Free Radical-Induced Tandem Base Damage in DNA Oligomers

A new tandem base lesion has been identified in two DNA oligomers, namely d(GpT) and d(CpGpTpA), exposed to X-irradiation in deoxygenated aqueous solution. In this lesion the C6 carbon atom of thymine is hydroxylated and a covalent link is formed between the C5 carbon atom of thymine and the C8 carbon atom of the adjacent guanine base. In addition, further evidence in the form of mass spectrometric data is presented confirming the structures of previously reported tandem base lesions that are produced by ionizing radiation in the presence of oxygen. New data is presented on the prevalence of a previously reported tandem base lesion in which the methyl carbon atom of thymine is covalently linked to the C8 carbon atom of the adjacent guanine base. The free radical-initiated processes by which tandem base damages are generated are discussed. To date four different radiation-induced tandem base lesion have been identified. The evidence suggests that tandem base damage is a significant component of free radical-induced DNA damage.     

Is the oxygen atom of carbon monoxide coordinated to the copper of hemocyanin?

The carbon monoxide binding site of hemocyanins was studied by comparing the isotope shift of the CO-stretching frequencies in CO-hemocyanins with that of carbon monoxide diethylenetriaminecopper(I)tetraphenylboron in which the carbon atom of CO is coordinated to the copper. Coordination by the carbon atom of CO in CO-hemocyanin is suggested.     

Kinetic resolution of organosilicon compounds by stereoselective dehydrogenation with horse liver alcohol dehydrogenase

Streoselective dehydrogenation of three isomers of trimethylsilypropanol was carried out with horse liver alcohol dehydrogenase (HLADH, EC 1.1.1.1.) and optically active organosilicon compounds were obtained in a water-organic solvent two-layer system with coenzyme regeneration. Furthermore, we examined the effects of the silicon atom on stereoselectivity of HLADH compared to the corresponding carbon compounds. Substitution of the silicon atom for the carbon atom was found to improve the stereoselectivity of HLADH. For example, the optical purity of the remaining 1-trimethylsilyl-2-propanol was higher than 99% enantiomeric excess (ee) at 50% conversion, whereas that of the carbon analogue was 84% ee. This phenomenon was probably ascribable to the bulkiness of the organosilicon compounds derived from their longer Si-C bond. Kinetic analysis in an aqueous monolayer system demonstrated that the specific properties of the silicon atom greatly affected the reactivity of these substrate compounds.Correspondence to: A. Tanaka     

Piperidinyl Peptide Nucleic Acids: Synthesis and DNA-Complementation Studies

Abstract

Synthesis of a new six membered PNA analogue by introducing a methylene bridge between β carbon atom of ethylene diamine and β′ carbon atom of linker to nucleobase.     

Bioconversion of organosilicon compounds by horse liver alcohol dehydrogenase: the role of the silicon atom in enzymatic reactions

Summary Bioconversion of three organosilicon compounds of different chain length between the silicon atom and the hydroxyl group (Me₃Si(CH₂)_nOH, n = 1–3) by horse liver alcohol dehydrogenase (HLADH, EC 1.1.1.1.) was studied. Furthermore, the effect of the silicon atom on the HLADH-catalysed reaction was examined in comparison with the corresponding carbon compounds. HLADH could catalyse the dehydrogenation of trimethylsilyeethanol (n = 2) and trimethylsilylpropanol (n = 3). Trimethylsilylethanol was a better substrate than both its carbon analogue, 3,3-dimethylbutanol, and ethanol. The improved activity of HLADH on trimethylsilylethanol could be accounted for by a higher affinity toward HLADH and a lower activation energy of the reaction by HLADH than those of the carbon counterpart. These are derived from physical properties of the silicon atom, that is, the lower electronegativity and the bigger radius than those of the carbon atom. In contrast, HLADH showed no activity on trimethylsilylmethanol (n = 1), whereas it catalysed the dehydrogenation of the carbon analogue, 2,2-dimethylpropanol, fairly well. The reason for the inactivity of HLADH in the case of trimethylsilylmethanol based on the electric effect of the silicon atom is also discussed. Offsprint requests to: A. Tanaka     

