Aqueous Hydration of Nucleic Acid Constituents: Monte Carlo Computer Simulation Studies

Abstract

Monte Carlo computer simulations were performed on dilute aqueous solutions of thymine, cytosine, uracil, adenine, guanine, the dimethyl phosphate anion in the gauche-gauche conformation and a ribose and deoxyribose derivative. The aqueous hydration of each molecule was analysed in terms of quasi-component distribution functions based on the Proximity Criterion, and partitioned into hydrophobic, hydrophilic and ionic contributions. Color stereo views of selected hydration complexes are also presented. A preliminary discussion of the transferability of functional group coordination numbers is given. The results enable to comment on two current problems related to the hydration of nucleic acids: a) the theory of Dickerson and coworkers on the role of water in the relative stability of the A and B forms of DNA and b) the idea of water bridges and filaments emerging from the computer simulation results on the hydration of DNA fragments by Clementi.     

Scorpion toxins that block T-type Ca2+ channels in spermatogenic cells inhibit the sperm acrosome reaction

The acrosome reaction (AR) is a Ca(2+)-dependent event required for sperm to fertilize the egg. The activation of T-type voltage-gated Ca(2+) channels plays a key role in the induction of this process. This report describes the actions of two toxins from the scorpion Parabuthus granulatus named kurtoxin-like I and II (KLI and KLII, respectively) on sperm Ca(2+) channels. Both toxins decrease T-type Ca(2+) channel activity in mouse spermatogenic cells and inhibit the AR in mature sperm. Saturating concentrations of the toxins inhibited at most approximately 70% of the whole-cell Ca(2+) current, suggesting the presence of a toxin-resistant component. In addition, both toxins inhibited approximately 60% of the AR, which is consistent with the participation of T-type Ca(2+) channels in the sperm AR.     

Nature of the Stacking of Nucleic Acid Bases in Water: a Monte Carlo Simulation

Abstract

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.     

Properties of a Zn2+-glycerophosphocholine cholinephosphodiesterase from bovine brain membranes

A Zn²⁺-glycerophosphocholine cholinephosphodiesterase was purified with a specific activity of 4.6 μmole/min·mg protein from bovine brain membranes by procedures involving PI-PLC solubilization, concanavalin A affinity chromatography, CM-sephadex chromatography and Sephadex G-150 chromatography. Based on molecular weight determination gel chromatography and SDS polyacrylamide gel electrophoresis, the phosphodiesterase activity appears to be a dimeric protein (110 kDa) composed of two subunits with a molecular weight of approximately 54 kDa. The Km value for p-nitrophenylphosphocholine and the optimum pH were found to be 16 μM and pH 10.5, respectively. The phosphodiesterase was inhibited by Cu²⁺, but not the other divalent metal ions. The activity of the apoenzyme was remarkably activated by Co²⁺ or Zn²⁺, but not Mn²⁺ or Mg²⁺. In addition, the inactivation of the enzyme in glycine buffer was prevented by Mn²⁺ or Zn²⁺, but not Co²⁺ or Mg². In a separate experiment, comparing properties of the purified and membrane-bound phosphodiesterases, the forms of two enzymes were quite similar except in stability. Both enzymes were more stable at pH 7.4 than pH 5 or 10. However, the membrane-bound enzyme was more stable than the soluble enzyme at all three pHs. These data suggest that the activity of the phosphodiesterase may be stabilized in-vivo.     

Two new scorpion toxins that target voltage-gated Ca2+ and Na+ channels

This report describes the isolation, primary structure determination, and functional characterization of two similar toxins from the scorpion Parabuthus granulatus named kurtoxin-like I and II (KLI and KLII, respectively). KLII from P. granulatus is identical to kurtoxin from Parabuthus transvaalicus (a 63 amino-acid long toxin) whereas KLI is a new peptide containing 62 amino acid residues closely packed by four disulfide bridges with a molecular mass of 7244. Functional assays showed that both toxins, KLI and kurtoxin from P. granulatus, potently inhibit native voltage-gated T-type Ca(2+) channel activity in mouse male germ cells. In addition, KLI was shown to significantly affect the gating mechanisms of recombinant Na(+) channels and weakly block alpha(1)3.3Ca(V) channels expressed in Xenopus oocytes. KLI and kurtoxin from P. granulatus represent new probes to study the role of ion channels in germ cells, as well as in cardiac and neural tissue.     

