Three dimensional structure of adenosine triphosphate

A System of Rapidly Detecting Escherichia Coli in Food Based on a Nanoprobe and Improved ATP Bioluminescence Technology

Bacterial contamination is an important factor causing food security issues. Among the bacteria, Escherichia coli is one of the main pathogens of food-borne microorganisms. However, traditional bacterial detection approaches cannot meet the requirements of real-time and on-site detection. Thus, it is of great significance to develop a rapid and accurate detection of bacteria in food to ensure food safety and safeguard human health. The pathogen heat-treatment module was designed in this paper based on the techniques including nanoprobe, pathogen heat-treatment, graphene transparent electrode (GTE), and adenosine triphosphate (ATP) bioluminescence technology. The system mainly consists of two parts: one is the optical detection unit; the other is the data processing unit. And it can quickly and automatically detect the number of bacterial colonies in food such as milk etc. The system uses not only the probe to capture and enrich E. coli by antigen-antibody interaction but also the heat treatment to increase the amount of ATP released from bacterial cells within five minutes. To enhance the detecting accuracy and sensitivity, the electric field generated by GTE is adopted in the system to enrich ATP. Compared to the other conventional methods, the linear correlation coefficient of the system can be reached 0.975, and the system meets the design requirements. Under the optimal experimental conditions, the detection can be completed within 25 min, and the detectable concentration of bacteria is in the range of 3.1 × 10¹–10⁶ CFU/mL. This system satisfies the demands of a fast and on-site inspection.

Fast energy minimization of the CCDC drug-subset structures by molecule-in-cluster computations allows independent structure validation and model completion

Optimizing structures with computations on clusters of molecules permits generation of structure-specific restraints for refinement and structure validation.

Structural characterization of nucleotide 5'-triphosphates by infrared ion spectroscopy and theoretical studies

The molecular family of nucleotide triphosphates (NTPs), with adenosine 5'-triphosphate (ATP) as its best-known member, is of high biochemical importance as their phosphodiester bonds form Nature's main means to store and transport energy. Here, gas-phase IR spectroscopic studies and supporting theoretical studies have been performed on adenosine 5'-triphosphate, cytosine 5'-triphosphate and guanosine 5'-triphosphate to elucidate the intrinsic structural properties of NTPs, focusing on the influence of the nucleobase and the extent of deprotonation. Mass spectrometric studies involving collision induced dissociation showed similar fragmentation channels for the three studied NTPs within a selected charge state. The doubly charged anions exhibit fragmentation similar to the energy-releasing hydrolysis reaction in nature, while the singly charged anions show different dominant fragmentation channels, suggesting that the charge state plays a significant role in the favorability of the hydrolysis reaction. A combination of infrared ion spectroscopy and quantum-chemical computations indicates that the singly charged anions of all NTPs are preferentially deprotonated at their β-phosphates, while the doubly-charged anions are dominantly αβ-deprotonated. The assigned three-dimensional structure differs for ATP and CTP on the one hand and GTP on the other, in the sense that ATP and CTP show no interaction between nucleobase and phosphate tail, while in GTP they are hydrogen bonded. This can be rationalized by considering the structure and geometry of the NTPs where the final three dimensional structure depends on a subtle balance between hydrogen bond strength, flexibility and steric hindrance.

Conformations of spermine in adenosine triphosphate complex: the structural basis for weak bimolecular interactions of major cellular electrolytes

Selectively (2)H- and (13)C-labeled spermines (SPM) were efficiently synthesized and analyzed by NMR spectroscopy to determine the spin-spin coupling constants for six conformationally relevant bonds. SPM that is composed of three alkyl moieties, a butanylene, and two propanylene chains undergoes a conformational change when interacting with multivalent anions (e.g., adenosine triphosphate (ATP), ATP-Mg(2+) , and tripolyphosphate). Upon interaction with ATP, the C-C bonds, which affect the distance between the neighboring pairs of ammonium groups (i.e., N1/N5 and N5/N5'), increase the population of gauche rotamers by 17-20% relative to those in the 4 HCl salt of SPM. However, the trend in increments of the gauche conformers for the SPM-ATP complex profoundly differs from that of the spermidine (SPD)-ATP complex. This implies that SPM may preferentially recognize the adenyl group of ATP rather than the tripolyphosphate moiety. This may account for the higher affinity of SPM to ATP-Mg(2+) than with that of SPD, which chiefly interacts with β- and γ-phosphates and is easily replaced by Mg(2+) . These results may provide a clue for the further understanding of the structural basis of polyamine biological functions.