Human plasma lecithin-cholesterol acyltransferase. Inhibition of the phospholipase A2-like activity by sn-2-difluoroketone phosphatidylcholine analogues

Lecithin-cholesterol acyltransferase (LCAT) is a plasma enzyme which catalyzes the transacylation of the sn-2-fatty acid of lecithin to cholesterol, forming lysolecithin and cholesteryl ester. We have recently proposed a covalent catalytic mechanism for LCAT in which lecithin cleavage proceeds via the formation of a transition state tetrahedral adduct between the oxygen atom of the catalytic serine residue and the sn-2-carbonyl carbon atom of the substrate (Jauhiainen, M., Ridgway, N.D., and Dolphin, P.J. (1987) Biochim. Biophys. Acta 918, 175-188). This proposal is evaluated here by use of nonhydrolyzable sn-2-difluoroketone phosphatidylcholine analogues, known to inhibit calcium-dependent phospholipase A2. These compounds inhibited the calcium-independent phospholipase A2 activity of LCAT in a time and concentration dependent manner. The most potent analogues had a 100-fold higher affinity for the enzyme than the substrate, lecithin, when present within lecithin/apoA-I proteoliposomes. The inhibition was dependent upon the presence of a difluoromethylene group alpha to the sn-2-carbonyl carbon of the analogues. The inhibition is attributed to the formation of a tetrahedral adduct between the catalytic serine residue of LCAT and the sn-2-carbonyl carbon atom of the analogues which is stabilized by the electronegative fluorine atoms present upon the carbon atom alpha to the carbonyl carbon. This adduct mimics that proposed by us to occur during lecithin cleavage by LCAT, and the data substantiate the existence of this transition state adduct prior to the release of lysolecithin and formation of a fatty acylserine oxyester of the enzyme.     

Cyclic thioether peptide mimetics as VCAM-VLA-4 antagonists

Selective substitution of a sulfur atom by carbon in a highly potent 13-membered cyclic disulfide was accomplished by intramolecular displacement of a bromide. The potency of the resulting thioethers in the VCAM/VLA-4 assay was dependent on ring size and the position of the sulfur atom.     

L-1-N-methyl-4-mercaptohistidine disulfide, a potential endogenous regulator in the redox control of chloroplast coupling factor 1 in Dunaliella.

A water-soluble, highly polar, heat-stable, small molecule has been isolated from cell-free extracts of the halotolerant green alga Dunaliella salina. This compound, soluble inhibitory factor (SIF), when added to in vivo light-activated, thylakoid membrane-bound preparations of the D. salina coupling factor 1 (CF1), causes a rapid inactivation of the ATPase activity. SIF must be in its oxidized form to inactivate the CF1 ATPase and probably functions by oxidizing the reduced form of the light-activated enzyme. SIF has been purified to homogeneity and characterized by UV-visible and IR absorption spectroscopy, 1H and 13C NMR spectroscopy, and mass spectrometry. SIF has five different kinds of nonexchangeable protons and seven different kinds of carbon atoms. Three of the carbon atoms and one proton are part of a heterocyclic (imidazole) ring. One carbon atom is a carbonyl (carboxylic acid). One carbon atom and three protons form a methyl group attached to the aromatic ring. One carbon atom and two protons are a methylene group, and one carbon atom (an alpha-amino carbon) is attached to a single proton. In addition, in its reduced form, SIF contains a thiol group attached to the heterocyclic ring. From high resolution mass spectrometry, the molecular weight of SIF was determined to be 401 (M + H+) and is consistent with the composition being C14H21N6O4S2. The UV absorption of SIF shows a large increase at 240 nm upon reduction. An effective difference extinction coefficient for this absorbance change has been calculated to be 6.84 meq/cm. A comparison of SIF with the oxidized form of ovothiol A (1-N-methyl-4-mercaptohistidine disulfide) shows the two compounds to be identical in all respects. In addition, ovothiol A disulfide is as effective as SIF in inhibiting the light-triggered, CF1 ATPase activity. It is concluded, therefore, that SIF and L-1-N-methyl-4-mercaptohistidine disulfide are identical.     