Biosorption Performance of Multimetal Resistant Fungus Penicillium chrysogenum XJ-1 for Removal of Cu2+ and Cr6+ from Aqueous Solutions

Adsorption for heavy metals via biomaterials such as fungal biomass presents a practical remediation technique for polluted water. Among all known filamentous fungi, Penicillium chrysogenum is widespread in nature and can serve as a biosorbent for heavy metals. In the current study, the ability of P. chrysogenum XJ-1 to remove copper (Cu²⁺) and chromium (Cr⁶⁺) from water was evaluated. The maximum biosorption capacity of XJ-1 for Cu²⁺ reached 42.83 ± 0.57 mg g^?1 dry biomass at pH 5.0 after the equilibrium time of 1.5 h. The maximum biosorption capacity for Cr⁶⁺ at pH 3.0 reached 52.69 ± 1.68 mg g^?1 dry biomass after the equilibrium time of 1.5 h. The biosorption data of XJ-1 biomass were well fitted to the Freundlich isotherm model and the pseudo-second-order Lagergren kinetic model. Laundry powder-treated and HCl-treated XJ-1 biomass significantly enhanced its adsorption capacity to Cu²⁺ and Cr⁶⁺, respectively. HCl and NaOH were suitable desorbents for Cu²⁺/Cr⁶⁺ loading biomass, respectively. Fourier transform infrared spectroscopy analyses revealed that hydroxyl, amine, and sulfonyl groups on the biosorbent contributed to binding Cu²⁺ and Cr⁶⁺ and that carbonyl and carboxyl groups were also vital binding sites of Cu²⁺. Scanning electron microscopy and energy-dispersive x-ray (SEM-EDX) analyses confirmed that considerable amounts of metals were precipitated on the cell surface of XJ-1. Our results suggested that XJ-1 might be used to purify multimetal-contaminated water. This low-cost and eco-friendly biomass of XJ-1 seems to have a broad use in the restoration of metal-contaminated water.     

Preconcentration with Bacillus subtilis–Immobilized Amberlite XAD-16: Determination of Cu2+ and Ni2+ in River,Soil, and Vegetable Samples

Solid-phase extraction (SPE) method was developed for the preconcentration of Cu²⁺ and Ni²⁺ before their determination by inductively coupled plasma optical emission spectrometry (ICP-OES). Bacillus subtilis–immobilized Amberlite XAD-16 was used as biosorbent. Effects of critical parameters such as pH, flow rate of samples, amount of Amberlite XAD-16 and biosorbent, sample volume, eluent type, and volume and concentration of eluent on column preconcentration of Cu²⁺ and Ni²⁺ were optimized. Applicability of the method was validated through the analysis of the certified reference tea sample (NCS ZC73014). Sensitivity of ICP-OES was improved by 36.4-fold for Cu²⁺ and 38.0-fold for Ni²⁺ by SPE-ICP-OES method. Limit of quantitation (LOQ) was found to be 0.7 and 1.1 ng/ml for Cu²⁺ and Ni²⁺, respectively. Concentrations of Cu²⁺ and Ni²⁺ were determined by ICP-OES after application of developed method. Relative standard deviations (RSDs) were lower than 4.9% for Cu²⁺ and 7.9% for Ni²⁺. The Tigris River that irrigates a large agricultural part of Southeast Turkey is polluted by domestic and industrial wastes. Concentrations of Cu²⁺ and Ni²⁺ were determined in water, soil, and some edible vegetables as a biomonitor for heavy metal pollution.     

