Conformation of ATP and ADP Molecules in Aqueous Solutions Determined by High-Energy X-ray Diffraction

High-energy X-ray diffraction measurements were carried out at 26 °C for aqueous 1.0, 2.0 and 2.05 mol% disodium adenosine 5′-triphosphate (ATP) and 2.0 and 2.05 mol% disodium adenosine 5′-diphosphate (ADP) solutions in order to obtain direct experimental information on the intramolecular conformations of ATP and ADP molecules in aqueous solutions. Observed interference terms were analyzed in terms of the intramolecular geometry of the ATP and ADP molecules. Dihedral angles between adenine and the ribose group (t ₁), ribose-ring and methylene group of ribose (t ₂), and the methylene group of ribose and triphosphate (or diphosphate) group (t ₃), were determined through the least-squares fitting procedure of the observed interference term.     

三元混配铂(Ⅱ)配合物的稳定性和分子内芳环堆积效应研究

用pH电位滴定法测定了铂(Ⅱ)与核苷酸NTP (NTP为腺苷5′-三磷酸和尿苷5′-三磷酸)和另一芳环系列配体ArL形成的三元混配配合物Pt(ArL)(NTP)n-(ArL=Phen, Bpy和Trp; n=2或3)在水溶液中的稳定常数(I=0.1 mol/L, KNO3; 25℃).用ΔlogKPt比较了二元和三元混配配合物的稳定性差异,认为三元混配配合物稳定性的增加可归因于π-酸与π-碱之间的合作效应和分子内芳环配体的堆积作用.     

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…     

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.     

Enzyme-catalyzed synthesis of nucleoside triphosphates from nucleoside monophosphates

Syntheses of adenosine 5′-triphosphate (ATP) from adenosine 5′-monophosphate (AMP) and ribavirin 5′-triphosphate (RTP) from ribavirin 5′-monophosphate (RMP) (1) were performed using enzymes as catalysts. Synthesis of ATP is based on acetyl phosphate as the phosphate donor, and acetate kinase (Bacillus stearothermophilus, EC 2.7.2.1), adenylate kinase (porcine muscle, EC 2.7.4.3), and inorganic pyrophosphatase (yeast, EC 2.6.1.1) as the catalysts. Three reactions on a 150-mmol scale provided ATP as its barium salt in 82% yield and 67% purity. Synthesis of RTP used phosphoenol pyruvate (PEP) as the phosphate donor, and pyruvate kinase (rabbit muscle, EC 2.7.1.40) and adenylate kinase (rabbit muscle) as the catalysts. A gram-scale reaction provided RTP as its barium salt in 93% yield and 97% purity. This work demonstrates the utility of the autoxidationresistant acetate kinase fromB. stearothermophilus, the value of pyrophosphatase in controlling the level of pyrophosphate in the reactions and the ability of adenylate kinase to accept at least one substrate other than a derivative of adenosine.     

Equilibre Ester Phosphorique,Hydroxyphosphorane Role des Liaisons Hydrogene,Acidite de Bronsted

A phosphoric ester elaborated from two butyltartrate moeities exists in solution as phosphoric ester because of intramolecular hydrogen bonds. In presence of triethylamine, it turns into the triethylammonium salt of its isomeric hydroxyspirophosphorane. Its pKa has been determined by titrimetry followed by potentiometry, in solution in DMF or (and) DMSO. Its values (7.4 and 4.4 respectively) correspond to an acid more dissociated than carboxylic acids. All these results have been rationalized by semiempiric quantic calculations.     

Oligonucleotides and nucleotidylpeptides. XXXII. Synthesis and hydrolytic stability of amino acid derivatives of adenosine 5′-di(tri)phosphates

The synthesis has been effected of the ethyl esters of adenosine-5′-diphospho-(P_β→N)-and adenosine-5′-triphospho(P_γ→N)-alanine. It has been shown that under the conditions of synthesis the serine analogues of ATP and ADP decompose. An investigation of the hydrolytic stability of the compounds synthesized has shown that they are unstable in acid and alkaline media. In an acid medium the phosphoramide bond is cleaved more rapidly than the phosphoric anhydride bond (in the case of the ADP analogue), while in an alkaline medium the ester bond is saponified and the phosphoric anhydride bond is cleaved. The ATP analogue is more labile both in acid and in alkaline media.     