底物中的硅原子对酶反应的影响

在酶工程学的研究史上,人们一方面不断地研制开发新的酶种;一方面利用固定化、酶分子改造和修饰等技术来提高酶的活性和稳定性;另一方面,则不断地开拓酶的新用途。酶催化非天然化合物的生物合成和转化（正是这一方面研究的新进展）。由于有机硅化合物在有机合成,尤其...     

A new electronic-topological investigation of the relationship between chemical structure and ambergris odour.

An electronic-topological approach has been used to define an active ambergris fragment (AAF) which correctly describes the presence (or absence) of the ambergris odour of all 181 compounds investigated. The AAF consists of one oxygen atom and three carbon atoms (alpha, beta, gamma) which are separated by certain key distances and which possess certain atomic charges. The C(alpha) atom must bear at least one hydrogen atom (H(alpha)) which is located at a certain distance from one of the unshared electronic pairs of the oxygen atom.     

Condensed State Molecular Dynamics in Sorbitol and Maltitol: Mobility Gradients and Conformation Transitions

Abstract

Molecular mobility in sorbitol and maltitol is studied in order to understand their differences near the junction between the α and β relaxations. The molecular dynamics simulations performed on the polyols in their bulk state give support to the ¹³C NMR results and imply that the mobility of a carbon atom located at the extremity of the chain is higher than that of any other carbon. Moreover, the difference in carbon atoms mobility is greater within the sorbitol moiety of maltitol than in sorbitol and seems intimately related to the junction temperature of the α and β relaxation processes. The reorientation of the C–H vectors as probed by NMR is shown to be mainly the effect of conformation transitions in the case of a carbon atom located at the end of the chain.     

Hydrogen-mediated Stone-Wales isomerization of dicyclopenta[de,mn]anthracene

The mechanism of transformation of two radicals (R1p and R1i) obtained by addition of a hydrogen atom to an external and internal carbon atom of dicyclopenta[de,mn]anthracene (P1) was investigated. Two pathways were revealed. The first mechanism is a one-step process, whereas the second mechanism includes two transition states and a cyclobutyl intermediate. The formation of R1p and R1i and the homolytic cleavage of the radicals obtained during the isomerization processes were also examined. In both pathways the addition of a hydrogen atom to the internal carbon significantly lowers the activation energy for hydrogen-mediated isomerization of P1 to acefluoranthene. This finding could be explained by the specific electronic structures of the transition states and intermediates participating in the isomerization processes.     

Diphosphonates are potent inhibitors of mammalian inorganic pyrophosphatase

Methanediphosphonate and 12 analogs thereof with different substituents at the carbon atom are potent competitive inhibitors of highly purified rat liver and bovine heart inorganic pyrophosphatases. The inhibition constants for the most effective diphosphonates, which contain an NH2 or OH group at the bridge carbon atom, are in the micromolar range. Yeast and Escherichia coli pyrophosphatases are markedly less sensitive to the diphosphonates. Pyrophosphatase inhibition may be related to the numerous biological effects exerted by diphosphonates.     

EPR study of hydrated testosterone monoclinic and orthorhombic single crystals gamma-irradiated at 295 K

The molecular structure of free radicals formed in gamma-irradiated monoclinic and orthorhombic single crystals of hydrated testosterone were investigated by EPR spectroscopy. Two different types of radical were observed. In the monoclinic form, the radical arises by the loss of a hydrogen atom from the carbon atom C(2), whereas, in the orthorhombic form, it arises by addition of a hydrogen atom to the oxygen atom O(3). The hyperfine spectrum of the radical formed in the monoclinic single crystal originates from the interaction of the unpaired electron with one alpha-proton in position 2 and two non equivalent beta-protons in position 1. In the orthorhombic single crystal, we observed interaction of the unpaired electron, which is delocalized on the carbons C(3), C(4) and C(5) with one alpha-proton in position 4 and with four nonequivalent beta-protons connected with the carbon atoms C(2) and C(6). The hyperfine tensors of the coupling and the g-tensor of the radicals are given.     