Conformational change of spermidine upon interaction with adenosine triphosphate in aqueous solution

Endogenous polyamines, represented by putrescine, spermidine, and spermine, are known to exert their physiological functions by interacting with polyanionic biomolecules such as DNA, RNA, adenosine triphosphate (ATP), and phospholipids. Very few examples of conformation analysis have been reported for these highly flexible polymethylene compounds, mainly due to the lack of appropriate methodologies. To understand the molecular basis of the weak interaction between polyamines and polyanions that underlies their physiological functions, we aimed to elucidate the solution conformation of spermidine by using diastereospecifically deuterated and (13)C-labeled derivatives (1-7), which were designed to diagnose the orientation of seven conformationally relevant bonds in spermidine. (1)H-(1)H and (13)C-(1)H NMR coupling constants ((3)J(H,H) and (3)J(C,H)) were successfully determined for a spermidine-ATP complex. The relevant coupling constants markedly decreased upon complexation. The results reveal that spermidine, when interacting with ATP, undergoes changes that make the conformation more bent and forms the complex with the triphosphate part of ATP in an orientation-sensitive manner.

Mathematical modelling of kinetics of adenosine 5'-triphosphate hydrolysis catalyzed by Zn2+ ion in the pH range 7.1-7.4

Kinetic data on hydrolysis of ZnATP2- complexes confirm the enzyme-like mechanism of the reaction. The whole sequence of steps for the formation and transformations of the intermediates is established by numerical modelling in a wide range of concentrations (4x10(-4)-0.3 M) in the pH range 7.1-7.4. The rates of active center formation and appropriate equilibria are governed by H+ transfer from coordinated water with formation of hydrogen bond between the (N1) atom of the second ZnATP2- molecule and the gamma-phosphate moiety of the first ZnATP2- molecule. The rate and equilibrium constants are higher in trimeric associates as compared to dimeric ones. Among the steps of ADP formation in the pH-independent channel, H+ transfer from the hydrogen bond with O(-)-Pgamma of ZnATP2- to the hydrogen bond with O(-)-Pbeta of ZnADP- forming in the course of general base catalysis is the rate determining step. It is followed by the rapid and reversible substitution of ligand H2PO4- by H2O in the Zn2+ coordination sphere. Hydrogen bond participation leads to reversible ADP formation. AMP is shown to be formed also via associates, and the conformation transformation determines the induction period. The induction period decreases as the concentration of ZnATP2- increases. The rate and equilibrium constants of all steps are evaluated and variation of the intermediate concentrations in the course of hydrolysis is presented.

Formation of a complex containing ATP, Mg2+, and spermine. Structural evidence and biological significance

The conformation of ATP in the presence of Mg2+ and/or spermine was studied by 31P and 1H NMR, to clarify how polyamines interact with ATP. Spermine predominantly interacted with the beta- and gamma-phosphates of ATP in the presence of Mg2+. A conformational change of the beta- and gamma-phosphate of ATP with spermine could not be observed in the absence of Mg2+ by 31P NMR. It was found by 1H NMR that the conformation of adenosine moiety of ATP was not influenced significantly by spermine. The binding of Mg2+ to ATP was slightly inhibited by spermine and vice versa. The results indicate that the binding sites of Mg2+ and spermine on ATP only partially overlap. The PotA protein, an ATP-dependent enzyme, was used as a model system to study the biological role of the ATP-Mg2+-spermine complex. The ATPase activity of PotA was greatly enhanced by spermine. Double reciprocal plots at several concentrations of spermine as an activator indicate that spermine interacts with ATP, but not with PotA. The activity of protein kinase A was also stimulated about 2-fold by spermine. The results suggest that a ternary complex of ATP-Mg2+-spermine may play an important role in some ATP-dependent reactions in vivo and in the physiological effects of endogenous polyamines.

Acid-base properties of nucleosides and nucleotides as a function of concentration. Comparison of the proton affinity of the nucleic base residues in the monomeric and self-associated, oligomeric 5'-triphosphates of inosine (ITP), guanosine (GTP), and adenosine (ATP)

