Labile zinc-assisted biological phosphate chemosensing and related molecular logic gating interpretations

Herein, molecular fluorescence 'OFF-ON' behavior with aqueous addition of biological phosphate and Zn(2+) is studied with Zn(2)(slys)(2)Cl(2) [H(2)slys = 6-amino-2-{(2-hydroxybenzylidene)amino}hexanoic acid], a fluorescent water-soluble complex, using various spectroscopic tools (e.g., (31)P NMR, UV-vis, emission, and CD spectroscopy) at the micromolar level. Adduct-dependent fluorescence intensity changes can be interpreted as a two-input (cation/anion) implication molecular logic gating system. A displacement study of PPi from the dizinc complex is also reported. Diphosphate and triphosphate addition/displacements were also studied. (31)P NMR spectroscopy shows gradual NMR peak shifts from bound ADP/GDP to free ADP/GDP with increasing [PPi]. In the emission spectrum, fluorescence quenching is shown: CD signal maxima decrease with addition of PPi. These displacement events are also tested with triphosphates (ATP, GTP), and their binding strength/displacement ability over ADP/GDP is quantified: PPi > ATP ≈ GTP (3.35 ± 0.77 × 10(4) M(-1) for PPi, 7.73 ± 1.79 × 10(3) M(-1) for ATP, 9.21 ± 2.88 × 10(3) M(-1) for GTP over 1·ADP). Many anions and cations were also screened for selectivity. Tubulin polymerization was assayed in the presence of 1 and its copper analogue which reflected a slight inhibition in polymerization.     

Fluorescent imidazolium-based cyclophane for detection of guanosine-5'-triphosphate and I(-) in aqueous solution of physiological pH

A new water-soluble and fluorescent imidazolium-anthracene cyclophane (1) effectively recognizes the biologically important GTP and I(-) over other anions in a 100% aqueous solution of physiological pH 7.4. Fluorescence and (1)H NMR spectra and ab initio calculations demonstrate that emission arises from the formation of an excimer state and quenching occurs upon GTP/I(-) binding through (C-H)(+)···A(-) hydrogen bond interactions.     

The specific vibrational modes of GTP in solution and bound to Ras: a detailed theoretical analysis by QM/MM simulations

The hydrolysis of guanosine triphosphate (GTP) in general, and especially by GTPases like the Ras protein, is in the focus of biological investigations. A huge amount of experimental data from Fourier-transformed infrared studies is currently available, and many vibrational bands of free GTP, GTP·Mg(2+), and Ras·GTP·Mg(2+) in solution have been assigned by isotopic labeling. In the Ras environment, bands between 800 cm(-1) and 1300 cm(-1) have already been assigned, but not those below 800 cm(-1). The combination of quantum and molecular mechanics (QM/MM) methods takes the quantum effects for selected relevant atoms into account. This provides structural details, vibrational frequencies and electron distributions of the region of interest. We therefore used MM and QM/MM simulations to investigate the normal vibrational modes of GTP, GTP·Mg(2+), and Ras·GTP·Mg(2+) in solution, and assigned the vibrational frequencies for each normal vibration mode. In this study, the quantum box contains the nucleoside and the Mg(2+). The comparison of calculated and experimental vibrational spectra provides a very good control for the quality of the calculations. Structurally, MM and QM/MM simulations reveal a stable tridentate coordination of the Mg(2+) by GTP in water, and a stable bidentate coordination by GTP in complex with Ras. For validation, we compare the calculated frequencies and isotopic shifts with the experimental results available in the range of 800 cm(-1) to 1300 cm(-1). For the first time we suggest band assignments of the vibrational modes below 800 cm(-1) by comparison of calculated and experimental spectra.     

Fluorescent GTP-sensing in aqueous solution of physiological pH

A new water-soluble imidazolium anthracene derivative not only differentiates two structurally similar compounds GTP and ATP but also acts as potential fluorescent chemosensors (as a quencher and an enhancer, respectively) for GTP and ATP in 100% aqueous solution (pH = 7.4, 10 mM HEPES).     

