing for surface-modified gold nanoparticle aggregates

Aggregation of gold nanoparticles of increasing size has been studied as a consequence of adsorption of 2-aminothiophenol (ATP) on gold nanoparticle surfaces. The capping property of ATP in the acidic pH range has been accounted from UV-vis absorption spectroscopy and surface-enhanced Raman scattering (SERS) studies. The effect of nanoparticle size (8-55 nm) on the nature of aggregation as well as the variation in the optical response due to variable degree of interparticle coupling effects among the gold particles have been critically examined. Various techniques such as transmission electron microscopy, X-ray diffraction, zeta-potential, and average particle size measurement were undertaken to characterize the nanoparticle aggregates. The aggregate size, interparticle distances, and absorption band wavelengths were found to be highly dependent on the pH of the medium and the concentration of the capping agent, ATP. The acquired SERS spectra of ATP relate the interparticle spacing. It has been observed that the SERS signal intensities are different for different sized gold nanoparticles.     

Motor protein nano-biomachine powered by self-supplying ATP

A new nano-biomachine has been created from microtubules (MTs) and hetero-bifunctional polymer particles bearing pyruvate kinase, which is propelled on glass surfaces coated with kinesin by use of self-supplying ATP.     

Electrochemical solid-state phase transformations of silver nanoparticles

Adenosine triphosphate (ATP)-capped silver nanoparticles (ATP-Ag NPs) were synthesized by reduction of AgNO(3) with borohydride in water with ATP as a capping ligand. The NPs obtained were characterized using transmission electron microscopy (TEM), UV-vis absorption spectroscopy, X-ray diffraction, and energy-dispersive X-ray analysis. A typical preparation produced ATP-Ag NPs with diameters of 4.5 ± 1.1 nm containing ~2800 Ag atoms and capped with 250 ATP capping ligands. The negatively charged ATP caps allow NP incorporation into layer-by-layer (LbL) films with poly(diallyldimethylammonium) chloride at thiol-modified Au electrode surfaces. Cyclic voltammetry in a single-layer LbL film of NPs showed a chemically reversible oxidation of Ag NPs to silver halide NPs in aqueous halide solutions and to Ag(2)O NPs in aqueous hydroxide solutions. TEM confirmed that this takes place via a redox-driven solid-state phase transformation. The charge for these nontopotactic phase transformations corresponded to a one-electron redox process per Ag atom in the NP, indicating complete oxidation and reduction of all Ag atoms in each NP during the electrochemical phase transformation.     

The effect of the oxidative properties of [Mg(H2O)6] in the triplet and singlet states on the energetics of adenosine triphosphate cleavage

The interaction of the adenosine triphosphate (ATP) molecule (the ATP subsystem) with the magnesium complex [Mg(H₂O)₆]²⁺ (the Mg subsystem) in the singlet (S) and triplet (T) states in an aqueous medium mimicked by 78 water molecules was studied by the molecular dynamics (density functional theory) method MD DFT:B3LYP with the 6–31G** basis set at T = 310 K. Potential energy surfaces for the S (lowest-lying) and T (highest-lying) states are significantly separated in space. The Mg complex moves along these surfaces to approach either oxygen atoms of the γ-β phosphate groups (O1–O2) (S PES) or oxygen atoms of β-α phosphate groups (O2–O3) (T PES). Chelation of the γ-β β-α and phosphates yields, respectively, a stable low-energy complex ([Mg(H₂O)₄-(O1–O2)ATP]²⁻) and a metastable high-energy complex ([Mg(H₂O)₂-(O2–O3)ATP]²⁻), which differ in the number of water molecules surrounding the Mg atom. Crossing of two triplet PESs is accompanied by the formation of an unstable state characterized by redistribution of spins between the Mg and ATP subsystems. This state, sensitive to interaction with the ²⁵Mg nuclear spin, induces an unpaired electron spin, which initiates the ATP cleavage by the ion-radical mechanism, yielding a reactive radical ion of adenosine monophosphate (•AMP⁻), which was earlier found experimentally by the of chemically induced dynamic nuclear polarization (CIDNP) method. Biological aspects of the results obtained are discussed. Original Russian Text ? A.A. Tulub, V.E. Stefanov, 2009, published in Zhurnal Neorganicheskoi Khimii, 2009, Vol. 54, No. 7, pp. 1188–1195.     