Purification and partial characterization of a novel phosphodiesterase from the venom of Trimeresurus stejnegeri: inhibition of platelet aggregation

The phosphodiesterases (PDEs) are a superfamily of enzymes that have multiple roles in extracellular nucleotide metabolism and in the regulation of nucleotide-based intercellular signaling. Here we describe for the first time the isolation and partial characterization of a novel phosphodiesterase from Trimeresurus stejnegeri venom, named TS-PDE, using ion exchange and gel filtration chromatography. The purified TS-PDE is shown to be homogeneous as judged by SDS-PAGE and capillary isoelectric focusing. TS-PDE is a glycoprotein which contains 2.48% carbohydrate. Unlike other PDEs which are usually single polypeptide chain proteins with isoelectric points between 7.5 and 10.5, TS-PDE is a disulfide-linked heterodimer with an isoelectric point of 5.1 and a molecular mass of 100 kDa. The N-terminal amino acids of two chains are valine and serine, respectively. Furthermore, among all identified PDEs, only TS-PDE contains both of endogenous Cu²⁺ and Zn²⁺ which are essential for its phosphodiesterase activity. The purified TS-PDE exhibits broad phosphodiesterase substrate range with the order of specificity: nicotinamide guanine dinucleotide > ATP > nicotinamide adenine dinucleotide > ADP. The purified TS-PDE shows an exonuclease activity and no contamination with either alkaline phosphatase or 5′-nucleotidase activity. TS-PDE strongly inhibits ADP-induced platelet aggregation in human platelet-rich plasma by hydrolyzing ADP. Altogether, these results indicate that the novel TS-PDE is a unique phosphodiesterase with different structure from the known PDEs.     

The whole hexapeptide repeats domain from avian PrP displays untypical hallmarks in aspect of the Cu2+ complexes formation

Prions, the infectious agents responsible for the transmissible spongiform encephalopathies (TSEs) have defied full characterization for decades. Although the interactions of Cu(2+) ions with PrP both in vivo and in vitro are well documented, there are still a lot of ambiguities concerning the biological and chemical nature of these effects. In this work, we have investigated the interactions of Cu(2+) ions with whole repeat region of the copper-binding domain (hexapeptide repeats) of chicken PrP. Our results provide explanations for the structural and chemical basis of the specific interactions of Cu(2+) ions with the hexapeptide repeat region. Furthermore, we show that SOD-like activity depends on Cu(2+) complexes.     

维生素C抑制低密度脂蛋白的氧化修饰

研究了不同浓度维生素 C 对 Cu²⁺诱导的低密度脂蛋白(LDL)氧化修饰的抑制作用,通过测定硫代巴比妥酸反应物质(TBARS),荧光物质(lipofusion)扫描及琼脂糖电泳,显示一定浓度的维生素 C 在24h 内对 LDL 的氧化修饰具有抑制作用,并呈现量效效应.提示维生素 C 作为体内存在的一种抗氧化物,可抑制 LDL的氧化修饰,从而在防治动脉粥样硬化的发生具有一定意义.     

A positive charge at the N-terminal segment of Discrepin increases the blocking effect of K channels responsible for the IA currents in cerebellum granular cells

Discrepin is a scorpion peptide that blocks preferentially the I_A currents of the voltage-dependent K⁺ channel of rat cerebellum granular cells. It was isolated from the venom of the buthid scorpion Tityus discrepans and contains 38 amino acid residues with a pyroglutamic acid at the N-terminal site. Discrepin has the lowest sequence identity (approx. 50%) among the six members of the α-KTx15 sub-family of scorpion toxins. In order to find out which residues are important for the blocking effects of Discrepin, six mutants were chemically synthesized (V6K, I19R, D20K, T35V, I19R-D20K, I19R-D20K-R21V), correctly folded and their physiological properties were examined. Substitution of residues V6 and D20 for basically charged amino acids increases the blocking activity of Discrepin, specially the mutation V6K at the N-terminal segment of the toxin. Analysis of 3D-structure models of the mutants V6K and D20K supports the idea that basic residues improve their blocking activities, similarly to what happens with BmTx3, a toxic peptide obtained from Buthus martensi scorpion, which has the highest known blocking effects of I_A currents in K⁺ channels of rat cerebellum granular cells.     

