A kinetic model for the B–Z transition of poly[d(G-C)]·poly[d(G-C)] and poly[d(G-m5C)]·poly[d(G-m5C)]

The analysis of the kinetic data of the B-Z conformational changes induced by salt in sized double-stranded poly[d(G-C)].poly[d(G-C)] and poly[d(G-m5C)].poly[d(G-m5C)] polymers indicated that there exists a salt threshold which reveals some largely, as yet, unrecognised characteristics of the transition. It was observed that there is a direct correlation between the length of the polymer and the rate of the B-Z transition when the salt concentration in the polymer solution is lower than the salt threshold. The correlation is inverse when the salt concentration is higher than the salt threshold. Thus, the molecular mechanism of the B- to Z-DNA transition varies depending on whether the salt concentration is higher or lower than the threshold. In this context, we have found that the contrasting results reported in the literature describing the rate of the B-Z transition are not contradictory but complementary. The finding of a salt threshold leads to the establishment of a relationship between the cooperativity index of the B-Z transition and the polymer chain length. That relationship is dependent on the chemical structure of the polymer but is temperature independent.     

Bh-DNA: Variations of the Poly[d(A)] · Poly[d(T)] Structure within the Framework of the Fibre Diffraction Studies

Abstract

A refinement of the recent results for poly[d(A)] · poly[d(T)] (Alexeev et al., J. Biomol. Struct. Dyn. 4, 989 (1987)) involving additional parameters of the base-pair structure and of the sugar- phosphate backbone expands the conformational potential of this polynucleotide of the B type to include the possibility of bifurcated hydrogen bonds of the kind recently discovered in crystalline deoxyoligonucleotide with lone d(A)_n · d(T)_n stretch (Nelson et al., Nature 330, 221 (1987)).

Still, analysis of the available data and energy calculations do not seem to indicate that the bifurcated H-bonds are a crucial factor responsible for the anomalous structure of the d(A)_n · d(T)_n sequence. The unique structural properties of poly [d(A)] · poly[d(T)] can hardly be explained without taking into account its interactions with the double-layer hydration spine in the minor groove. In view of the hydration mechanism stabilizing poly [d(A)] · poly [d(T)] and of the polynucleotide's heteronomous prehistory (Arnott et al., Nucleic Acids Res. 11, 4141 (1983)) we suggest that this B-type structure be called B_h.     

Effect of the β-amyloid peptide Aβ<Subscript>25–35</Subscript> and fullerene C<Subscript>60</Subscript> on the activity of enzymes in erythrocytes

The effect of the β-amyloid peptide Aβ_25–35 and fullerene C₆₀ on the activity of the cytoplasmic enzymes lactate dehydrogenase (LDH) and glutathione peroxidase (GLP), and membrane-bound phosphofructokinase (PFK) and Na⁺,K⁺-ATPase in human erythrocytes has been studied. When used in combination, the cytotoxins decrease the activity of LDH and PFK in a nonadditive manner; in this case, Aβ_25–35 protects PFK against the inhibitory effect of C₆₀. The activity of LDH, GLP, and PFK decreases within the first 2–20 min of incubation of erythrocytes with Aβ_25–35 in the absence of glucose. The addition of glucose sharply decreases the inhibitory action of Aβ_25–35 on LDH and GLP but does not affect the fourfold decrease in activity of PFK; the activity of membrane-bound Na⁺,K⁺-ATPase does not depend on the presence of glucose. Possible mechanisms of interaction of Aβ_25–35 and fullerene C₆₀ with the erythrocyte membrane and enzymes are discussed.     

The nature of different influence of Cd<Superscript>2+</Superscript> ions on the conformational equilibrium of triple-stranded polyribonucleotides poly(U)•poly(A)•poly(U) and poly(I)•poly(A)•poly(I) in aqueous solutions

The influence of Cd²⁺ ions on the conformational equilibrium of single-stranded (poly(U), poly(A), poly(I)) and triple-stranded polyribonucleotides (A2I, A2U) in aqueous solutions (0.1 M Na⁺ pH 7) has been investigated using difference UV spectroscopy and thermal denaturation. Analysis of the shape and intensity of the DUV spectra of poly(A), poly(I), and A2I has revealed the presence of two types of complex formed as a result of (i) interaction between Cd²⁺ and the N7 atoms of purines, producing macrochelates; and (ii) binding of Cd²⁺ to the N1 atoms of poly(A) and poly(I). Since Cd²⁺ ions are not bound to heteroatoms of the bases in A2U, the conformation of the structure remains stable up to 0.02 M Cd²⁺. There is a critical Cd²⁺ concentration (～1.5?10^?4 M) above which A2I assumes a new helical conformation with lower thermal stability. It is supposed that, upon the formation of the “metallized” A2I triplex, the Cd²⁺ ions are located inside the triple helix and form bridges between the hypoxanthine and adenine of the homopolynucleotide strands.     