核苷酸碱基堆积导致的分子间NOE交叉峰

ＡＴＰ(三磷酸腺苷)是生命活动中不可缺少的能量物质,它的各种结合状态都是与生物功能密切相关的.在生物体内,它常常以很高的浓度存在[1-3].由于碱基芳环部分的电子云形成环流,两两堆积可以降低能量.因此在ＡＴＰ浓溶液中,它们可能倾向于以碱基堆积方式形成自聚体,使能量得到降低.已有不少报导指出核苷酸在溶液中有碱基堆积现象.人们通过改变样品的浓度、ｐＨ值、实验温度等条件,发现ＡＴＰ溶液的1ＨＮＭＲ谱中各质子的化学位移有很大变化,据此提出了多种可能的堆积模型[4-7],并通过实验数据计算了它们的变化规律[8,9],认为在酸度较高的情况…     

Europium tetracycline as a luminescent probe for nucleoside phosphates and its application to the determination of kinase activity

The determination of enzyme activities and the screening of enzyme regulators is a major task in clinical chemistry and drug development. A broad variety of enzymatic reactions is associated with the consumption of adenosine triphosphate (ATP), including, in particular, phosphorylation reactions catalyzed by kinases, formation of adenosine cyclic monophosphate (cAMP) by adenylate cyclases, and ATP decomposition by ATPase. We have studied the effect of a series of adenosine (ATP, ADP, AMP, cAMP) and guanosine (GTP, GDP) phosphoric esters, and of pyrophosphate (PP) on the fluorescence emission of the europium tetracycline (EuTC) complex. We found that these compounds have strongly different quenching effects on the luminescence emission of EuTC. The triphosphates ATP and GTP behave as strong quenchers in reducing the fluorescence intensity of EuTC to 25 % of its initial value by formation of a ternary 1:1:1 complex. All other phosphate esters showed a weak quenching effect only. The applicability of this fluorescent probe to the determination of the activity of phosphorylation enzymes is demonstrated by means of creatine kinase as a model for non-membrane-bound kinases. In contrast to other methods, this approach does not require the use of radioactively labeled ATP substrates, additional enzymes, or of rather complex immunoassays.     

Capillary electrophoresis apparatus equipped with a bioluminescence detector using a batch- or flow-type detection cell

We developed a capillary electrophoresis (CE) apparatus equipped with a batch- or flow-type bioluminescence (BL) detection cell. Firefly luciferin-luciferase BL reaction was used to analyze samples of nucleotides, such as ATP, dATP, ADP, GTP, UTP, CTP, ITP, and TTP. In the CE apparatus with the batch-type cell, ATP was detected at concentrations of 5-100 microM, while the other nucleotides were not detected at concentrations less than 500 microM. The electropherogram of ATP included two BL peaks; the latter peak showed peculiar broadening, which continued up to ca. 2.5 h. In the CE apparatus with the flow-type cell, ATP, dATP, and ADP were detected with single peaks with detection limits of 1, 75, and 100 microM, respectively. The other nucleotides, GTP, UTP, CTP, ITP, and TTP, were not detected at concentrations less than 0.5 mM. A mixture of 10 microM ATP and 100 microM dATP was examined using the CE apparatus with the flow-type BL detection cell. ATP and dATP were separated using running buffer at pH 10 containing 1 mM phenylboronic acid. The interaction between ATP and phenylboronic acid delayed the migration time of ATP.     

Nucleotide recognition by protonated aminoglycosides

Interactions of protonated forms of kanamycin A with nucleotides and several simple phosphate anions have been studied by potentiometric and NMR titrations. The affinity of kanamycin A to anions is comparable to that observed with other aliphatic polyammonium receptors of similar charge, but it discriminates triphosphate nucleotides with different nucleobases with binding constants following the order GTP?CTP ≈ ATP. Kanamycin A also binds the respective uncharged nucleosides with the same selectivity. Binding of ATP is exothermic with a negative entropic contribution in contrast to what is expected for simple ion pairing. Other tested aminoglycosides, amikacin and streptomycin, bind ATP less efficiently than kanamycin A. Models of structures of kanamycin A complexes with ATP and GTP obtained by molecular mechanics (OPLS-2005) calculations based on ¹H and ³¹P NMR data confirm the possibility of nucleotide discrimination by simultaneous ion pairing of terminal nucleotide phosphate groups with ammonium sites of rings B and C and hydrogen bonding of the nucleobase at the ring A of the aminoglycoside.     