Efficient embedded atom method interatomic potential for graphite and carbon nanostructures

A new interatomic potential for graphite and graphene based on embedded atom method is proposed in this paper. Potential parameters were determined by fitting to the equilibrium lattice constants, the binding energy, the vacancy formation energy and elastic constants. The agreement between the calculated properties of graphite and experimental data is very good. In addition, the proposed potential quite accurately reproduces the surface energy of graphite and the binding energies of carbon atom in fullerene C60 and in SWNTs. The proposed potential is computationally more efficient than the existing widely used carbon potentials. It is intended for use in large-scale molecular dynamics simulations of carbon structures.     

Simulation of carboxymyoglobin photodissociation

Computer-generated models of the structures of deoxymyoglobin and CO-bound myoglobin show that the CO molecule is not packed so tightly by the amino acid residues of the distal pocket to prevent its motion away from the iron atom upon photodissociation. A simulation of low temperature photodissociation by energy minimization techniques shows that the CO moves to a position approximately 4 A away from the iron atom due to the van der Waals forces. The final position of the CO molecule requires far larger motion of the carbon atom than the oxygen atom and thereby suggests that the isotope dependence of the molecular tunneling is a consequence of the orientation of the photodissociated CO.     

Biosynthesis of the modified nucleoside Q in transfer RNA.

During biosynthesis of the modified nucleoside Q, 7-(4,5-DIHYDROXYL-1-1-CYCLOPENTEN-3-YL-AMINOMETHYL)-7-DEAZAGUANOSINE, IN TRNA, the carbon atom at position 8 in precursor molecule guanine was expelled together with the nitrogen atom N-7 in a fashion similar to that in the biosynthesis of the nucleoside antibiotic toyocamycin.     

Carbon analogs of antifungal dioxane-triazole derivatives: synthesis and in vitro activities

A new series of triazole compounds possessing a carbon atom in place of a sulfur atom were efficiently synthesized and their in vitro antifungal activities were investigated. The carbon analogs showed excellent in vitro activity against Candida, Cryptococcus, and Aspergillus species. The MICs of compound 1c against C. albicans ATCC24433, C. neoformans TIMM1855, and A. fumigatus ATCC26430 were 0.016, 0.016, and 0.125 microg/mL, respectively (MICs of fluconazole: 0.5, >4, and >4 microg/mL; MICs of itraconazole: 0.125, 0.25, and 0.25 microg/mL).     

The electron spin resonance and absorption spectra of microsomal cytochrome P-450 and its isocyanide complexes

The absorption spectra of oxidized P-450-isocyanide complexes were the same in difference spectra irrespective of the isocyanide derivative tested. However, with these reduced P-450-isocyanide complexes, absorption at 455 mμ increased, and that at 430 mμ decreased, with increasing carbon atom number of the isocyanide derivative at a definite pH. The same changes were seen with individual complexes with increasing pH.

The dissociation constants of oxidized P-450-isocyanide complexes decreased with increase in carbon atom number of the isocyanide. These results were confirmed by electron spin resonance (ESR) spectroscopy. However, the dissociation constants of reduced P-450-isocyanide complexes were essentially identical and the dissociation constants of the oxidized and reduced P-450-isocyanide complexes were little affected by pH.

The oxidized P-450-isocyanide complexes gave magnetically specific ESR signals. The orbital energy differences of d orbitals of the heme iron of the complexes increased with increase in the carbon atom number of the isocyanide.

Purified P-450 and its isocyanide complexes were rapidly reduced by a ferredoxin-NADP⁺ reductase system.     

Transformation of carbon tetrachloride via sulfur and oxygen substitution by Pseudomonas sp. strain KC.

Pseudomonas sp. strain KC transforms carbon tetrachloride into carbon dioxide and nonvolatile products, without chloroform as an intermediate. To define the pathway for hydrolysis, nonvolatile products were analyzed. Condensation products containing the carbon atom of carbon tetrachloride as carbonyl and thioxo moieties were identified, indicating the intermediacy of phosgene and thiophosgene in the pathway.