Identification of the active site of human mitochondrial malonyl‐coenzyme a decarboxylase: A combined computational study

Malonyl‐CoA decarboxylase (MCD) can control the level of malonyl‐CoA in cell through the decarboxylation of malonyl‐CoA to acetyl‐CoA, and plays an essential role in regulating fatty acid metabolism, thus it is a potential target for drug discovery. However, the interactions of MCD with CoA derivatives are not well understood owing to unavailable crystal structure with a complete occupancy in the active site. To identify the active site of MCD, molecular docking and molecular dynamics simulations were performed to explore the interactions of human mitochondrial MCD (HmMCD) and CoA derivatives. The findings reveal that the active site of HmMCD indeed resides in the prominent groove which resembles that of CurA. However, the binding modes are slightly different from the one observed in CurA due to the occupancy of the side chain of Lys183 from the N‐terminal helical domain instead of the adenine ring of CoA. The residues 300 ? 305 play an essential role in maintaining the stability of complex mainly through hydrogen bond interactions with the pyrophosphate moiety of acetyl‐CoA. Principle component analysis elucidates the conformational distribution and dominant concerted motions of HmMCD. MM_PBSA calculations present the crucial residues and the major driving force responsible for the binding of acetyl‐CoA. These results provide useful information for understanding the interactions of HmMCD with CoA derivatives. Proteins 2016; 84:792–802. © 2016 Wiley Periodicals, Inc.     

南海北部生态系统食物网结构、能量流动及系统特征

根据20072008年在南海北部(107°00'120°00'E、17°00'23°30'N)进行的海洋生态综合调查数据,应用Ecopath with Ecosim软件构建了南海北部生态系统的生态通道模型,并通过模型分析了南海北部海洋生态系统的食物网结构、能量流动和系统的总体特征,并简要总结过度捕捞生态系统的基本特征。结果表明,南海北部海洋生态系统以捕食食物链为主要能流通道,初级生产者是系统能量的主要来源。各功能群的营养级范围为13.99,哺乳动物占据了最高的营养层,平均渔获物营养级为2.93。利用生态网络分析,系统的能量流动主要有6级,来自初级生产者的能流效率为12.6%,来自碎屑的转换效率为10.4%,平均能量转换效率为11.5%。系统连接指数(Connectance Index,CI)和系统杂食指数(System Omnivory Index,SOI)分别为0.290和0.239;Finn’s循环指数(Finn’scy cling index,FCI)和系统平均路径长度(Finn’s mean path length,MPL)分别为4.380和2.476;总初级生产力/总呼吸为2.596,综合研究表明当前南海北部海洋生态系统处于不成熟阶段。     

Mitochondrial Oxidative Phosphorylation Regulates the Fate Decision between Pathogenic Th17 and Regulatory T Cells

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混合盐碱胁迫对青山杨渗透调节物质及活性氧代谢的影响

为研究青山杨(Populus pseudo-cathayana × P. deltoides)对盐碱的适应能力,对青山杨2年生扦插苗进行不同盐度和碱度的28组胁迫处理.结果表明：随盐浓度增加,青山杨叶片的电解质外渗率、丙二醛和脯氨酸含量呈上升趋势,可溶性糖、SOD和POD活性先升后降.pH值升高使电解质外渗率、丙二醛和POD活性呈上升趋势,脯氨酸和可溶性糖含量先升后降,SOD活性上升趋势不明显.盐浓度低于100 mmol·L^-1时,随pH值升高,各项生理指标的变化不明显,SOD具有较高的活性;盐浓度在200 mmol·L^-1、pH 8.99以上时,其电解质外渗率在50%以上,POD活性和丙二醛含量大幅度增加,脯氨酸和可溶性糖含量下降,SOD活性较低.推断盐浓度>200 mmol·L^-1、pH>8.99的盐碱条件不适宜青山杨的生长.     