A supramolecular ON-OFF-ON fluorescence assay for selective recognition of GTP

With the objective of developing small molecule based receptors for nucleosides and nucleotides, interactions of a cyclic donor-acceptor conjugate 1 with adenosine, AMP, ADP, CTP, UTP, ITP, ATP, and GTP have been investigated by absorption, steady-state, and time-resolved fluorescence, cyclic voltammetry (CV), NMR, and fluorescence indicator displacement techniques. Titration of 1 with the fluorescent indicator, 8-hydroxy-1,3,6-pyrene trisulfonate (HPTS), resulted in nearly complete fluorescence quenching of HPTS, along with 25% hypochromicity in its absorption spectrum. Benesi-Hildebrand analysis gave a 1:1 stoichiometry for the complex between the receptor 1 and HPTS with an association constant (Kass) of 4.66 x 104 M-1 in buffer. The driving force for such a complexation was evaluated to be the synergistic effects of pi-stacking and electrostatic interactions inside the cavity as confirmed by the effect of ionic strength, temperature, and the negative results obtained with the model compound 2. Titration of the nonfluorescent complex [1.HPTS] with various nucleosides and nucleotides resulted in revival of fluorescence of the indicator, HPTS. It was observed that GTP induces maximum displacement of HPTS from the complex [1.HPTS] with an overall fluorescence enhancement of ca. 150-fold. The addition of adenosine, AMP, ADP, CTP, and UTP showed negligible changes, whereas ca. 45- and 50-fold enhancement was observed with ATP and ITP, respectively. The competitive displacement of the indicator by various analytes is found to be in the order GTP (buffer) approximately GTP (biofluid) > ITP approximately ATP > UTP > CTP approximately ADP approximately AMP approximately Ade. By virtue of having a better pi-electron cloud, GTP undergoes effective electronic, pi-stacking, and electrostatic interactions inside the cavity and forms a stable complex with the receptor 1. The uniqueness of this assay is that it differentiates GTP from ATP and other nucleotides and signals the event through a visual "turn on" fluorescence mechanism in buffer as well as in biological fluids.     

ATP-GTP-BINDING PROTEINS AND ENDOGENOUS ADP-RIBOSYL TRANSFERASE IN Lemna paucicostata 441

Abstract— A crude extract containing membrane components of Lemna paucicostata was treated with 1% Lubrol PX and fractionated by gel nitration. Binding activities to non-hydrolyzable analogues of ATP, [³⁵S]ATPγS (adenosine 5'[;γ-thio]triphosphate) and that of GTP, [³⁵S]GTPγS (guanosine 5'[γ-thiojtriphosphate) were detected in some fractions, and these activities were prevented in the presence of 0.1 mM ATP or GTP. ATP and GTP were 2 to 3 orders of magnitude more effective than CTP or UTP in preventing this binding activity. These fractions showed ATPase and GTPase activities with 1 nM [γ-³²P]ATP or [γ–³²P]GTP substrate. Analyses by sodium dodecyl sulfate polyacrylamide gel electrophoresis of these fractions after binding with [³⁵S]ATPγS or [³⁵S]GTP-γ S revealed that these fractions contained [³⁵S]ATPγS and [³⁵S]GTPγS binding proteins with molecular weights of 53 000 and 60 000, respectively. Both of these proteins were [³²P]ADP-ribosylated by endogenous ADP-ribosyl transferase. Three proteins with molecular weights of 11 000, 12 000 and 13 000 which could bind [³⁵S]ATP7S or [-³⁵S]GTP-γ S were ADP-ribosylated by endogenous ADP-ribosyl transferase. Pertussis toxin stimulated ADP-ribosylation of these proteins. Four proteins with molecular weight of 37 000, 50 000, 80 000 and 115 000 with P^SS]ATP7S and [^,3S]GTP7S binding activities were also detected. The signal transduction of light to underlying clock mechanism in Lemna may be controlled by ATP-GTP-binding proteins and by the ADP-ribosylation of these proteins.     