Semiconductor cadmium sulphide nanoparticles as matrices for peptides and as co-matrices for the analysis of large proteins in matrix-assisted laser desorption/ionization reflectron and linear time-of-flight mass spectrometry

The use of semiconductor cadmium sulphide nanoparticles (CdS NPs) capped with 4-aminothiophenol (ATP) and 11-mercaptoundecanoic acid (MUA) is described for the first time as matrices and as co-matrices for the analysis of peptides and proteins in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). UV-visible spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) were applied for the characterization of functionalized CdS NPs. The synthesized CdS-ATP and CdS-MUA NPs exhibit uniform size distribution with diameter of 15-25 nm and 20-30 nm, respectively. The -NH(2) (ATP) and -COOH (MUA) groups modified on the surfaces of CdS NPs provide ionizable moieties for efficient transfer of protons during the desorption/ionization of analytes. The functionalized CdS NPs have desirable properties for the analysis of peptides in reflectron MALDI-TOF-MS with suppressed background noise and increased mass resolution (4-13-fold) in linear MALDI-TOF-MS. The application of CdS-MUA NPs and SA as the co-matrices in MALDI-MS is demonstrated for the analysis of hydrophobic proteins from soybean.     

Second-harmonic generation for studying structural motion of biological molecules in real time and space

SHG and sum-frequency generation (SFG) are surface-selective, nonlinear optical techniques whose ability to measure the average tilt angle of molecules on surfaces is well known in non-biological systems. By labeling molecules with a second-harmonic-active dye probe, SHG detection is extended to any biological molecule. The method has been used in previous work to detect biomolecules at an interface and their ligand-induced conformational changes. Here I demonstrate that SHG can be used to study structural motion quantitatively using a probe placed at a specific site (Cys-77) in adenylate kinase, a protein. The protein is also labeled non-site-specifically via amines. Labeled protein is absorbed to a surface and a baseline SH signal is measured. Upon introducing ATP, AMP or a specific inhibitor, AP(5)A, the baseline signal changes depending on the ligand and the labeling site. In particular, a substantial change in SH intensity is produced upon binding ATP to the amine-labeled protein, consistent with the X-ray crystal structures. In contrast, SHG polarization measurements are used to quantitatively determine that no rotation occurs at site Cys-77, in agreement with the lack of motion observed at this site in the X-ray crystal structures. A method for building a global map of conformational change in real time and space is proposed using a set of probes placed at different sites in a biomolecule. For this purpose, SH-active unnatural amino acids are attractive complements to exogenous labels.     

分子动力学研究F1-ATP合酶对三磷酸腺苷的稳定和定位作用

F₁-ATP合酶通过与ATP之间建立广泛的相互作用,实现对ATP的位置进行精确的定位.这些相互作用为ATP的合成/水解创造了稳定的环境.理解这些相互作用是理解ATP的合成/水解机理的基础.我们通过分子动力学模拟方法研究这些相互作用,找出在稳定化过程中起到重要作用的残基.通过检测ATP和F₁-ATP合酶之间的非键相互作用,发现残基段158-164所形成的loop区域及残基R189, Y345对ATP存在显著相互作用.其中,该loop区域对ATP的三磷酸部分形成一个半包围结构,封闭活性位点区域,并通过氢键网络约束ATP三磷酸的运动,为ATP合成/水解创造稳定的环境.此外,关键残基Y345通过π-π叠加相互作用对ATP的碱基进行约束,但是ATP的碱基可以在平行于Y345芳香环的平面内进行滑动,我们推断这种滑动运动有利于促进ATP的水解.     

A Multisite‐Binding Switchable Fluorescent Probe for Monitoring Mitochondrial ATP Level Fluctuation in Live Cells

Adenosine triphosphate (ATP), commonly produced in mitochondria, is required by almost all the living organisms; thus fluorescent probes for monitoring mitochondrial ATP levels fluctuation are essential and highly desired. Herein, we report a multisite‐binding switchable fluorescent probe, ATP‐Red 1 , which selectively and rapidly responds to intracellular concentrations of ATP. Live‐cell imaging indicated that ATP‐Red 1 mainly localized to mitochondria with good biocompatibility and membrane penetration. In particular, with the help of ATP‐Red 1 , we successfully observed not only the decreased mitochondrial ATP levels in the presence of KCN and starvation state, but also the increased mitochondrial ATP levels in the early stage of cell apoptosis. These results indicate that ATP‐Red 1 is a useful tool for investigating ATP‐relevant biological processes.     