Mono- and bis-N-functionalised cyclen with benzimidazolylmethyl pendant arms: Sensitive and selective fluorescent probes for zinc and copper ions

The Zn²⁺ and Cu²⁺ complexes of L¹ and L² ligands (L¹: 1-(benzimidazol-2-ylmethyl)-1,4,7,10-tetraazacyclododecane, L²: 1,7-bis(benzimidazol-2-ylmethyl)-1,4,7,10-tetraazacyclododecane) were synthesised and characterised by means of NMR, EPR, and UV-Vis spectroscopies, X-ray determination and molecular modelisation (HF-DFT(B3LYP)/LANL2DZ). These studies showed that the 1:1 complexes were formed in which the benzimidazole arm(s) are coordinated to the metal ion. On addition of successive amounts of Zn²⁺ in CH₃CN, the fluorescence emission of L¹ increased linearly by a factor of 50 and the one of L² by a factor of 5 while on addition of successive amounts of Cu²⁺ in CH₃CN, the fluorescence emission of L² decreased linearly to 80% of its initial value.     

Pro-sequence and Ca2+-binding: implications for folding and maturation of Ntn-hydrolase penicillin amidase from E. coli

Penicillin amidase (PA) is a bacterial periplasmic enzyme synthesized as a pre-pro-PA precursor. The pre-sequence mediates membrane translocation. The intramolecular pro-sequence is expressed along with the A and B chains but is rapidly removed in an autocatalytic manner. In extensive studies we show here that the pro-peptide is required for the correct folding of PA. Pro-PA and PA unfold via a biphasic transition that is more pronounced in the case of PA. According to size-exclusion chromatography and limited proteolysis experiments, the inflection observed in the equilibrium unfolding curves corresponds to an intermediate in which the N-terminal domain (A-chain) still possesses native-like topology, whereas the B-chain is unfolded to a large extent. In a series of in vitro experiments with a slow processing mutant pro-PA, we show that the pro-sequence in cis functions as a folding catalyst and accelerates the folding rate by seven orders of magnitude. In the absence of the pro-domain the PA refolds to a stable inactive molten globule intermediate that has native-like secondary but little tertiary structure. The pro-sequence of the homologous Alcaligenes faecalis PA can facilitate the folding of the hydrolase domain of Escherichia coli PA when added in trans (as a separate polypeptide chain). The isolated pro-sequence has a random structure in solution. However, difference circular dichroism spectra of native PA and native PA with pro-peptide added in trans suggest that the pro-sequence adopts an alpha-helical conformation in the context of the mature PA molecule. Furthermore, our results establish that Ca2+, found in the crystal structure, is not directly involved in the folding process. The cation shifts the equilibrium towards the native state and facilitates the autocatalytic processing of the pro-peptide.     

Calcium and copper transport ATPases: analogies and diversities in transduction and signaling mechanisms

The calcium transport ATPase and the copper transport ATPase are members of the P-ATPase family and retain an analogous catalytic mechanism for ATP utilization, including intermediate phosphoryl transfer to a conserved aspartyl residue, vectorial displacement of bound cation, and final hydrolytic cleavage of Pi. Both ATPases undergo protein conformational changes concomitant with catalytic events. Yet, the two ATPases are prototypes of different features with regard to transduction and signaling mechanisms. The calcium ATPase resides stably on membranes delimiting cellular compartments, acquires free Ca²⁺ with high affinity on one side of the membrane, and releases the bound Ca²⁺ on the other side of the membrane to yield a high free Ca²⁺ gradient. These features are a basic requirement for cellular Ca²⁺ signaling mechanisms. On the other hand, the copper ATPase acquires copper through exchange with donor proteins, and undergoes intracellular trafficking to deliver copper to acceptor proteins. In addition to the cation transport site and the conserved aspartate undergoing catalytic phosphorylation, the copper ATPase has copper binding regulatory sites on a unique N-terminal protein extension, and has also serine residues undergoing kinase assisted phosphorylation. These additional features are involved in the mechanism of copper ATPase intracellular trafficking which is required to deliver copper to plasma membranes for extrusion, and to the trans-Golgi network for incorporation into metalloproteins. Isoform specific glyocosylation contributes to stabilization of ATP7A copper ATPase in plasma membranes.     