Bis- and tris-naphthoimidazolium derivatives for the fluorescent recognition of ATP and GTP in 100% aqueous solution

Naphthoimidazolium groups can form unique ionic hydrogen bonds with anions as imidazolium moieties, and in addition, they are fluorescent, so no further elaborative synthesis is needed to introduce a fluorescent group. In this paper, three naphthoimidazolium derivatives were synthesized and studied for the recognition of nucleotides. Compound 1 composed of a single naphthoimidazolium group and quaternary ammonium group did not show any significant fluorescent changes with various anions and nucleotides, such as ATP, GTP, CTP, TTP, UTP, ADP and AMP. A tripodal compound 3 bearing three naphthoimidazolium groups and three quaternary ammonium groups, respectively, showed large fluorescence enhancements with UTP, CTP and TTP and moderate fluorescence enhancements with ATP and pyrophosphate and a fluorescence quenching effect with GTP. On the other hand, compound 2 bearing two naphthoimidazolium groups and two quaternary ammonium groups displayed a selective fluorescence enhancement with ATP and a selective fluorescence quenching effect with GTP in 100% aqueous solution.     

Exploring sites on mitochondrial ATPase for catalysis, regulation, and inhibition.

Evidence is presented that mitochondrial ATPase has two types of sites that bind adenine nucleotides. The catalytic site, C, binds the substrates ATP, GTP, or ITP and the inhibitor guanylyl imidodiphosphate (GMP-PNP). A second type of site, R, binds ATP, ADP, adenylyl imidodiphosphate (AMP-PNP), and the chromium complexes of ATP or ADP. All of these substances binding to the R site inhibit the hydrolysis of ATP in a competitive manner; their inhibition of hydrolysis of ITP and GTP is noncompetitive. GMP-PNP inhibits oxidative phosphorylation in submitochondrial particles but AMP-PNP does not. The localization on mitochondrial membranes of sites for the binding of various antibiotics that inhibit oxidative phosphorylation is discussed.     

Structure effect of nucleotides in terbium(III)—nucleotide fluorescent reaction New evidence for the binding sites of terbium(III) on nucleotides

Upon addition of Tb³⁺ to 16 nucleotides and homopolynucleotides, all of them showed a characteristic green emission from Tb³⁺, but with much different intensity, upon excitation in the aromatic region of bases. The result suggested that nucleotides with at least one carbonyl group in nucleotide bases are better enhancers to the fluorescence of Tb³⁺. The complexes of ATP, GDP and GTP with Tb³⁺ are synthesized as two types of models. Guanine type nucleotides with one carbonyl group in the bases are the best enhancers, while adenine type nucleotides with no carbonyl group in the bases are poorest enhancers to the fluorescence of Tb³⁺. Comparing the IR spectra of ATP, GTP, GDP and their Tb³⁺ complexes suggested that C-6 carbonyl group in GTP and GDP may be involved in complex formation, which may be responsible for the effective energy transfer. This is further supported by comparing the UV spectra of ATP, Poly(A), GTP, and Poly(G) with their Tb³⁺ complexes in water solution.     

A cholic acid-based fluorescent chemosenor for the detection of ATP

A novel ditopic cholic acid-based fluorescent chemosensor for ATP, 1a, was designed and synthesized. Its interactions with phosphates, AMP, ADP, ATP, CTP, GTP, and TTP have been investigated. When ATP was added to a 1:1 aqueous CH3CN solution of the sensor at pH 7.4, a significant decrease in fluorescence of 1a was observed, whereas other guest molecules showed a much smaller effect. The complex between 1a and ATP was confirmed through combined UV, 1H, 13C and 31P NMR spectroscopic methods. The uniqueness of the new sensor is that it binds with ATP 33-124 times more selectively than other nucleotides, as evidenced from the respective binding constants. 1a is a highly sensitive sensing probe; as little as 30 nM ATP can cause 15% fluorescence quenching of the sensor.     