Aryl urea substituted fatty acids: a new class of protonophoric mitochondrial uncoupler that utilises a synthetic anion transporter

Respiring mitochondria establish a proton gradient across the mitochondrial inner membrane (MIM) that is used to generate ATP. Protein-independent mitochondrial uncouplers collapse the proton gradient and disrupt ATP production by shuttling protons back across the MIM in a protonophoric cycle. Continued cycling relies on the formation of MIM-permeable anionic species that can return to the intermembrane space after deprotonation in the mitochondrial matrix. Previously described protonophores contain acidic groups that are part of delocalised π-systems that provide large surfaces for charge delocalisation and facilitate anion permeation across the MIM. Here we present a new class of protonophoric uncoupler based on aryl-urea substituted fatty acids in which an acidic group and a π-system are separated by a long alkyl chain. The aryl-urea group in these molecules acts as a synthetic anion receptor that forms intermolecular hydrogen bonds with the fatty acid carboxylate after deprotonation. Dispersal of the negative charge across the aryl-urea system produces lipophilic dimeric complexes that can permeate the MIM and facilitate repeated cycling. Substitution of the aryl-urea group with lipophilic electron withdrawing groups is critical to complex lipophilicity and uncoupling activity. The aryl-urea substituted fatty acids represent the first biological example of mitochondrial uncoupling mediated by the interaction of a fatty acid and an anion receptor moiety, via self-assembly.

A new mitochondrial uncoupler that forms membrane permeable dimers through interactions of remote acidic and anion receptor groups.     

Ratiometric fluorescence and visual sensing of ATP based on gold nanocluster-encapsulated metal-organic framework with a smartphone

Adenosine triphosphate (ATP) plays an important role in various biological processes and the ATP level is closely associated with many diseases. Herein, we designed a novel dual-emissive fluorescence nanoplatform for ATP sensing based on red emissive europium metal-organic framework (Eu-MOF) and blue emissive gold nanoclusters (AuNCs). The presence of ATP causes the decomposition of Eu-MOF owing to strong affinity of Eu³⁺ with ATP. As a result, the red emission of Eu-MOF decreases while the blue emission of AuNCs remains unchanged. The distinct red/blue emission intensity change enables the establishment of a ratiometric fluorescent and visual sensor of ATP. Moreover, a fluorescent paper-based sensor was fabricated with the ratiometric ATP probes, which enabled easy-to-use and visual detection of ATP in serum samples with a smartphone.     

Enhanced Anticancer Efficacy by ATP‐Mediated Liposomal Drug Delivery

A liposome‐based co‐delivery system composed of a fusogenic liposome encapsulating ATP‐responsive elements with chemotherapeutics and a liposome containing ATP was developed for ATP‐mediated drug release triggered by liposomal fusion. The fusogenic liposome had a protein–DNA complex core containing an ATP‐responsive DNA scaffold with doxorubicin (DOX) and could release DOX through a conformational change from the duplex to the aptamer/ATP complex in the presence of ATP. A cell‐penetrating peptide‐modified fusogenic liposomal membrane was coated on the core, which had an acid‐triggered fusogenic potential with the ATP‐loaded liposomes or endosomes/lysosomes. Directly delivering extrinsic liposomal ATP promoted the drug release from the fusogenic liposome in the acidic intracellular compartments upon a pH‐sensitive membrane fusion and anticancer efficacy was enhanced both in vitro and in vivo.     

