Quantitative determination of the conformation of ATP in aqueous solution using the lanthanide cations as nuclear-magnetic-resonance probes.

Chemical shift perturbations of the eight 1H resonances and of the three 31P resonances in the nuclear magnetic resonance spectra of ATP in 2H2O, pH 6.0, have been induced by specifically bound lanthanide cations Ln3+ (Ln = Pr, Nd, Eu, Yb). After separation of contact (through bond) perturbations the resultant through-space shifts, which are found to have axial symmetry, are used in an analysis of the conformation of the Ln3+ -ATP complex. A computer program was used to search for the conformations of the molecule which fit the nuclear magnetic resonance data. The "best" solutions obtained represent a small closely interrelated family of conformations. Effects of the cation Gd3+ on the longitudinal relaxation rates of five of the protons of ATP were also measured and used to confirm the conformational family. One of these conformations corresponds closely to one of the crystal structure forms, with an anti arrangement of the base-ribose unit and and a right-hand helical phosphate chain folded towards the adenine part of the molecule. The lanthanide ion binds predominantly to the beta and gamma phosphates and does not interact with the purine ring, these two centres being separated by at least one water molecule.     

Self-association of some anthocyanins in neutral aqueous solution

A good contrast in optical properties caused by self-association was found between malvin and cyanin quinonoidal bases. Circular dichroism measurements of the pigments in neutral aqueous solutions show that molecules of the malvin quinonoidal base self-associate quickly and the conformational orientation of the aggregates is opposite to those formed by cyanin quinonoidal bases. Hypsochromism and hypochromism in the visible absorption also occurred on the formation of malvin aggregates. CD comparisons of malvin, hirsutin and 4′-O-methylmalvin suggest that a methoxyl group in the B-ring of the anthocyanidin strongly suppresses self-association. It is proposed that the driving forces for self-association are mainly hydrophobic interactions among the aromatic nuclei stacked parallel to each other which are surrounded by the hydrophilic glucose moieties in a suitable spatial arrangement. Furthermore, the glucose moiety at the 5-position rather than that at the 3-position plays an important role in the self-association of these anthocyanidin 3,5-diglucosides. Addition of sodium chloride promotes self-association and the greater stability of the anthocyanins in solution.     

Recent progress in artificial receptors for phosphate anions in aqueous solution

Phosphate esters exist ubiquitously in nature in the form of nucleoside phosphates (nucleotides) as components of RNA (or DNA), sugar nucleotides for glycosylation of oligosaccharides or proteins, activated form of proteins responding to extracellular signals, and chemical mediators playing central roles in intracellular signaling signals. Phosphorylation of anti-viral nucleoside analogues by intracellular kinases yields nucleoside phosphates (nucleotide) as biologically active forms as anti-viral agents. Development of artificial phosphate receptors would afford new methodologies for detection, separation, or transport of biologically important phosphates. Herein, a recent progress of artificial phosphate receptors is reviewed with special focus on macrocyclic polyamines and their metal complexes as a new prototype. In comparison to most of the previous artificial receptors (most of them are organic molecules), our system characteristically works in aqueous solution at neutral pH with extremely strong affinities with phosphate anions. Moreover, zinc(II)-macrocyclic tetraamine (cyclen) complexes were discovered to selectively bind thymine and uracil, so that nucleotides of these bases are specifically recognized by the bis(Zn2+-cyclen) complexes.     

The behavior of inososes in neutral and basic aqueous solution

N.m.r. spectra (¹H and ¹³C) have shown that, of three inososes studied, the 2,3,4,6/5-isomer exists in solution as the keto form, and the 2,4,6/3,5-isomer is partially, and the 2,3,5/4,6-isomer is almost fully, hydrated. In alkaline solution, each of the inososes rapidly loses a molecule of water, to give trans-2,3,4,5-tetrahydroxy-2-cyclohexen-1-one. On acetylation in the presence of a base, this compound gives tetraacetoxybenzenes; hydrogenation yields several cyclohexanepentols.     