The acid-base properties of the nucleic base residues of ITP, GTP, and ATP, and for comparison also as far as possible of the corresponding nucleosides, were studied in dependence on their concentration, i.e. on the effect of self-association. From the dependence between the 1H-NMR chemical shifts of H-2 (where applicable), H-8, and H-1', and the pD of the solutions, the acidity constants for the deprotonation of the D+(N-7) site in D2(ITP)2-, D2(GTP)2-, D(Ino)+, and D(Guo)+, and of the D+(N-1) site in D2(ATP)2- and D(Ado)+ were calculated. Chemical shift/pD profiles for a whole series of varying concentrations of the nucleic base derivatives (= N) were constructed, including those for infinite dilution (delta o), which give the acidity constant for the monomeric N, and for infinitely concentrated solutions (delta infinity), which give the acidity constant of an N in an infinitely long stack. The acidity constants determined from the delta o/pD plots are in excellent agreement with the pKa values measured by potentiometric pH titrations of highly diluted solutions of N. The effects of self-association are striking; e.g. the pKa value of the D+(N-7) site in D2(GTP)2- is lowered by about 1 (as calculated from the delta o/pD and delta infinity/pD profiles), while the pKa value of the D+(N-1) site in D2(ATP)2- is increased by approximately 0.3; i.e. in the first case deprotonation is facilitated and in the second it is inhibited. The increasing inhibition of the H+(N-1) deprotonation with an increasing ATP concentration is due to the high stability of the dimeric [H2(ATP)]2(4-) stack for which the intermolecular H+(N-1)/gamma-P(OH)(O)2- ion pairs between the two ATP molecules are crucial. In those cases where no other significant interaction but aromatic-ring stacking in the self-association process occurs, the release of protons from protonated nitrogen-ring sites is facilitated with increasing stacking; this holds not only for D2(GTP)2- as indicated above, but also for D2(ITP)2-, D(Ino)+, and D(Ado)+. The latter example especially suggests that the situation for the D2(ATP)2- system is exceptional. Some consequences of the considered acid-base properties for biological systems are indicated.

Comparison of the self-association properties of the 5'-triphosphates of inosine (ITP), guanosine (GTP), and adenosine (ATP). Further evidence for ionic interactions in the highly stable dimeric [H2(ATP)]2(4-) stack

The concentration dependence of the chemical shifts for the hydrogens H-2, H-8 and H-1' of ITP and for H-8 and H-1' of GTP has been measured in D2O at 25 degrees C under several degrees of protonation in the pD range 1.2-8.4. For reasons of comparison, inosine and guanosine have been included in the study The results are consistent with the isodesmic model of indefinite noncooperative stacking. The association constants for the nucleosides (Ns) inosine and guanosine decrease with increasing protonation: Ns greater than D(Ns)+/Ns in a 1:1 ratio greater than D(Ns)+. In contrast, a maximum is observed with ITP and GTP; the stacking tendency of GTP following the series: GTP4- less than or equal to D(GTP)3- (K approximately 0.7 M-1) less than D(GTP)3-/D2(GTP)2- in a 1:1 ratio (K approximately 2.9 M-1) greater than D2(GTP)2- greater than D3(GTP)- (K approximately 1.5 M-1). The order of the series with ITP corresponds to that with GTP, but the association constants are slightly smaller. At the maximum of the self-association tendency the triphosphate residue has only a minor influence; this follows from the fact that the association constants for the 1:1 ratios of Ino/D(Ino)+ and D(ITP)3-/D2(ITP)2- are identical within experimental error; this holds also for Guo/D(Guo)+ and D(GTP)3-/D2(GTP)2-; in all these pairs the K-7 site is 50% protonated. Comparison of the association constant for the deprotonated species shows that here charge effects, i.e. repulsion between the negatively charged triphosphate chains, are important: Ino (K approximately 3.3 M-1) greater than ITP4- (K approximately 0.4 M-1) and Guo (K approximately 8 M-1) greater than GTP4- (K approximately 0.8 M-1). In addition the series holds: Ado (K approximately 15 M-1) greater than Guo greater than Ino. However, most important is the comparison of the ITP and GTP series with previous data for ATP: ATP4- (K approximately 1.3 M-1) less than D(ATP)3- (2.1 M-1) less than 1:1 ratio of D(ATP)3-/D2(ATP)2- (6 M-1) much less than D2(ATP)2- (approximately 200 M-1) much greater than D3(ATP)- (K less than or equal to 17 M-1).(ABSTRACT TRUNCATED AT 400 WORDS)

Influence of the protonation degree on the self-association properties of adenosine 5'-triphosphate (ATP)

The concentration dependence of the chemical shifts for the protons H-2, H-8 and H-1' of ATP has been measured in D2O at 27 degrees C under several degrees of protonation in the pD range from 1.5 to 8.4. The results at pD greater than 4.5 are consistent with the isodesmic model of indefinite noncooperative stacking, while those at pD less than 4.5 indicate a preference for the formation of dimeric stacks. The stacking tendency follows the series, ATP4- (K = 1.3 M-1) less than D(ATP)3- (2.1 M-1) less than 1:1 ratio of D(ATP)3-/D2(ATP)-2- (6.0 M-1) much less than D2(ATP)2- (approximately 200 M-1) much greater than D3(ATP)- (K approximately less than 17 M-1) (for reasons of comparison all constants are expressed in the isodesmic model). These results are compared with previous data for adenosine [Ado (K = 15 M-1) greater than 1:1 ratio of Ado/D(Ado)+ (6.0 M-1) greater than D(Ado)+ (0.9 M-1)] and AMP [AMP2- (K = 2.1 M-1) less than D(AMP)- (3.4 M-1) less than 1:1 ratio of D(AMP)-/D2(AMP) +/- (5.6 M-1) greater than D2(AMP) +/- (approximately equal to 2 M-1) greater than D3(AMP)+ (K less than or equal to 1 M-1)] to facilitate the interpretation of the results for the ATP systems. Stack formation of H2(ATP)2- is clearly favored by additional ionic interactions; this is confirmed by measuring via potentiometric pH titrations the acidity constants of H2(ATP)2- in solutions containing different concentrations of ATP. It is suggested that in the [H2(ATP)]4-(2) dimer intermolecular ion pairs (and hydrogen bonds) are formed between the H+(N-1) site of one H2(ATP)2- and the gamma-P(OH)(O)-2 group of the other; in this way (a) the stack is further stabilized, and (b) the positive charges at the adenine residues are compensated (otherwise repulsion would occur as is evident from the adenosine systems). A detailed structure for the [H2(ATP)4-(2) dimer is proposed and some implications of the described stacking properties of ATP for biological systems are indicated.