Measuring the simultaneous effects of hypoxia and deformation on ATP release from erythrocytes

It is known that adenosine triphosphate (ATP) is released from red blood cells (RBCs) due to various forms of stimulation such as deformation, pharmacological stimuli, and hypoxia. To date, these various stimuli have been investigated individually. Here, we have combined a microflow system capable of initiating deformation-induced release of ATP from the RBCs at various levels of hypoxia as measured by percent oxygen saturation in the RBC sample. When values of ATP released from deformation and hypoxia are compared to values of ATP release due to hypoxia alone, the relationship between the two stimuli can be deduced. Measurement of RBC-derived ATP with the well-known chemiluminescence assay employing luciferin/luciferase indicates that RBCs deoxygenated for 4 min released 1.84 +/- 0.075 microM ATP. The largest decrease in oxygen saturation was found to be between 0 s (66.3% O(2) saturation) and 15 s (22.3% O(2) saturation). RBCs deoxygenated to a 22.3% O(2) saturation released 0.374 +/- 0.011 microM ATP when pumped through the microflow system. This value is an increase from 0.281 +/- 0.007 microM ATP in the presence of flow alone. The ATP release after exposure to hypoxia at 22.3% O(2) saturation was 0.381 +/- 0.014 microM ATP, a value statistically equivalent to that of hypoxia and flow combined. These data suggest that, at an oxygen saturation point of around 25.0% or above, deformation contributes to ATP release from the RBC; however, beyond this saturation point, the ATP release is largely due to hypoxia.     

Water‐Soluble Triarylboron Compound for ATP Imaging In Vivo Using Analyte‐Induced Finite Aggregation

Adenosine 5′‐triphosphate (ATP) is a multifunctional molecule that participates in many important biological processes. Currently, fluorescence indicators for ATP with high performance are in demand. Reported herein is a novel water‐soluble triarylboron compound which displays an apparent ATP‐dependent fluorescence enhancement when dispersed in water. It can selectively recognize ATP from other bioactive substances in vitro and in vivo. The ATP‐induced finite aggregation endows the indicator with appreciable photostability and superior tolerance to environmental electrolytes. This indicator has been successfully applied to the ATP imaging in NIH/3T3 fibroblast cells. The difference in the ATP levels within the membrane and cytosol is clearly visible.     

Extracellular ATP is generated by ATP synthase complex in adipocyte lipid rafts

Mitochondrial biogenesis is known to accompany adipogenesis to complement ATP and acetyl-CoA required for lipogenesis. Here, we demonstrated that mitochondrial proteins such as ATP synthase alpha and beta, and cytochrome c were highly expressed during the 3T3-L1 differentiation into adipocytes. Fully-differentiated adipocytes showed a significant increase of mitochondria under electron microscopy. Analysis by immunofluorescence, cellular fractionation, and surface biotinylation demonstrated the elevated levels of ATP synthase complex found not only in the mitochondria but also on the cell surface (particularly lipid rafts) of adipocytes. High rate of ATP (more than 30 microM) synthesis from the added ADP and P(i) in the adipocyte media suggests the involvement of the surface ATP synthase complex for the extracellular ATP synthesis. In addition, this ATP synthesis was significantly inhibited in the presence of oligomycin, an ATP synthase inhibitor, and carbonyl cyanide m-chlorophenylhydrazone (CCCP), an ATP synthase uncoupler. Decrease of extracellular ATP synthesis in acidic but not in basic media further indicates that the surface ATP synthase may also be regulated by proton gradient through the plasma membrane.     

A Novel Fluorescent Probe for ATP Detection Based on Synergetic Effect of Aggregation-induced Emission and Counterion Displacement

In this work,a fluorescent probe(TPEBe-I)was developed for adenosine triphosphate(ATP)detection based on the synergetic effect of aggregation-induced emission and counterion displacement.TPEBe-I gave weak emission in aqueous solution due to the heavy-atom effect of counter iodide ion.However,upon the addition of ATP,the new aggregate complex(TPEBe-ATP)was formed between the cationic unit of TPEBe-I and ATP through electrostatic interactions,which not only restricted the intramolecular motion of luminogen but also eliminated the quenching effect of iodide ion.As a result,the fluorescent light-up detection for ATP was successfully achieved.Moreover,TPEBe-I exhibited high selectivity towards ATP and showed a wide linear detection region towards the logarithm of ATP concentration(5—600μmol/L)with a detection limit of 1.0μmol/L,enabling TPEBe-I as a promising probe for ATP quantitative analysis.     