Fluorescence of proteins in aqueous neutral salt solutions. I. Influence of anions

The effects of anions of neutral salts on the fluorescence emission of six proteins as well as on tryptophan and tyrosine were studied in relation to the structure of proteins. Most anions are good quenchers of tryptophyl and tyrosyl fluorescence, free or in proteins. The results with tryptophan and tyrosine indicate involvement of a collisional quenching mechanism due to agreement with Stern–Volmer law. The deactivation of fluorescence probably occurs because of the transition from singlet state to triplet state. Lehrer's modification of Stern–Volmer law was applied to proteins. The effective quenching constants ([K_Q]eff) and the fraction of fluorescence available ([f_a]eff) to the quencher are also calculated. In contrast to its effect on tryptophan, CH₃COO^? quenches tyrosyl fluorescence and ClO₄^? does not. The effects on fluorescence of ribonuclease and free tyrosine are similar and without any changes in emission maximum. The anions are divided into three groups based on the effect they have on tryptophan-containing proteins. (1) NO₃^?, NO₂^?, Br^?, and I^? have high [K_Q]eff values and readily quench tryptophyl fluorescence of proteins causing a shift of emission maximum to a shorter wavelength. This change is due to the specific quenching of “exposed” tryptophan residues which are accessible to quenchers and the observed residual fluorescence is from the “buried” tryptophyls. (2) ClO₄^? and SCN^? also quench fluorescence of tryptophan in proteins and have lower ([K_Q]eff) values. In their presence the fluorescence maximum is shifted to a longer wavelength, which indicates the unfolding of a protein with [(f_a)eff] = 1. (3) Cl^?, CH₃COO^?, and SO₄? do not have a direct effect on the fluorescence of tryptophan. Besides the “direct” effects, “indirect” effects on fluorophors in protein are also seen, pointing out that the neutral salts can interact in more than one manner with proteins. The effectiveness of anions in quenching fluorescence of proteins follows similar sequences which almost resemble the Hofmeister series, viz., SO₄⁼, CH₃COO^? ? Cl^? < ClO₄^? < SCN^? < Br^? < I^? < NO₃^? < NO₂^?.     

Oligonucleotides as probes for studying polymerization reactions in dilute aqueous solution

We have prepared a [³²P]-labeled oligonucleotide probe carrying a free primary amine at its 3′terminus. This probe is used to initiate polymerization of aziridine (ethyleneimine) in aqueous solution. The nature of the oligomeric products and the kinetics of their formation are then monitored by gel electrophoresis. Our results are generally consistent with those obtained using conventional techniques. We have also investigated the effect of polyanionic templates on the rate of oligomerization of aziridine. We find that water-soluble polyanions generally accelerate the polymerization. The sodium salt of polymethacrylic acid is the most effective of the templates that we studied. The methods introduced in this paper should be applicable to a variety of polymerization reactions in aqueous solution. They should greatly simplify the screening of potentially prebiotic polymerization reactions. Correspondence to: L.E. Orgel on sabbatical leave     

Changes in conformation of reduced cytochrome c in neutral aqueous solution.

In neutral aqueous solution, high concentrations of alcohols perturb cytochrome c in such a way that reduction by means of ionizing radiation results in the formation of abnormal conformers of ferrocytochrome c resembling those previously seen on reduction in alkaline solution. These relax to normal ferrocytochrome c in about 0.1 s.     

Time-resolved fluorescent chirality sensing and imaging of malate in aqueous solution

Chiral discrimination of malates in aqueous solutions at near-neutral pH is achieved through fluorescence measurement and imaging using the europium-tetracycline complex (EuTc) as a fluorescent probe. The method is based on the significantly different fluorescence properties of the ternary complexes (Eu-Tc-malate) formed between EuTc and the enantiomeric malates. The enantiomeric excess (ee) of chiral malates can be quantified by both steady-state and time-resolved fluorescence, using either a conventional fluorescence microplate reader or fluorescence imaging. It offers a facile and sensitive method for high-throughput chiral discrimination.     