Preparation of a mixture of nucleoside triphosphates suitable for use in synthesis of nucleotide phosphate sugars from ribonucleic acid using nuclease P1, a mixture of nucleoside monophosphokinases and acetate kinase

This paper (1) describes the enzymatic synthesis of a mixture of adenosine, guanosine, cytidine, and uridine triphosphates (ATP, GTP, CTP, and UTP) from ribonucleic acid (RNA). RNA was hydrolyzed by nuclease P1 to a mixture of 5'-nucleoside monophosphates. This mixture was converted to the nucleoside triphosphates using a mixture of nucleoside monophosphate kinases and acetate kinase, with acetyl phosphate as the ultimate phosphoryl donor. The nucleoside monophosphokinases were extracted from brewer's yeast in a four-step procedure. The specific activity of the yeast enzyme preparation after gel permeation chromatography was sufficiently high that the yeast kinases could be immobilized in volumes that were practical for laboratory scale syntheses. Conversions from NMP to NTP in a mixture containing 0.34 mol of total nucleoside phosphates were: ATP, 90%; GTP, 90%; CTP, 60%; and UTP, 40%.     

Fluorescence enhancement of terbium(III) by nucleotides and polyhomonucleotides in the presence of phenanthroline

Summary The fluorescence enhancement of terbium(III) by nucleotides (AMP, ADP, ATP, GMP, GDP, GTP) and polyhomonucleotides [poly(A), poly(G), poly(C), poly(U)] in the presence of phenanthroline (phen) was studied. Investigation of the composition of the terbium(III)/ANP(AMP, ADP, ATP)/phen complexes and conditions of optimization suggest a 1:2 molar ratio of terbium(III) and phen for the ternary complexes. The results showed that the presence of phen enhanced the net fluorescence of terbium(III)/ANP, poly(A), poly(C) or poly(U) from several fold to more than one-hundred fold, while it has little effect on the fluorescence of terbium(III)/GNP(GMP, GDP and GTP) or the poly(G) system. The possibility of spectrofluorimetric measurements of these compounds were studied under optimal conditions (pH 7.0 in tris-HCl buffer; E_x=298 nm, E_m=543.5 nm). The detection limits were 2.0×10^–7, 6.0×10^–7 and 1.0×10^–6 mol/l for AMP, ADP and ATP, respectively. The relative standard deviations (6 replicates) were within 2.0% in the middle of the linear range.     

Characterization of phosphate-containing metabolites by calcium adduction and electron capture dissociation

Several phosphate-containing metabolites, including nicotinamide adenine dinucleotide (NAD), nicotinamide adenine dinucleotide phosphate (NADP), adenosine 5'-diphosphate ribose (ADP-r), adenosine 5'-triphosphate (ATP), and guanosine 5'-triphosphate (GTP), have been characterized with electron capture dissociation (ECD) and sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) tandem mass spectrometry (MS/MS) in positive-ion mode. Calcium complexation was used to successfully produce abundant doubly charged cationic precursor ions with or without hydration. This approach enabled application of ECD to acidic metabolites for the first time. Fragmentation pathways observed in ECD and SORI-CAD of calcium-adducted phosphate-containing metabolites were complementary. Unique fragmentation was observed in ECD compared to SORI-CAD MS/MS, including ribose cross-ring cleavage for NAD and NADP, and generation of hydrated product ions, including cross-ring fragments, for hydrated ATP and GTP. A combination of ECD and CAD appears promising for maximizing structural information about metabolites.     

Using a deoxyribozyme ligase and rolling circle amplification to detect a non-nucleic acid analyte, ATP

An allosteric ribozyme (aptazyme) has been used to transduce the binding of a small organic analyte (ATP) into the ligation of a circular template for rolling circle amplification (RCA). An ATP-activated deoxyribozyme ligase was immobilized on a glass slide and, upon addition of ATP, catalyzed the ligation of a circular padlock probe. The ligated products could be directly amplified and visualized via RCA. The coupled reaction exhibited could detect as little as 1 muM of ATP and could discriminate against structurally similar nucleotides such as GTP, CTP, and UTP. Cooperative ATP activation of the deoxyribozyme was faithfully mimicked by RCA, yielding an amplified "switch" that was responsive to ATP concentration.     

