Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta

X-ray analysis of enzyme–DNA interactions is very informative in revealing molecular contacts, but provides neither quantitative estimates of the relative importance of these contacts nor information on the relative contributions of specific and nonspecific interactions to the total affinity of enzymes for specific DNA. A stepwise increase in the ligand complexity approach is used to estimate the relative contributions of virtually every nucleotide unit of synthetic DNA containing abasic sites to its affinity for apurinic/apyrimidinic endonuclease (APE1) from human placenta. It was found that APE1 interacts with 9–10 nt units or base pairs of single-stranded and double-stranded ribooligonucleotides and deoxyribooligonucleotides of different lengths and sequences, mainly through weak additive contacts with internucleotide phosphate groups. Such nonspecific interactions of APE1 with nearly every nucleotide within its DNA-binding cleft provides up to seven orders of magnitude (ΔG° ~ −8.7 to −9.0 kcal/mol) of the enzyme affinity for any DNA substrate. In contrast, interactions with the abasic site together with other specific APE1–DNA interactions provide only one order of magnitude (ΔG° ~ −1.1 to −1.5 kcal/mol) of the total affinity of APE1 for specific DNA. We conclude that the enzyme's specificity for abasic sites in DNA is mostly due to a great increase (six to seven orders of magnitude) in the reaction rate with specific DNA, with formation of the Michaelis complex contributing to the substrate preference only marginally.     

Synthesis of polyglycerol phosphate by Bacillus stearothermophilus.

A particulate enzyme preparation from Bacillus stearothermophilus synthesized 1,3-poly(glycerol phosphage) from CDPglycerol at an optimum pH of 8.0 and the reaction was stimulated by divalent cations. Km for CDPglycerol was 0.18 mM. The synthesis was inhibited by CMP, CDP, and CTP and by concentrations of CDP-glycerol above 0.49 mM. The reaction was irreversible, The product had an average chain length of 8 glycerol units. About two thirds of the polymers were synthesized in entirety while the ramainder were attached to some acceptor by their phosphate end. The enzome was able to synthesize only a limited amount of polymer.     

Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase

We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1 interactions with 10–13 nt pairs within its DNA-binding cleft provides approximately 5 orders of magnitude of its affinity for DNA (ΔG° approximately −6.7 kcal/mol). The relative contribution of the oxoG unit of DNA (ΔG° approximately −3.3 kcal/mol) together with other specific interactions (ΔG° approximately −0.7 kcal/mol) provide approximately 3 orders of magnitude of the affinity. Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the k_cat term instead; the rate increases by 6–7 orders of magnitude for cognate DNA as compared with non-cognate one. The k_cat values for substrates of different sequences correlate with the DNA twist, while the K_M values correlate with ΔG° of the DNA fragments surrounding the lesion (position from −6 to +6). The functions for predicting the K_M and k_cat values for different sequences containing oxoG were found.     

Dynamic compression counteracts IL-1β induced inducible nitric oxide synthase and cyclo-oxygenase-2 expression in chondrocyte/agarose constructs

Background  

Nitric oxide and prostaglandin E₂ (PGE₂play pivotal roles in both the pathogenesis of osteoarthritis and catabolic processes in articular cartilage. These mediators are influenced by both IL-1β and mechanical loading, and involve alterations in the inducible nitric oxide synthase (iNOS) and cyclo-oxygenase (COX)-2 enzymes. To identify the specific interactions that are activated by both types of stimuli, we examined the effects of dynamic compression on levels of expression of iNOS and COX-2 and involvement of the p38 mitogen-activated protein kinase (MAPK) pathway.     

Interactions of human 8-oxoguanine-DNA glycosylase with single- and double-stranded DNA

Interactions of human 8-oxoguanine-DNA glycosylase (hOGG1) with single- and double-stranded oligodeoxyribonucleotides (ODN) have been studied by the method of stepwise increase in ligand complexity. The ODNs have been found to inhibit the glycosylase-catalyzed reaction competitively. The K1 values have been determined for a set of ODNs. All units of non-specific DNA within the enzyme footprint have been shown to interact with the protein globule in an additive manner. An increase in the d(pN)n length (n) by one unit caused a monotonous 1.4-1.5-fold increase in their affinity for the glycosylase ODN until n = 10, mostly due to weak nonspecific contacts of the enzyme and the sugar-phosphate backbone. The weak nonspecific additive interactions contributed about five orders of magnitude in the affinity of hOGG1 for specific DNA (Kd approximately 10(-5) M), whereas introduction of a 8-oxoguanine residue added about three orders of magnitude to this affinity (Kd approximately 10(-8) M). Quantitative features of recognition of specific DNA by the enzyme are analyzed.     