Nuclear Overhauser effects in aqueous solution as dynamic probes in short linear peptides

The possibility of obtaining interresidue NOEs from short linear peptides in aqueous solution has been investigated from an experimental point of view using peptides of various lengths (namely GGRA, LHRH and RNase S-peptide). It is shown that, provided that long (approximately 800 ms) NOESY mixing times are used, complete sets of sequential alpha N NOEs are obtainable. From the intensities and signs of the observed NOEs, the relative mobilities of different parts of the polypeptide chain can be determined.     

Molecular dynamics simulation of the calmodulin-trifluoperazine complex in aqueous solution

Trifluoperazine (TFP) has been widely studied in relation to its mode of binding and its inactivation of calmodulin (CaM). Most studies in solution have indicated that CaM has two high-affinity binding sites for TFP. The crystal structure of the 1:4 CaM-TFP complex (CaM-4TFP) shows that three TFP molecules bind to the C-domain of CaM, and that one TFP molecule binds to the N-domain. In contrast, the crystal structure of the 1:1 CaM-TFP complex (CaM-1TFP) shows that one TFP molecule binds to the C-domain. It has been thought that the binding of one TFP molecule to the C-domain is followed by binding to the N-domain. The crystal structure of the 1:2 CaM-TFP complex (CaM-2TFP), moreover, has recently been determined, showing that two TFP molecules bind to the C-domain. In order to determine the structure of the CaM-TFP complex and to clarify the interaction between CaM and TFP in solution, we performed a molecular dynamics simulation of the CaM-TFP complex in aqueous solution starting from the CaM-4TFP crystal structure. The obtained solution structure is very similar to the CaM-2TFP crystal structure. The computer simulation showed that the binding ability of the secondary binding site of the C-domain is higher than that of the primary binding site of the N-domain.     

Reversible oxygenation of protoheme-imidazole complex in aqueous solution (1,2)

Solutions of protohemin in aqueous buffer containing imidazole were reduced and exposed to carbon monoxide forming the carbon monoxide-imidazole complex similar to that in carboxyhemoglobin. This complex is stable for long periods in the presence of low pressures of oxygen and thus the standard flash photolysis methods can be used to determine rates of combination of the heme-imidazole complex with oxygen. Combination rates for both carbon monoxide and oxygen are faster than any on rates for hemoglobin and oxygen dissociation rates are also faster. But the equilibrium constant for binding of this isolated site is larger than that for hemoglobin.     

Efficient oligoadenylate synthesis catalyzed by uranyl ion complex in aqueous solution

Polymerization of adenosine-5'-phosphorimidazolide in an aqueous solution was conducted with uranyl ion as a catalyst. Oligoadenylate formation took place efficiently with high regio-selectivity (2'-5' linkage). The oligoadenylates up to hexadecamer were obtained in a high total yield. The chain length and the regio-selectivity of the resulting oligoadenylates varied greatly depending on the concentration of the uranyl ion catalyst. The oligonucleotide formation is likely to be mediated by uranylnucleotide complex.     

A ratiometric fluorescent chemosensor for the detection of cysteine in aqueous solution at neutral pH

A ratiometric fluorescent chemosensor 2‐(2′‐hydroxy‐3′‐formyl‐5′‐methoxyphenyl)benzothiazole ( 1 ) was developed for the detection of cysteine (Cys). In aqueous solution at neutral pH, 1 exhibited a ratiometric fluorescent response to Cys with a remarkable red‐to‐green shift in the emission wavelength. This fluorescence change was attributed to the cyclization reaction between the formyl group in 1 and the amino and sulfhydryl group in Cys in a stoichiometry of 1: 1 according to the proposed mechanism. At neutral pH, 1 displayed a significant fluorescence ratio signal enhancement with the addition of Cys. Furthermore, 1 showed good selectivity toward Cys. The detection limit and linear range were 5.6 and 0–100 μmol/L, respectively, which demonstrated that 1 could recognize relatively low concentrations of Cys and is a good candidate for applications in detecting Cys.     