Influence of Cu2+ on the Amino Acids Profile of Saccharomyces cerevisiae RD1 during Growth

The growth and the amino acid composition of the strain Saccharomyces cerevisiae RD1 were studied in the presence of copper ions. The accumulation of biomass was inhibited with the increase of Cu²⁺ concentration. It should be noted that the synthesis of aromatic amino acids was promoted at lower Cu²⁺ concentration (100 mg·L^?1), but at higher concentrations the inhibiting effect was significant. The decreases of the amino acid contents with the increase of Cu²⁺ concentration varied upon their type. The total amount of amino acids was much lower at 300 and 400 mg·L^?1 Cu²⁺.     

重金属Cd2+和Cu2+胁迫下泥蚶消化酶活性的变化

为了探讨重金属Cd²⁺和Cu²⁺胁迫对泥蚶消化酶活性的影响,运用酶学分析的方法,按《渔业水质标准》（GB 11607）规定的Cd²⁺、Cu²⁺最高限量值的1、2、5、10倍设置重金属离子Cd²⁺、Cu²⁺浓度及其组合,研究了在重金属Cd²⁺、Cu²⁺胁迫下,30d内泥蚶3种消化酶活性的变化规律。结果表明：与空白对照组相比,在重金属Cd²⁺、Cu²⁺或其组合的胁迫下,较低浓度组泥蚶的淀粉酶活性实验前期增强（即被诱导）,实验后期减弱（即被抑制）,较高浓度组泥蚶的淀粉酶活性从实验一开始就减弱,并保持在较低水平,毒性比较,同一重金属高浓度 > 低浓度,不同重金属及其组合Cu²⁺ > （Cd²⁺+Cu²⁺）组合 > Cd²⁺;泥蚶脂肪酶的活性实验前期增强,实验后期转为微减弱或减弱,毒性比较,同一重金属高浓度 > 低浓度,不同重金属及其组合（Cd²⁺+Cu²⁺）组合 > Cu²⁺ > Cd²⁺;泥蚶胃蛋白酶的活性实验前期增强,且活性呈现升高-降低-再升高-再降低的变化,实验后期分别表现微增强、微减弱和减弱,毒性比较,同一重金属高浓度 > 低浓度,不同重金属及其组合（Cd²⁺+Cu²⁺）组合 > Cu²⁺ > Cd²⁺。可见：环境中的Cd²⁺和Cu²⁺对泥蚶的消化酶活性起着明显的影响作用。     

Differences in the binding modes of phytochelatin to cadmium (II) and Zinc(II) ions

An ¹H NMR (nuclear magnetic resonance) spectroscopic structural analysis of Cd²⁺ complexes formed with the pentapeptide phytochelatin, (NH₃)⁺−(ψ-Glu-Cys)₂−Gly−COO−(PC₂), at a pH of 7.5 showed that the two thiol groups of the Cys residues and either the carbonyl or amide group of the peptide bond between Glu1 and Cys1 act as possible donor groups in the complexes at Cd²⁺/PC₂ ratios up to 0.4. As the ratio increases, the carboxylate group of Glu2 and either the carbonyl or amide group of the peptide bond between Cys1 and Glu2 comes to serve as a donor group. The manner in which Cd²⁺ forms complexes with PC₂ is distinctly different from Zn²⁺ and might account for the role of phytochelatin in Cd²⁺ detoxification. Electron absorption spectrometry demonstrated that the Cd²⁺ complexes are coordinated in a tetrahedral fashion by four thiol groups and that several sulfur atoms might bridge Cd²⁺ ions, resulting in the formation of polynuclear complexes. This contrasts with Zn²⁺ complex formation, which consists exclusively of a 1:1 complex.     