X-ray structure of the ternary complex Zn(II)-ATP-2,2'-bipyridyl and possible model for ATP transport

Ternary complexes between metal ions, nucleotides and aromatic heterocyclic amines are being investigated by X-ray diffraction as possible models for enzyme-metal-substrate interactions. Kennard and coworkers have reported the crystal structure of the ATP disodium salt. Although more recently several crystal structures of binary and ternary complexes between metal ions and nucleoside monophosphates have been reported, no structure combining metal complexes with nucleoside di- or triphosphates has been reported. Most divalent metal ions catalyse the nonenzymatic transfer of phosphate from nucleoside polyphosphates to various acceptors. Therefore, these compounds in water solution undergo extensive hydrolysis in the presence of metal ions, leading to the formation of the monophosphates; for instance, at pH 6.5, Cu2+ accelerates the hydrolysis of ATP by a factor of about 300 (ref. 5). We report here the crystal and molecular structure of the complex [Zn(II)-H2ATP-2,2'-bipyridyl]2.4H2O, determined by single crystal X-ray analysis. The complex molecule provides a possible model for ATP transport and phosphate group transfer mechanism.

Phenylalanyl-tRNA and seryl-tRNA synthetases from baker's yeast. Substrate specificity with regard to ATP analogs and mechanism of the aminoacylation reaction

Eighteen analogs of ATP have been tested in the aminoacylation reaction of phenylalanyl-tRNA and seryl-tRNA synthetases from baker's yeast. Four compounds are substrates for phenylalanyl-tRNA synthetase, five for seryl-tRNA synthetase, one compound is an inhibitor for both enzymes; their Km and Ki and V values have been determined. The substrate specificity shows that for the catalytic action of both enzymes with these substrates positions 6, 7, 8 and 9 of the purine moiety and positions 2' and 3' of the ribose moiety are important.

The self-association of adenosine-5'-triphosphate studied by circular dichroism at low ionic strengths

The self-association of adenosine-5'-triphosphate (ATP) was studied as a function of pH, additional counterions, concentration and temperature. Circular dichroism measurements were employed as a measure of the base-stacking. The self-association of ATP is pH dependent with the protonation of the adenine ring helping stabilize the association. Highly charged counterions alter this aggregation. At pH 2.8 and 20 degrees C, a dimerization constant of 88 M-1 is obtained, while an isodesmic model leads to an equilibrium constant of 158 M-1. With increasing pH, the association constants decrease. At pH 2.8 there is a very strong temperature dependence of the CD amplitude. These results indicate the existence of additional electrostatic stabilization for the stacking of the adenine rings. At acidic pHs, models are proposed to explain this high degree of stability and a calculation of the approximate electrostatic contribution to the aggregation shows it to be of the proper magnitude.

Properties of the ribose-ring-opened adenine nucleotide, 2,2'(1-(9-adenyl)-1'-(tri-,diphosphoryl-oxymethyl))-dihydroxydiethylether in mitochondrial adenine-nucleotide translocation

(Adenine-14C) or (gamma-32P)-labelled 2,2'[1-(9-adenyl)-1'-(tri-, diphosphoryl-oxymethyl]-dihydroxydiethylether (rroANP) was obtained from ANP by cleavage of the C-2--C-3' bond by sodium periodate oxidation and subsequent borohydride reduction. Binding of rroANP to rat liver mitochondria revealed carrier-linked (atractyloside-sensitive) and unspecific (atractyloside-insensitive) binding but no transfer across the inner mitochondrial membrane. Kinetic data indicate rroANP as a competitive inhibitor for ANP uptake with Ki = 9.3 X 10(-5) M. Experimental rroANP confirmed that an intact adenine base and three anio.nic charges of the phosphate chain are essential for the recognition between ANP-carrier and nucleotide but insufficient for the induction of a transmembrane ANP exchange. In addition mobilisation of the carrier-nucleotide complex requires an intact ribofuranoside ring system.