Closed-tube human leukocyte antigen DQA1∗05 genotyping assay based on switchable lanthanide luminescence probes

Genotyping in closed tube is commonly performed using polymerase chain reaction (PCR) amplification and allele-specific oligonucleotide probes using fluorescence resonance energy transfer (FRET). Here we introduce a homogeneous human leukocyte antigen (HLA)–DQA1∗05 end-point PCR assay based on switchable lanthanide luminescence probe technology and a simple dried blood sample preparation. The switchable probe technology is based on two non-luminescent oligonucleotide probes: one carrying a non-luminescent lanthanide chelate and the other carrying a light-absorbing antenna ligand. Hybridization of the probes in adjacent positions to the target DNA leads to the formation of a highly luminescent lanthanide chelate complex by self-assembly of the reporter molecules. Performance of the HLA–DQA1∗05 assay was evaluated by testing blood samples collected on sample collection cards and was prepared by lysing the punched samples (3-mm discs) using alkaline reaction conditions and high temperature. Testing of 147 blood samples yielded 100% correlation to the heterogeneous DELFIA technology-based reference assay. Genotyping requires carefully designed probe sequences able to discriminate matched and mismatched target sequences by hybridization. Furthermore, definite genotype discrimination was achieved because inherently non-luminescent switchable probes together with time-resolved measurement mode led to very low background signal level and, therefore, very high signal differences averaging 54-fold between DQA1∗05 and other alleles.     

Colorimetric detection of oxalate in aqueous solution by a pyrogallol red‐based Cu2+ complex

The pyrogallol red (PR)‐based Cu²⁺ complex was proven to be an effective and selective colorimetric chemosensing ensemble for recognition of oxalate over other anions in a perfect aqueous solution. The addition of oxalate to the PR–Cu²⁺ complex resulted in a colour change from purple to orange colour due to the regeneration of PR by the chelation of oxalate with Cu²⁺, while other anions did not induce any significant colour change. Moreover, it was revealed that no obvious interference was observed during the titrations with oxalate into each other anion. Therefore, the PR–Cu²⁺ complex can be used as a simple and practical colorimetric chemosensor for detecting oxalate.     

Kinetics of the formation and hydrolysis reactions of some thiomolybdate(VI) anions in aqueous solution

The kinetics of the formation of the thiomolybdate ions MoOS₃²⁻ and MoS₄²⁻ were determined spectroscopically from the addition of excess sulphide to MoO₂S₂²⁻ in pH buffered media (6–8) at 30 °C. The reverse (hydrolysis) reactions of MoO₂S₂²⁻ and MoOS₃²⁻ were measured under the same conditions. The reaction rates measured are shown below:

Values of the rate-constants (s⁻¹) obtained at pH 7.0 were k₁₀ 2.4 × 10⁻³, k₂₁ 1.5 × 10⁻⁵, k₃₀ 2.1 × 10⁻⁵, k₂₃ 6.0 × 10⁻⁴, and k₃₄ 1.9 × 10⁻⁵; where the results are comparable they are in good agreement with those obtained by earlier workers, although different conditions were used. However, in this work it was found that certain reactions had to be mathematically treated as two consecutively occurring reactions. There is also a difference in interpretation of the mechanism of the hydrolysis reactions of the tri- and tetrathio ions. In general the lability towards further S replacement of O atoms, and the reverse reaction, decreased with increased S substitution. All reaction rates increased with increasing H⁺ ion concentration, mostly this was a linear relationship over the limited pH range examined. The effect of the H⁺ ion is interpreted in terms of protonation of the oxythiomolybdate ions at an O atom leading to increased lability.     

Determination of the solution conformation of dephospho coenzyme A by nuclear-magnetic-resonance spectroscopy with lanthanide probes. A method for analysis when more than one complex species is present

The aqueous solution conformation of the 1 : 1 complex of dephospho CoA bound to a lanthanide ion has been determined by examination of the dipolar shift and induced relaxation at pH 6.4. The experimental data are shown to arise from the presence of both 1 : 1 and 1 : 2 metal : ligand complexes and a graphical method is described to divide the experimental data into information corresponding to each of the two species. The formation constants are also derived. For the 1 : 1 complex the ribose is found in a 2E conformation with the adenine base predominantly anti. A small contribution from a syn conformation is evident. The pantoinic acid fragment of the chain is folded back towards the pyrophosphate while the remainder of the chain is extended.     