The Effects of FeCl<Subscript>3</Subscript> and Fe–EDTA on the Development of Psoriasis

The effects of FeCl₃ and Fe–EDTA on the development of psoriasis were studied in the mouse model of vaginal epithelium and tail epidermis. The mitoses of vaginal epithelial cell in female mice of their estrogenic stage and the formation of granular cell layers in male mouse tail scale were observed. Mice were randomly divided into eight groups and treated with normal saline, methotrexate, and different doses of two iron forms, FeCl₃ and Fe–EDTA, respectively, for 10 days. To explore the influence of FeCl₃ and Fe–EDTA on the excretion of Cu, Fe, Zn, Ca, Mg, Mn, and Se, the concentration of those elements in liver and kidney was analyzed by atomic absorption spectrometry. The different doses of FeCl₃ or Fe–EDTA could obviously inhibit the mitoses of vaginal epithelial cell (p< 0.05) and promote the formation of granular cell layers in mice tail scale (p < 0.05). No statistically significant results were found between the groups of FeCl₃ and Fe–EDTA, and between experimental groups and methotrexate group acted as the positive control (p>0.05). Compared with the negative group, the concentrations of Cu, Fe, Zn, Ca, Mg, Mn, and Se in liver and kidney of experimental groups and positive control group were not significantly changed (p > 0.05). FeCl₃ and Fe–EDTA are as effective as methotrexate on inhibiting hyperplasia of epidermal cells and increasing the formation of granular cell layers, and the concentrations of Cu, Fe, Zn, Ca, Mg, Mn, and Se in liver and kidney of experimental groups and positive control group were not significantly changed compared with the negative group, possibly retarding the development of psoriasis.     

Protease-catalyzed synthesis of the tripeptide CCK<Subscript>26–28</Subscript>, a fragment of CCK-8

Summary. Two enzymatically synthetic strategies of the tripeptide derivative PhAc-Asp(OMe)-Tyr-Met-OAl are reported. The second strategy gains the advantage of more economical starting materials, less reaction steps and a higher overall isolated yield of this tripeptide fragment over the first strategy. The effect of the acyl-donor ester concentration and structure, the C-α protecting group of the nucleophile, reaction media, enzyme and the carrier on the tripeptide derivative synthesis were studied. This tripeptide selected is a fragment of the cholecystokinin C-terminal octapeptide (CCK-8), a potential therapeutic agent in the control of gastrointestinal function and also a drug candidate for the treatment of epilepsy.     

Hydrogen-bonding behavior of various conformations of the HNO<Subscript>3</Subscript>…(CH<Subscript>3</Subscript>OH)<Subscript>2</Subscript> ternary system

Nine minima were found on the intermolecular potential energy surface for the ternary system HNO₃(CH₃OH)₂ at the MP2/aug-cc-pVDZ level of theory. The cooperative effect, which is a measure of the hydrogen-bonding strength, was probed in these nine conformations of HNO₃…(CH₃OH)₂. The results are discussed here in terms of structures, energetics, infrared vibrational frequencies, and topological parameters. The cooperative effect was observed to be an important contributor to the total interaction energies of the cyclic conformers of HNO₃…(CH₃OH)₂, meaning that it cannot be neglected in simulations in which the pair-additive potential is applied.

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Graphical abstract The H-bonding behavior of various conformations of the HNO₃(CH₃OH)₂ trimer was investigated

     

Structure of the Mn<Subscript>4</Subscript>–Ca cluster as derived from X-ray diffraction

The catalytic centre for light-induced water oxidation in photosystem II (PSII) is a multinuclear metal cluster containing four manganese and one calcium cations. Knowing the structure of this biological catalyst is of utmost importance for unravelling the mechanism of water oxidation in photosynthesis. In this review we describe the current state of the X-ray structure determination at 3.0 A resolution of the water oxidation complex (WOC) of PSII. The arrangement of metal cations in the cluster, their coordination and protein surroundings are discussed with regard to spectroscopic and mutagenesis studies. Limitations of the presently available structural data are pointed out and possible perspectives for the future are outlined, including the combination of X-ray diffraction and X-ray spectroscopy on single crystals.     