文山松毛虫质型多角体病毒形态结构及理化性质的研究

对文山松毛虫质型多角体病毒的形态结构及理化特性进行了研究,多角体大部分为六边形,少数为四边形及近园形,其大小在0.47～2.45μ之间,平均为1.1μ。病毒粒子呈球形,无囊膜,致密的核芯区由一层外壳包裹,直径为60nm。病毒粒子表面有12个刺突,放大图象可见其亚单位排列。多角体蛋白的主要成分为一种,分子量为26200道尔顿,多角体蛋白氨基酸组成中不含半胱氨酸;其碱性氨基酸与酸性氨基酸之比为1:2.16。病毒粒子结构蛋白含五条多肽组分。用SDS-热酚法提取所得核酸,其热变性紫外吸收OD_(260)值增加51.6％。抗核酸酶S_1。Tm值为86℃。在1％琼脂糖凝胶电泳中可分为9个片段,而在5％PAGE中,则可分为10个片段。各片段大小在0.66×10~6～2.85×10~6道尔顿之间,总分子量为15.35×10~6。电镜分析研究显示了CPV RNA在0.4μ、0.8μ和1.2μ处有三个分布峰。     

An Investigation into the Rate and Control of Assimilate Movement from Leaves in Pisum sativum

Export studies were made on leaves of Pisum by monitoring the¹⁴CO₂-treated source leaf at its surface at frequent intervals.Radiocarbon levels of fresh leaf samples showed a good correlationwith results from the more conventional methods of radiocarbonestimation which involve destructive analysis. The rate of export was highest in plants which had been defoliated,except for the source leaf 20 h or more before the start ofthe export study. Removal of the shoot apex reduced export andprogressive reduction in sink capacity was associated with decreasedexport rates, particularly over short time periods. Export rateswere similar in defoliated and non-defoliated plants where theshoot apex and the roots had been excised. This suggested thata decrease in the source resulted in higher export rates fromthe remaining source only when active sinks were present; thisin turn suggests that, at least under these conditions, activeremoval of photosynthate is more important in controlling exportthan the photosynthate build-up in the leaf itself. The non-destructive technique enabled comparisons to be madebetween export curves for individual plants. It was found thatin experiments replicated in time, the same relationship betweentreatments was present on different days and the shape of theexport curves was similar but the absolute values for exportedradiocarbon sometimes varied considerably.     

Interactions of human 8-oxoguanine DNA glycosylase with single-and double-stranded DNAs

The interaction of human 8-oxoguanine (8-oxoG) DNA glycosylase (hOGG1) with single-and double-stranded oligodeoxyribonucleotides (ODNs) was studied by a method of stepwise increase in ligand complexity. ODNs were shown to act as competitive inhibitors with respect to the substrate of the reaction catalyzed by hOGG1. K _I was estimated for various homo-and hetero-ODNs. All nucleotides covered by the enzyme globule proved to additively interact with hOGG1. An increase in the ODN size n by one nucleotide or base pair in d(pN)_n and their duplexes monotonically increased their affinity for hOGG1 by a factor of 1.4–1.5 until n = 10, mostly due to weak nonspecific additive contacts between hOGG1 and the sugar-phosphate backbone. Weak nonspecific additive interactions contributed about five orders of magnitude to the total affinity of hOGG1 for specific DNA (K _d ～ 10^?5 M). Specific 8-oxoG increased the affinity of DNA for the enzyme by three orders of magnitude (K _d ～ 10^?8 M). The main features of the recognition of specific DNA by hOGG1 were analyzed.     

Chilling-induced Lipid Hydrolysis in the Oil Palm (Elaeis guineensis) Mesocarp

Oil palm fruits exposed to temperatures of 15 °C and belowshowed a significant increase in free fatty acid (FFA) contentin the mesocarp. This effect was most pronounced in fruits exposedto 5 °C when FFA levels exceeding 70% of the total oil wereobserved. The increase in FFA was accompanied by an increasein lipid-soluble phosphorus levels and a decrease in carotenecontent. Chilling did not have an effect on palm kernel oil.The results suggest the activation of a lipase in the mesocarpby low temperature stress. Key words: Lipase, oil palm, free fatty acid