Mercury(II) complex formation with glutathione in alkaline aqueous solution

The structure and speciation of the complexes formed between mercury(II) ions and glutathione (GSH = L-glutamyl-L-cysteinyl-glycine) have been studied for a series of alkaline aqueous solutions (\( C_{{{\text{Hg}}^{{2 + }}}}\,{\sim18\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}}\) and C _GSH = 40–200 mmol dm^?3 at pH ～10.5) by means of extended X-ray absorption fine structure (EXAFS) and ¹⁹⁹Hg NMR spectroscopy at ambient temperature. The dominant complexes are [Hg(GS)₂]^4? and [Hg(GS)₃]^7?, with mean Hg–S bond distances of 2.32(1) and 2.42(2) Å observed in digonal and trigonal Hg–S coordination, respectively. The proportions of the Hg²⁺–glutathione complexes were evaluated by fitting linear combinations of model EXAFS oscillations representing each species to the experimental EXAFS spectra. The [Hg(GS)₄]^10? complex, with four sulfur atoms coordinated at a mean Hg–S bond distance of 2.52(2) Å, is present in minor amounts (<30%) in solutions containing a large excess of glutathione (C _GSH ≥ 160 mmol dm^?3). Comparable alkaline mercury(II) cysteine (H₂Cys) solutions were also investigated and a reduced tendency to form higher complexes was observed, because the deprotonated amino group of Cys^2? allows the stable [Hg(S,N-Cys)₂]^2? chelate to form. The effect of temperature on the distribution of the Hg²⁺–glutathione complexes was studied by comparing the EXAFS spectra at ambient temperature and at 25 K of a series of glycerol/water (33/67, v/v) frozen glasses with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}} \) and C _GSH = 16–81 mmol dm^?3. Complexes with high Hg–S coordination numbers, [Hg(GS)₃]^7? and [Hg(GS)₄]^10?, became strongly favored when just a moderate excess of glutathione (C _GSH ≥28 mmol dm^?3) was used in the glassy samples, as expected for a stepwise exothermic bond formation. Addition of glycerol had no effect on the Hg(II)–glutathione speciation, as shown by the similarity of the EXAFS spectra obtained at room temperature for two parallel series of Hg(II)-glutathione solutions with \( C_{{{\text{Hg}}^{{2 + }} }} \,{\sim7\,{\rm{mmol}}\,{\rm{{dm^{-3}}}}},\) with and without 33% glycerol. Also, the ¹⁹⁹Hg NMR chemical shifts of a series of ～18 mmol dm^?3 mercury(II) glutathione solutions with 33% glycerol were not significantly different from those of the corresponding series in aqueous solution.     

Antimony(V) complex formation with adenine nucleosides in aqueous solution

Despite the clinical use of pentavalent antimonial drugs for over half a century, their mode of action against leishmaniasis remains poorly understood. In this paper, we investigated the ability of Sb(V) to form in aqueous solution complexes with adenine nucleosides and deoxynucleosides, using circular dichroism (CD) and (1)H and (13)C NMR spectroscopies. We report that the ribonucleosides, adenosine (A) and adenosine monophosphate (AMP), form in water complexes with Sb(V), as evidenced by the changes induced in their CD spectra. On the other hand, 2'-deoxyadenosine (dA) did not show such a change. CD titration of the ribonucleosides with Sb(V) suggests the formation of 1:2 Sb(V)-nucleoside complexes. NMR analysis indicates that Sb(V) binds to the sugar moiety at the 2' position. Furthermore, the incubation of the antimonial drug, meglumine antimonate, with adenosine at 37 degrees C led to the transfer of Sb(V) from its original ligand to the nucleoside molecule, at acidic pH (pH 5), but not at neutral pH (7.2). Our data therefore suggests that the formation of such complexes may take place in vivo within the acidic cell compartments, including the phagolysosome of macrophage in which Leishmania resides.