ATP‐Mediated Transient Behavior of Stomatocyte Nanosystems

In nature, dynamic processes are ubiquitous and often characterized by adaptive, transient behavior. Herein, we present the development of a transient bowl‐shaped nanoreactor system, or stomatocyte, the properties of which are mediated by molecular interactions. In a stepwise fashion, we couple motility to a dynamic process, which is maintained by transient events; namely, binding and unbinding of adenosine triphosphate (ATP). The surface of the nanosystem is decorated with polylysine (PLL), and regulation is achieved by addition of ATP. The dynamic interaction between PLL and ATP leads to an increase in the hydrophobicity of the PLL–ATP complex and subsequently to a collapse of the polymer; this causes a narrowing of the opening of the stomatocytes. The presence of the apyrase, which hydrolyzes ATP, leads to a decrease of the ATP concentration, decomplexation of PLL, and reopening of the stomatocyte. The competition between ATP input and consumption gives rise to a transient state that is controlled by the out‐of‐equilibrium process.     

Intramitochondrial co-assembly between ATP and nucleopeptides induces cancer cell apoptosis

Mitochondria are essential intracellular organelles involved in many cellular processes, especially adenosine triphosphate (ATP) production. Since cancer cells require high ATP levels for proliferation, ATP elimination can be a unique target for cancer growth inhibition. We describe a newly developed mitochondria-targeting nucleopeptide (MNP) that sequesters ATP by self-assembling with ATP inside mitochondria. MNP interacts strongly with ATP through electrostatic and hydrogen bonding interactions. MNP exhibits higher binding affinity for ATP (−637.5 kJ mol⁻¹) than for adenosine diphosphate (ADP) (−578.2 kJ mol⁻¹). To improve anticancer efficacy, the small-sized MNP/ADP complex formed large assemblies with ATP inside cancer cell mitochondria. ATP sequestration and formation of large assemblies of the MNP/ADP–ATP complex inside mitochondria caused physical stress by large structures and metabolic disorders in cancer cells, leading to apoptosis. This work illustrates a facile approach to developing cancer therapeutics that relies on molecular assemblies.

Mitochondria-targeting nucleopeptide (MNP) can sequester ATP by self-assembling with ATP. A small nanosized MNP/ADP complex forms a large assembly with ATP. Thus, intramitochondrial co-assembly causes stress by large structures and apoptosis.     

Dynamic mechanism for the autophosphorylation of CheA histidine kinase: molecular dynamics simulations

The two-component system (TCS) is an important signal transduction component for most bacteria. This signaling pathway is mediated by histidine kinases via autophosphorylation between P1 and P4 domains. Taking chemotaxis protein CheA as a model of TCS, the autophosphorylation mechanism of the TCS histidine kinases has been investigated in this study by using a computational approach integrated homology modeling, ligand-protein docking, protein-protein docking, and molecular dynamics (MD) simulations. Four nanosecond-scale MD simulations were performed on the free P4 domain, P4-ATP, P4-TNPATP, and P1-P4-ATP complexes, respectively. Upon its binding to the binding pocket of P4 with a folded conformation, ATP gradually extends to an open state with help from a water molecule. Meanwhile, ATP forms two hydrogen bonds with His413 and Lys494 at this state. Because of the lower energy of the folded conformations, ATP shrinks back to its folded conformations, leading to the rupture of the hydrogen bond between ATP and Lys494. Consequently, Lys494 moves away from the pocket entrance, resulting in an open of the ATP lid of P4. It is the open state of P4 that can bind tightly to P1, where the His45 of P1 occupies a favorable position for its autophosphorylation from ATP. This indicates that ATP is not only a phosphoryl group donor but also an activator for CheA phosphorylation. Accordingly, a mechanism of the autophosphorylation of CheA is proposed as that the ATP conformational switch triggers the opening of the ATP lid of P4, leading to P1 binding tightly, and subsequently autophosphorylation from ATP to P1.     

Electrochemical/electrospray mass spectrometric studies of electrochemically stimulated ATP release from PP/ATP films

Polypyrrole (PP)/adenosine triphosphate (ATP) was chosen as a conducting polymer/anionic drug model to serve as a bioactive releasing material for ATP. The process of ATP release from PP/ATP films was investigated for the first time by electrochemical electrospray ionization mass spectrometry (EC/ESMS). This technique allowed the simultaneous and direct detection of ATP and its related species during electrochemical release. In the experiments, suitable solvent conditions were found for both the electrochemical release and the electrospray mechanisms. EC/ESMS results showed that continuous potential cycles allowed a higher ATP release rate than potential steps. It was also found that the film thickness is an important factor affecting the rate and the amount of electrochemical ATP release.