Convenient syntheses of adenosine 5′-diphosphate,adenosine 5′-methylenediphosphonate,and adenosine 5′-triphosphate

Adenosine 5′-tosylate is converted to adenosine 5′-diphosphate (ADP), adenosine 5′-methylenediphosphonate, and adenosine 5′-triphosphate (ATP) in good yields by direct displacement with the appropriate inorganic salt.     

Highly selective recognition of adenosine 5′-triphosphate against other nucleosides triphosphate with a luminescent metal-organic framework of [Zn（BDC）（H2O）2]n（BDC = 1,4-benzenedicarboxylate）

Selective recognition of adenosine 5′-triphosphate(ATP)is of great significance owing to its indispensable functions to organisms.Also,it is a challenging task because other nucleosides triphosphate hold the same triphosphate group and structurally planar bases as ATP.It is known that metal-organic frameworks(MOFs)are a new type of sensing material.In this work,highly selective recognition of ATP against other nucleosides triphosphate is successfully achieved with a luminescent MOF of[Zn(BDC)(H2O)2]n(BDC2=1,4-benzenedicarboxylate).[Zn(BDC)(H2O)2]n dispersed in water shows a remarkable redshift of the emission wavelength upon addition of ATP,while cytidine 5′-triphosphate(CTP),uridine 5′-triphosphate(UTP),and guanosine 5′-triphosphate(GTP),as well as some inorganic anions such as P2O74 or PO43 can’t induce such spectral change as ATP.1H NMR,31P NMR and Raman spectra indicate that both-stacking interactions and the coordination of Zn(II)with adenine and the phosphate group are involved in the interaction of[Zn(BDC)(H2O)2]n with ATP.In addition,the experimental results showed that the redshift extent of the emission wavelength of[Zn(BDC)(H2O)2]n has the linear relationship with the concentration of ATP in the range of 0.3–1.8 mmol/L.Based on this,the detection of ATP content in the sample of ATP injection was made with satisfactory results.This system pioneers the application of MOFs in the recognition of nucleotides,and testifies that the participation of base in the recognition process can improve the selectivity against the other nucleotides.     

脱铁伴清蛋白两结合位点不同酪氨酸氢键的特性

The interaction of gallium（Ⅲ） with the ligands containing phenolic group（s）, such as salicylic acid, 8-hydroxyquinoline, N,N＇-bis（2-hydroxybenzyl）ethylenediamine-N,N＇diacetic acid （HBED）, N,N＇-ethylenebis[2-（o- hydroxyphenyl）glycine （EHPG）, and ovotransferrin, was studied, respectively, by means of fluorescence in 0.01 mol/L Hepes at pH 7.4 and room temperature. Fluorescence intensity showed an increase when gallium（Ⅲ） was bound to 8-hydroxyquinoline and HBED. In contrast, it was decreased with the interaction of gallium（Ⅲ） with salicylic acid and EHPG. At pH 7.4, there was N…H-O type intramolecular hydrogen bond in the former, and the latter existed O…H-O type intramolecular hydrogen bond. Fluorescence titration of apoovotransferrin with gallium（Ⅲ） displayed that the fluorescence intensity was decreased at the N-terminal binding site, while enhanced at the C-terminal binding site. It can account for the O…H-O type intramolecular hydrogen bonds for the phenolic groups of Tyr92 and Tyr191 residues at the N-terminal binding site. And there are N…H-O type intramolecular hydrogen bonds for Tyr431 and Tyr524 residues at the C-terminal binding site. In addition, under the same conditions, the conditional binding constant of gallium（Ⅲ） with EHPG or HBED determined by fluorescence method is lg KGa-EHPG=19.18 or lg KGa-HBED= 19.08.     

Effect of peracylation of beta-cyclodextrin on the molecular structure and on the formation of inclusion complexes: an X-ray study.