Copper-Ligand Interactions and Physiological free Radical Processes. Part 2. Influence of Cu2+ Ions on Cu+-Driven Oh Generation and Comparison with Their Effects on Fe2+-Driven Oh Production

In our search to establish a reference ·OH production system with respect to which the reactivity of copper(II) complexes could then be tested, the influence of free Cu²⁺ ions on the Cu⁺/H₂O₂ reaction has been investigated.

This influence depends on the C_Cu²⁺/C_Cu⁺ ratio. At low Cu²⁺ concentrations, ·OH damage to various detector molecules decreases with increasing Cu²⁺ concentrations until C_Cu²⁺/C_Cu⁺ reaches unity. Above this value, ·OH damage increases sharply until C_Cu²⁺/C_Cu⁺ becomes equal to 5 with salicylate and 2 with deoxyribose, ratios for which the protective effect of Cu²⁺ cancels. Finally, at higher concentrations, Cu²⁺ ions logically add their own ·OH production to that normally expected from Cu⁺ ions. The possible origin of this unprecedented alternate effect has been discussed. The possible influence of Cu⁺ ions on the generation of ·OH radicals by water gamma radiolysis has also been tested and, as already established for Cu²⁺ in a previous work, shown to be nonexistent. This definitely confirms that either form of ionised copper cannot scavenge ·OH radicals in the absence of a Iigand.     

TUNEL法检测Cu~(2+)胁迫诱导的中国树花共生藻细胞的死亡

为了探讨铜离子胁迫对中国树花共生藻细胞毒害作用的机制及细胞死亡的原因,通过徒手切片,采用两种TUNEL检测法(Promega和Roche试剂盒)对2mmol/L和4mmol/L Cu~(2+)胁迫24h的中国树花地衣体共生藻细胞凋亡情况进行观察。结果表明:(1)伊文思蓝染色法检测结果显示,中国树花共生藻细胞活力在2和4mmol/L Cu~(2+)胁迫下显著降低,其细胞的死亡率随着Cu~(2+)浓度的提高和处理时间的延长而明显增加;(2)在2和4mmol/L Cu~(2+)胁迫条件下,中国树花共生藻细胞的TUNEL阳性细胞率在Promega试剂盒中检测结果分别为50.30%和31.21%,而在Roche试剂盒中共生藻细胞TUNEL阳性标记核分别为53.17%和36.88%,两种TUNEL检测法结果类似。(3)与伊文思蓝染色法检测的Cu~(2+)胁迫中国树花共生藻细胞活力相比,发现较低浓度的Cu~(2+)(2mmol/L)胁迫对地衣共生藻细胞的毒害作用可诱导启动细胞凋亡程序,而较高浓度的Cu~(2+)(4mmol/L)胁迫对地衣共生藻产生较严重的毒害则导致大部分细胞的坏死,只有极少数细胞出现细胞凋亡。(4)两种试剂盒均可用于较低浓度Cu~(2+)胁迫引起的地衣体共生藻细胞凋亡的检测;直接将徒手切片材料用于TUNEL细胞凋亡原位检测中也得到了较理想的结果,避免了制备石蜡切片的繁琐步骤,缩短实验时间,简化了实验流程。     

Effect of Cu2+-ascorbic acid on lipid peroxidation,Mg2+-ATPase activity and spectrin of RBC membrane and reversal by erythropoietin

The effect of erythropoietin (Ep), a glycoprotein hormone, has been studied on lipid peroxidation induced by Cu²⁺ and ascorbate in vitro, Mg²⁺ ATPase activity and spectrin of RBC membrane. Our present investigation reveals that Cu²⁺ and ascorbic acid increases lipid peroxidation of RBC membrane significantly. It has further been observed that under the same experimental condition spectrin, a major cytoskeleton membrane protein, and Mg²⁺-ATPase activity of RBC membrane decrease significantly. However, exogenous administration of Ep completely restores lipid peroxidation and Mg²⁺-ATPase activity and partially recovers spectrin of RBC membrane.