Charge ordering in the metal–insulator transition of V-doped CrO<Subscript>2</Subscript> in the rutile structure

Electronic, magnetic, and structural properties of pure and V-doped CrO₂ were extensively investigated utilizing density functional theory. Usually, pure CrO₂ is a half-metallic ferromagnet with conductive spin majority species and insulating spin minority species. This system remains in its half-metallic ferromagnetic phase even at 50% V-substitution for Cr within the crystal. The V-substituted compound Cr_0.5V_0.5O₂ encounters metal–insulator transition upon the application of on-site Coulomb repulsion U?=?7 eV preserving its ferromagnetism in the insulating phase. It is revealed in this study that Cr³⁺-V⁵⁺ charge ordering accompanied by the transfer of the single V-3d electron to the Cr-3dt_2g orbitals triggers metal–insulator transition in Cr_0.5V_0.5O₂. The ferromagnetism of Cr_0.5V_0.5O₂ in the insulating phase arises predominantly due to strong Hund’s coupling between the occupied electrons in the Cr-t_2g states. Besides this, the ferromagnetic Curie temperature (T_c) decreases significantly due to V-substitution. Interestingly, a structural distortion is observed due to tilting of CrO₆ or VO₆ octahedra across the metal–insulator transition of Cr_0.5V_0.5O₂.

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Graphical abstract The V-doped compound Cr_0.5V_0.5O₂ is found a half-metallic ferromagnet (HMF) in the absence of on-site Coulomb interaction (U). This HMF behavor maintains up to U?=?6 eV. Eventually, this system encounters metal-insulator transition (MIT) upon the application of U?=?7 eV with a band gap of E_g ~ 0.31 eV. Nevertheless, applications of higher U widen the band gaps. In this figure, calculated total (black), Cr-3d (red), V-3d (violet), and O-2p (blue) DOS of Cr_0.5V_0.5O₂ for U?=?8 eV are illustrated. The system is insulating with a band gap of E_g ~ 0.7 eV.

     

A theoretical study on the reaction mechanism of O<Subscript>2</Subscript> with C<Subscript>4</Subscript>H<Subscript>9</Subscript>• radical

Ab initio calculations have been performed using the complete basis set model (CBS-QB3) to study the reaction mechanism of butane radical (C₄H₉•) with oxygen (O₂). On the calculated potential energy surface, the addition of O₂ to C₄H₉• forms three intermediates barrierlessly, which can undergo subsequent isomerization or decomposition reaction leading to various products: HOO• + C₄H₈, C₂H₅• + CH₂CHOOH, OH• + C₃H₇CHO, OH• + cycle-C₄H₈O, CH₃• + CH₃CHCHOOH, CH₂OOH• + C₃H₆. Five pathways are supposed in this study. After taking into account the reaction barrier and enthalpy, the most possible reaction pathway is C₄H₉• + O₂ → IM1 → TS5 → IM3 → TS6 → IM4 → TS7 → OH• + cycle-C₄H₈O.     

NMR solution structure of the N-terminal domain of subunit E (E<Subscript>1–52</Subscript>) of A<Subscript>1</Subscript>A<Subscript>O</Subscript> ATP synthase from <Emphasis Type="Italic">Methanocaldococcus jannaschii</Emphasis>

The N-termini of E and H of A₁A_O ATP synthase have been shown to interact and an NMR structure of N-terminal H_1–47 has been solved recently. In order to understand the E-H assembly and the N-terminal structure of E, the truncated construct E_1–52 of Methanocaldococcus jannaschii A₁A_O ATP synthase was produced, purified and the solution structure of E_1–52 was determined by NMR spectroscopy. The protein is 60.5 Å in length and forms an α helix between the residues 8–48. The molecule is amphipathic with a strip of hydrophobic residues, discussed as a possible helix-helix interaction with neighboring subunit H.     

A DFT study of the catalytic pyrolysis of benzaldehyde on ZnO, γ-Al<Subscript>2</Subscript>O<Subscript>3</Subscript>, and CaO models

The catalytic pyrolysis pathways of carbonyl compounds in coal were systematically studied using density functional theory (DFT), with benzaldehyde (C₆H₅CHO) employed as a coal-based model compound and ZnO, γ-Al₂O₃, and CaO as catalysts. The results show that the products of both pyrolysis and catalytic pyrolysis are C₆H₆ and CO. However, the presence of any of the catalysts changes the reaction pathway and reduces the energy barrier, indicating that these catalysts promote C₆H₅CHO decomposition.