Stabilities and isomeric equilibria in solutions of monomeric metal-ion complexes of guanosine 5'-triphosphate (GTP4-) and inosine 5'-triphosphate (ITP4-) in comparison with those of adenosine 5'-triphosphate (ATP4-)

Under experimental conditions in which the self-association of the purine-nucleoside 5'-triphosphates (PuNTPs) GTP and ITP is negligible, potentiometric pH titrations were carried out to determine the stabilities of the M(H;PuNTP) and M(PuNTP)2-complexes where M2+ = Mg2+, Ca2+, Sr2+. Ba2+, Mn2+, Co2+, Ni2+, Cu2+, Zn2+, or Cd2+ (I = 0.1 M, 25 degrees C). The stabilities of all M(GTP)2- and M(ITP)2- complexes are significantly larger than those of the corresponding complexes formed with pyrimidine-nucleoside 5'-triphosphates (PyNTPs), which had been determined previously under the same conditions. This increased complex stability is attributed, in agreement with previous 1H MNR shift studies, to the formation of macrochelates of the phosphate-coordinated metal ions with N7 of the purine residues. A similar enhanced stability (despite relatively large error limits) was observed for the M(H;PuNTP) complexes, in which H+ is bound to the terminal y-phosphate group, relative to the stability of the M(H;PyNTP)- species. The percentage of the macrochelated isomers in the M(GTP)2- and M(ITP)2- systems was quantified by employing the difference log KMM(PuNTP)-log KMM(PyNTP); the lowest and highest formation degrees of the macrochelates were observed for Mg(ITP)2- and Cu(GTP)2- with 17 +/- 11% and 97 +/- 1%, respectively. From previous studies of M(ATP)2- complexes, it is known that innersphere and outersphere macrochelates may form; that is, in the latter case a water molecule is between N7 and the phosphate-coordinated M2+. Similar conclusions are reached now by comparisons with earlier 1H MNR shift measurements, that is, that Mg(GTP)2- (21 +/- 11%), for example, exists largely in the form of an outersphere macrochelate and Zn(GTP)2- (68 +/- 4%) as an innersphere one. Generally, the overall percentage of macrochelate falls off for a given metal ion in the order M(GTP)2- > M(ITP)2- > M(ATP)2-; this is in accord with the decreasing basicity of N7 and the steric inhibition of the (C6)NH2 group in the adenine residue. Furthermore, although the absolute stability constants of the previously studied M(GMP), M(IMP), and M(AMP) complexes differ by about two to three log units from the present M(PuNTP)2- results, the formation degrees of the macrochelates are astonishingly similar for the two series of nucleotides for a given metal ion and purine-nucleobase residue. The conclusion that N7 of the guanine residue is an especially favored binding site for metal ions is also in accord with observations made for nucleic acids.     

Borate-nucleotide complex formation depends on charge and phosphorylation state

Flow injection analysis with electrospray ionization mass spectrometry was used to investigate borate-nucleotide complex formation. Solutions containing 100 microM nucleotide and 500 microM boric acid in water-acetonitrile-triethylamine (50:50:0.2, v/v/v; pH 10.3) showed that borate complexation with nicotinamide nucleotides was significantly influenced by the charge on the nicotinamide group and the number of phosphate groups on the adenine ribose. Borate binding decreased in the order of NAD(+), NADH, NADP(+) and NADPH. To investigate the relationship between complex formation and phosphorylation, association constants (K(A)) of borate-adenine (AMP, ADP, ATP), -guanine (GMP, GDP, GTP), -cytidine (CMP, CDP, CTP) and -uridine (UMP, UDP, UTP) complexes were compared. The results showed that the number of nucleotide phosphate groups was inversely proportional to the relative abundance of the borate complexes, with the K(A) of borate-nucleotide complex decreasing in the order mono-, di- and tri-phosphates (AMP approximately GMP approximately CMP approximately UMP > ADP approximately GDP approximately CDP approximately UDP > GTP > ATP approximately CTP approximately UTP). At pH 7.4, using ammonium bicarbonate buffer, only borate-NAD(+) complex was observed. This indicates that the borate-NAD(+) complex may be the most physiologically relevant of those studied.