Block of mitochondrial apoptotic pathways in lizard ovarian follicle cells as an adaptation to their nurse function

Pyriforms are ovarian follicle nurse cells that undergo apoptosis at the end of previtellogenesis and are completely eliminated by the epithelium. This event is accompanied by the active transfer of organelles and macromolecules to the oocyte via an intercellular bridge. Since it would be a nonsense for damaged mitochondria to reach the oocyte, we have postulated that pyriform cells have adapted their apoptotic machinery to prevent mitochondrial degradation. To verify this hypothesis, we have studied mitochondrial morphology and functionality during follicle cell regression. Cytological and biochemical evidence indicates that mitochondria in pyriforms maintain their size, organization and membrane potential. This clearly indicates that they are not involved in apoptosis signalling/progression. This block would favour both the oocyte, by increasing the pool of organelles available from follicle cells, and also the regressing pyriforms, by maintaining the energy resources required for completion of their nurse function. The block is probably attributable to an over-expression of Bcl-2 and might be carried out by sequestering cytochrome c inside the organelles. As demonstrated by in vitro experiments, the mitochondrial apoptosis pathway can be activated by stress induction, such as serum deprivation, but not following physiological pro-apoptotic signalling, such as treatment with gonadotrophin-releasing hormone. These studies were supported by a grant from the MIUR (PRIN project: Molecular responses of embryonic, differentiated and tumoral cells exposed to cadmium intoxication).     

The effects of cultural conditions on growth and secondary metabolism in Streptomyces thermoviolaceus

Abstract Granaticin, an isochromate quinone antibiotic is synthesized as a secondary metabolite by Streptomyces thermoviolaceus . Antibiotic productivity was investigated under a variety of cultural conditions, including complex and defined media, mesophilic and thermophilic temperatures and a variety of sole carbon sources. In a defined medium growth was supported, to varying extents, by different carbon sources and in most cases granaticin production was observed. Highest biomass and granaticin yields were obtained when cultures were grown in the presence of xylan, fructose, glutamate or proline as carbon source. Changes in pH during growth affected both the timing and extent of granaticin production.     

Disturbed nitrogen metabolism associated with the hyperhydric status of fully habituated callus of sugarbeet

The content of polyamines and proline was much lower in a normal (N) callus of Beta vulgaris L. than in a fully habituated hyperhydric (H) callus. The H callus also contained more glutamate and had a higher glutamate dehydrogenase activity. The excess of glutamate, in this chlorophyll-deficient callus, was linked to accumulation of proline and polyamines. Experiments with α-difluoromethylornithine (DFMO) and α-difluoromethylarginine (DFMA) showed that both ornithine decarboxylase and arginine decarboxylase participated in the synthesis of polyamines (especially spermidine and putrescine) and removal of ammonia. It is hypothesized that the H callus was subjected to ammonia stress from the start of the culture. Experiments with gabaculine, an inhibitor of ornithine aminotransferase, showed that this enzyme linked proline degradation to polyamine synthesis through the production of ornithine. This disturbed nitrogen metabolism appeared to be characteristic of the fully habituated callus and might explain the low growth of this hyperhydric tissue.     

The Serine Hydroxymethyltransferase of Plasmodium lophurae*

SYNOPSIS. Plasmodium lophurae serine hydroxymethyltransferase (EC 2.1.2.1) was partially purified and characterized by (NH₄)₂SO₄ fractionation and chromatography on Sephadex G-100. The enzyme, precipitated by 3.0–3.3 m (NH₄)₂SO₄, had a molecular weight of 68,300 as estimated by exclusion chromatography on G-100. The pH optimum of the enzyme was 6.8–7.6 in sodium phosphate-citrate buffer. Citrate stabilized the enzyme during storage in phosphate buffer at 4 C. The K_m was 4.3 × 10^?3m for l -serine and 2.5 × 10^?4m for tetrahydrofolate.     

The systematic substitutions around the conserved charged residues of the cytoplasmic loop of Na+-driven flagellar motor component PomA

PomA, a homolog of MotA in the H+-driven flagellar motor, is an essential component for torque generation in the Na+-driven flagellar motor. Previous studies suggested that two charged residues, R90 and E98, which are in the single cytoplasmic loop of MotA, are directly involved in this process. These residues are conserved in PomA of Vibrio alginolyticus as R88 and E96, respectively. To explore the role of these charged residues in the Na+-driven motor, we replaced them with other amino acids. However, unlike in the H+-driven motor, both of the single and the double PomA mutants were functional. Several other positively and negatively charged residues near R88 and E96, namely K89, E97 and E99, were neutralized. Motility was retained in a strain producing the R88A/K89A/E96Q/E97Q/E99Q (AAQQQ) PomA protein. The swimming speed of the AAQQQ strain was as fast as that of the wild-type PomA strain, but the direction of motor rotation was abnormally counterclockwise-biased. We could, however, isolate non-motile or poorly motile mutants when certain charged residues in PomA were reversed or neutralized. The charged residues at positions 88-99 of PomA may not be essential for torque generation in the Na+-driven motor and might play a role in motor function different from that of the equivalent residues of the H+-driven motor.