The molecular structures of peracylated beta-cyclodextrins (CDs)--heptakis(2,3,6-tri-O-acetyl)-beta-CD (TA), heptakis(2,3,6-tri-O-propanoyl)-beta-CD (TP), and heptakis(2,3,6-tri-O-butanoyl)-beta-CD (TB)--have been determined by single crystal X-ray structure analysis. Due to the lack of O2...O3' hydrogen bonds between adjacent glucose units of the peracylated CDs, the macrocycles are elliptically distorted into nonplanar boat-shaped structures. The glucose units are tilted with respect to the O4 plane to relieve steric hindrance between adjacent acyl chains. In TB, all glucose units adopt the common (4)C(1)-chair conformation and one butanoyl chain intramolecularly penetrates the cavity, whereas, in TA and TP, one glucose unit each occurs in (O)S(2)-skew-boat conformation and one acyl chain closes the O6 side like a lid. In each of the three homologous molecules the intramolecular self-inclusion and lidlike orientation of acyl chains forces the associated O5-C5-C6-O6 torsion angle into a trans-conformation never observed before for unsubstituted CD; the inclusion behavior of TA, TP, and TB in solution has been studied by circular dichroism spectroscopy with the drug molsidomine and several organic compounds. No inclusion complexes are formed, which is attributed to the intramolecular closure of the molecular cavity by one of the acyl chains.     

Nucleoside und Nucleotide. Teil 15. Synthese von Desoxyribonucleosid-monophosphaten und -triphosphaten mit 2(1H)-Pyrimidinon, 2(1H)-Pyridinon und 4-Amino-2(1H)-pyridinon als Basen

Nucleosides and Nucleotide. Part 15. Synthesis of Deoxyribonucleoside Monophosphates and Triphosphates with 2(1H)-Pyrimidinone, 2(1H)-Pyridinone and 4-Amino-2(1H)-pyridinone as the Bases The phosphorylation of the modified nucleosides 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyrimidinone (M_d, 4 ), 4-amino-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone (Z_d, 6 ) and the synthesis of 1–2′-deoxy-β-D -ribofuranosyl-2(1 H)-pyrimidinone-5′-O-triphosphate (pppM_d, 1 ), 1-(2′-deoxy-β-D ribofuranosyl)-2(1 H)-pyridinone-5′-O-triphosphate (pppII_d, 2 ), and 4-amino-1-(2′-deoxy-βD -ribofuranosyl)-2(1 H)-pyridinone-5′-O-triphosphate (pppZ_d, 3 ) are described. The nucleoside-5′-monophosphates pM_d (5) and pZ_d (7) were obtained by selective phosphorylation of M_d (4) and Z_d (6) , respectively, using phosphorylchloride in triethyl phosphate or in acetonitril. The reaction of pM_d (5) pII _d (8) or pZ_d (7) with morpholine in the presence of DCC led to the phosphoric amides 9, 10 and 11 , respectively, which were converted with tributylammonium pyrophosphate in dried dimethylsulfoxide to the nucleoside-5′triphosphates 1, 2 and 3 , respectively.     

A Novel Fluorescent Probe for Lead Ions

A new fluorescent probe for lead ions, p-nitrophenyl 3H-phenoxazin-3-one-7-yl phosphoric acid (NPPA), has been synthesized by linking resorufLn (serving as a fluorophore and electron acceptor) to p-nitrophenol (serving as a fluorescence quencher and electron donor) through phosphodiester bonds. When NPPA was irradiated with light, intramolecular fluorescence self-quenching took place due to the PET (photoinduced electron transfer) from the donor to the acceptor. However, upon addition of Pb^Ⅱ, the phosphate ester bonds in the probe were cleaved and the fluorophore was released, accompanying the retrievement of fluorescence.     