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Graphical abstract The presence of catalysts changes the reaction pathway and the energy barrier decreases in the order Ea (no catalyst)> Ea (CaO)> Ea (γ-Al₂O₃)> Ea (ZnO), indicating that these catalysts promote C₆H₅CHO decomposition.

     

The effect of NBD-Cl in nucleotide-binding of the major subunit α and B of the motor proteins F<Subscript>1</Subscript>F<Subscript>O</Subscript> ATP synthase and A<Subscript>1</Subscript>A<Subscript>O</Subscript> ATP synthase

Subunit α of the Escherichia coli F₁F_O ATP synthase has been produced, and its low-resolution structure has been determined. The monodispersity of α allowed the studies of nucleotide-binding and inhibitory effect of 4-Chloro-7-nitrobenzofurazan (NBD-Cl) to ATP/ADP-binding. Binding constants (K _d ) of 1.6 μM of bound MgATP-ATTO-647N and 2.9 μM of MgADP-ATTO-647N have been determined from fluorescence correlation spectroscopy data. A concentration of 51 μM and 55 μM of NBD-Cl dropped the MgATP-ATTO-647N and MgADP-ATTO-647N binding capacity to 50% (IC₅₀), respectively. In contrast, no effect was observed in the presence of N,N′-dicyclohexylcarbodiimide. As subunit α is the homologue of subunit B of the A₁A_O ATP synthase, the interaction of NBD-Cl with B of the A-ATP synthase from Methanosarcina mazei Gö1 has also been shown. The data reveal a reduction of nucleotide-binding of B due to NBD-Cl, resulting in IC₅₀ values of 41 μM and 42 μM for MgATP-ATTO-647N and MgADP-ATTO-647N, respectively.     

Structure of the δ-Chain of Chimpanzee Haemoglobin A<Subscript>2</Subscript>

STUDIES of adult¹ and foetal² haemoglobin from the chimpanzee (Pan troglodytes) have shown that the amino-acid compositions of tryptic and chymotryptic peptides of the α, β and γ-chains are indistinguishable from those of man. The primary structures of chimpanzee α, β and γ-chains are therefore almost certainly identical to the homologous human chains. The two types of γ-chains found in man³, ^Gγ and ^Aγ, with glycine and alanine in position γ136, respectively, are likewise present in the chimpanzee².     

Cooperation of adenosine and prostaglandin E<Subscript>2</Subscript> (PGE<Subscript>2</Subscript>) in amplification of cAMP–PKA signaling and immunosuppression

INTRODUCTION: We hypothesize that adenosine and PGE(2) could have a complementary immunosuppressive effect that is mediated via common cAMP-PKA signaling. MATERIALS AND METHODS: To test this hypothesis, the effect of adenosine and PGE(2) on the cytotoxic activity and cytokine production of lymphokine activated killer (LAK) cells was investigated. RESULTS: PGE(2) and adenosine inhibited LAK cells cytotoxic activity and production of INF-gamma, GM-CSF and TNF-alpha. In combination they showed substantially higher inhibition than each modality used alone. Using agonists and antagonists specific for PGE(2) and adenosine receptors we found that cooperation of PGE(2) and adenosine in their inhibitory effects are mediated via EP(2) and A(2A) receptors, respectively. LAK cells have 35-fold higher expression of EP(2) than A(2A). Combined PGE(2) and adenosine treatment resulted in augmentation of cAMP production, PKA activity, CREB phosphorylation and inhibition of Akt phosphorylation. Wortmannin and LY294002 enhanced the suppressive effects of adenosine and PGE(2). In contrast, Rp-8-Br-cAMPS, an inhibitor of PKA type I blocked their immunosuppressive effects, suggesting that the inhibitory effects of PGE(2) and adenosine are mediated via common pathway with activation of cAMP-PKA and inhibition of Akt. CONCLUSION: In comparison to other immunosuppressive molecules (TGF-beta and IL-10), adenosine and PGE(2) are unique in their ability to inhibit the executive function of highly cytotoxic cells. High intratumor levels of adenosine and PGE(2) could protect tumor from immune-mediated destruction by inactivation of the tumor infiltrating functionally active immune cells.