On the Position of the Intramolecular Equilibrium between Opened and Aromatic-Ring Stacked Forms in Ternary Complexes Composed of Adenosine 5′-triphosphate,Mg2+ or Zn2+, and L-Tryptophanate,and in Related Ternary Systems

The intramolecular and dimensionless equilibrium constant, K′, for the equilibrium between open and aromatic-ring stacked isomers of ternary complexes formed between adenosine 5′-triphosphate, inosine 5′-triphosphate, or uridine 5′-triphosphate, Mg²⁺ or Zn²⁺, and L -tryptophanate, 2,2′-bipyridyl (bipy), or 1,10-phenanthroline (phen) have been estimated by ¹H-NMR. shift measurements in D₂O (I = 0.1M , NaNO₃; 27°). The approximate equilibrium constants K′ are ≥ 20, ≥ 20, 1.2, 0.9, 0.7, 0.5, and 0.3 for the ternary complexes Zn (phen) (ATP)^2?, Mg (phen) (ATP)^2?, Zn (bipy) (ATP)^2?, Zn (bipy) (ITP)^2?, Zn (bipy) (UTP)^2?, Zn (trp) (ATO) ^3?, and Mg (trp) (ATP)^3?, respectively. The percentages of the stacked isomers decrease in the order Zn (phen) (ATP)^2? (≥ 95%) ? Zn (bipy) (ATP)^2? (55%) > Zn (bipy) (ITP)^2? (48%) > Zn (bipy) (UTP)^2? (～ 40%), which coincides with the order of stability of the binary metal-free adducts (phen) (ATP)^4? > (bipy) (ATP)^4? ? (bipy) (ITP)^4? > (bipy) (UTP)^4?; the corresponding stability constants are K = 28.2 ± 4.7, 8.1 ± 2.6, 8.8 ± 1.8, and ～ 1 (M ^?1), respectively (D₂O; I = 0.1 M , NaNO₃; 27°): these series reflect the decreasing size of the aromatic-ring systems forming the stacks. The indole moiety of tryptophan resembles 2,2′-bipyridyl rather than 1,10-phenanthroline and K = 6.2 ± 1.8 M ^?1 for (trp) (ATP)^4?. Implications with respect to the stability of ternary complexes, and to biological systems are indicated briefly.     

Molecular dynamics of (Z)-1-(2-hydroxy-5-methyl-3-nitrophenyl)ethanone oxime and (E)-2-hydroxy-5-methylacetophenone thiosemicarbazone in solution studied by NMR spectroscopy

The formation of hydrogen bonds and the molecular dynamics for molecules (Z)-1-(2-hydroxy-5-methyl-3-nitrophenyl)ethanone oxime and (E)-2-hydroxy-5-methylacetophenone thiosemicarbazone, (E)-4-bromoacetophenone thiosemicarbazone have been investigated in solution using NMR. The results confirm the formation of different O-H…O type intramolecular hydrogen bonds in the oxime molecule. The rotational barrier energy and energy of intramolecular hydrogen bonds have been determined.     

In silico studies of 1,3(R):2,4(S)‐dibenzylidene‐D‐sorbitol as a gelator for polypropylene

The organic gelator 1,3(R):2,4(S)‐dibenzylidene‐D‐sorbitol (DBS) self‐organizes to form a 3‐D network at relatively low concentrations in a variety of nonpolar organic solvents and polymer melt. In this work, we have investigated the interactions between DBS molecules in polypropylene (PP) by molecular modeling. We have used quantum mechanics to elucidate the preferred geometry of one molecule and a dimer of DBS, and molecular mechanics and molecular dynamics to simulate pure DBS, pure PP, and mixture of DBS and PP as condensed phases, at various temperatures. It was found that inter‐ and intramolecular H‐bonds between DBS molecules are formed in PP in a much more pronounced manner than those formed in pure DBS. The most significant intermolecular H‐bonds are formed between the terminal hydroxyl groups. The most significant intramolecular H‐bonds are formed between O5 /H‐O6 groups. Due to the H‐bonds, DBS molecules form a rigid structure similar to liquid crystal forming molecules, which might explain their tendency to create nanofibrils. It seems that the aromatic rings do not contribute significantly to the intermolecular interactions. Their main role is probably to stiff the molecular structure. Temperature dependences of inter‐ and intramolecular interactions are different. Whereas intermolecular interactions peak heights decrease when temperature increases for pure DBS, the intramolecular interaction almost does not change. Copyright © 2012 John Wiley & Sons, Ltd.     

Conformational structures and vibrational spectra of isolated pyrimidine nucleosides: Fourier transform infrared matrix isolation study of 2-deoxyuridine

The conformational structures of 2-deoxyuridine (dU) were investigated using Fourier transform infrared (FTIR) matrix isolation spectroscopy. For the first time the FTIR spectra of dU in Ar matrices were obtained in the range 4000-200 cm(-1). The stabilities of conformers were estimated by the methods HF/3-21G (p), HF/6-31G (d,p) and MP2/6-31G (d,p). Ab initio calculations of the infrared spectra were performed by the methods HF/3-21G (p) and HF/6-31G (d,p). The actual occupancy of conformational isomers in matrix samples was determined. It was shown that anti-conformers of dU are dominant. The ribose rings of the main anti-conformers dU _a0, dU _a1 are in the C2'-endo conformation, but the ribose rings of minor anti-conformers dU_a2, dU_a3 have the C3'-endo conformation, stabilized by intramolecular hydrogen bonds O3'H...O5' and O5'H...O3', accordingly. Syn-conformers of dU are stabilized by the intramolecular hydrogen bond O5'H...O2 and the dominant conformation of the ribose ring is C2'-endo.     

Stepwise conformational transition of crystalline disodium adenosine 5′-triphosphate with relative humidity as studied by high resolution solid state 13C and 31P NMR

Stepwise conformational transition of disodium adenosine 5′-triphosphate (Na₂ATP) crystals as a function of relative humidity (RH), was examined by means of high resolution solid state NMR spectroscopy. The presence of two types of molecules, A and B, with altered conformations in an asymmetric unit, is evident from both ³¹P and ¹³C NMR spectra, irrespective of the three different crystalline forms, mono-, di- and trihydrates, in which, cell parameters changed linearly with RH. Hydration-dependent conformational transition from the monohydrate (RH 0–10%) through dihydrate (20–40%) to trihydrate (60–90%), was well monitored by stepwise upfield displacements of the C1′ ¹³C signals of ribose moiety (molecule B), although, the corresponding peak for the molecule A, is almost unchanged. This means that, adaptation of stepwise structural transitions to the linear expansion of cell parameters is almost entirely ascribed to the conformational readjustment of the molecule B, together with varying proportion of two types of hydrate forms, at the RH range of 20–40%. We consider that, small clusters or thin layers are formed in the beginning of the transition and subsequently, the number of them, rather than the size or thickness increases, because the phosphorous spin–lattice relaxation times, T₁^P, for the three phosphorous nuclei, including those of mixed state, of the two hydrate forms, turned out to be similar due to sufficient fast spin diffusion rates among them. Since only one direction of the cell parameters is changed, as determined by the previous X-ray diffraction study, we conclude that thin layer type micro crystals might be produced during the stepwise transition. Further, it was found that, these molecules acquired motional flexibility mainly at the bound water molecules, together with increased relative humidity, as determined by a variety of relaxation parameters.     

A study of the binding of manganese (II) with the sodium salts of nucleosides in aqueous solutions by the13C NMR method

The binding of manganese(II) with nucleosides — adenosine (A), guanosine (G), cytidine (C), and uridine (U) — in an alkaline D₂O solution has been investigated by the¹³C NMR method. It has been established that the structure of the paramagnetic Mn(II)—nucleoside complexes differs substantially in neutral and in alkaline media. The broadening of the resonance lines (C-2′, C-3′ > C-1′, C-4′ > C-5′) shows the localization of the Mn(II) in the C-2′ and C-3′ hydroxyls of the ribose in an alkaline medium. It has been shown for the case of U that the degree of complex-formation depends on the pH of the solution. It is assumed that the nucleoside forms intramolecular complexes (I) with Mn(OH)₂.     

Intramolecular oxidative coupling of 3-indolylarylketones with Pd(II)-catalysis under air: convenient access to indenoindolones

A Pd-catalyzed method has been developed for the intramolecular oxidative coupling of 3-indolylarylketones under open air as terminal oxidant toward the synthesis of indeno[1,2-b]indol-10(5H)-ones. This reaction represents an intramolecular coupling with dual activation of C-H bonds for electron-deficient arenes, while such reactions are common for electron-rich arenes. Pd(II)-catalysis with pivalic acid as co-catalyst has been found to be crucial. The reaction undergoes without indole N-H-protection.