Neural network-based analysis of thiol proteomics data in identifying potential selenium targets

Generation of a monomethylated selenium metabolite is critical for the anticancer activity of selenium. Because of its strong nucleophilicity, the metabolite can react directly with protein thiols to cause redox modification. Here, we report a neural network-based analysis to identify potential selenium targets. A reactive thiol specific reagent, BIAM, was used to monitor thiol proteome changes on 2D gel. We constructed a dynamic model and evaluated the relative importance of proteins mediating the cellular responses to selenium. Information from this study will provide new clues to unravel mechanisms of anticancer action of selenium. High impact selenium targets could also serve as biomarkers to gauge the efficacy of selenium chemoprevention.     

Mapping of a new autosomal dominant spinocerebellar ataxia to chromosome 22.

The autosomal dominant cerebellar ataxias (ADCAs) are a clinically and genetically heterogeneous group of disorders. The clinical symptoms include cerebellar dysfunction and associated signs from dysfunction in other parts of the nervous system. So far, five spinocerebellar ataxia (SCA) genes have been identified: SCA1, SCA2, SCA3, SCA6, and SCA7. Loci for SCA4 and SCA5 have been mapped. However, approximately one-third of SCAs have remained unassigned. We have identified a Mexican American pedigree that segregates a new form of ataxia clinically characterized by gait and limb ataxia, dysarthria, and nystagmus. Two individuals have seizures. After excluding all known genetic loci for linkage, we performed a genomewide search and identified linkage to a 15-cM region on chromosome 22q13. A maximum LOD score of 4.3 (recombination fraction 0) was obtained for D22S928 and D22S1161. This distinct form of ataxia has been designated "SCA10." Anticipation was observed in the available parent-child pairs, suggesting that trinucleotide-repeat expansion may be the mutagenic mechanism.     

A protein-protein docking algorithm dependent on the type of complexes

An efficient 'soft docking' algorithm is described to assist the prediction of protein-protein association using three-dimensional structures of molecules. The basic tools are the 'simplified protein' model and the docking algorithm of Wodak and Janin. The side chain flexibility of Arg, Lys, Asp, Glu and Met residues at the protein surface is taken into account. The complex type-dependent filtering technique on the basis of the geometric matching, hydrophobicity and electrostatic complementarity is used to select candidate binding modes. Subsequently, we calculate a scoring function which includes electrostatic and desolvation energy terms. In the 44 complexes tested including enzyme-inhibitor, antibody-antigen and other complexes, native-like structures were all found, of which 30 were ranked in the top 20. Thus, our soft docking algorithm has the potential to predict protein-protein recognition.     

低氧预适应增高小鼠脑组织内cPKCγ的膜转位水平

本实验拟通过观察重复性低氧对经典型蛋白激酶C(cPKC)膜转位水平(激活程度)的影响,初步探讨cPKC特定亚型在脑低氧预适应发生过程中的作用。按我室已建立的小鼠低氧预适应模型方法,制备重复性低氧1-4次的小鼠(H1-H4)。应用SDS-聚丙烯酰胺凝胶电泳(SDS-PAGE)、蛋白印迹(Western bolt)等生化技术,并结合Gel Doc凝胶成像系统,半定量检测小鼠海马和大脑皮层组织内cPKCα和γ的膜转位水平。实验结果表明,随低氧次数(H1-H4)的增加,小鼠海马组织内cPKCγ的膜转位水平明显增高,且在H2、H3和H4组的变化具有统计学显著意义(P<0.05,n=6);同样,大脑皮层内cPKCγ膜转位水平也随低氧次数的增加(H1-H4)而明显增高,且在H2、H3和H4组的变化具有统计学显著意义(P<0.05,n=6):而cPKCα亚型无论在大脑皮层还是在海马组织内的膜转位变化均无统计学意义。上述观察结果提示,cPKCγ膜转位可能在脑低氧预适应的发生发展过程中发挥着重要作用;但cPKCβ Ⅰ、β Ⅱ以及其它新奇型和非典型PKC特定亚型的变化还有待于进一步的研究和探讨。     

Reduction potentials of Rieske clusters: importance of the coupling between oxidation state and histidine protonation state

Rieske [2Fe-2S] clusters can be classified into two groups, depending on their reduction potentials. Typical high-potential Rieske proteins have pH-dependent reduction potentials between +350 and +150 mV at pH 7, and low-potential Rieske proteins have pH-independent potentials of around -150 mV at pH 7. The pH dependence of the former group is attributed to coupled deprotonation of the two histidine ligands. Protein-film voltammetry has been used to compare three Rieske proteins: the high-potential Rieske proteins from Rhodobacter sphaeroides (RsRp) and Thermus thermophilus (TtRp) and the low-potential Rieske ferredoxin from Burkholderia sp. strain LB400 (BphF). RsRp and TtRp differ because there is a cluster to serine hydrogen bond in RsRp, which raises its potential by 140 mV. BphF lacks five hydrogen bonds to the cluster and an adjacent disulfide bond. Voltammetry measurements between pH 3 and 14 reveal that all the proteins, including BphF, have pH-dependent reduction potentials with remarkably similar overall profiles. Relative to RsRp and TtRp, the potential versus pH curve of BphF is shifted to lower potential and higher pH, and the pK(a) values of the histidine ligands of the oxidized and reduced cluster are closer together. Therefore, in addition to simple electrostatic effects on E and pK(a), the reduction potentials of Rieske clusters are determined by the degree of coupling between cluster oxidation state and histidine protonation state. Implications for the mechanism of quinol oxidation at the Q(O) site of the cytochrome bc(1) and b(6)f complexes are discussed.     

Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater

Nitrate-contaminated groundwater samples were analysed for nirK and nirS gene diversity. The samples differed with respect to nitrate, uranium, heavy metals, organic carbon content, pH and dissolved oxygen levels. A total of 958 nirK and 1162 nirS clones were screened by restriction fragment length polymorphism (RFLP) analysis: 48 and 143 distinct nirK and nirS clones, respectively, were obtained. A single dominant nirK restriction pattern was observed for all six samples and was 83% identical to the Hyphomicrobium zavarzinii nirK gene. A dominant nirS pattern was observed for four of the samples, including the background sample, and was 95% identical to the nirS of Alcaligenes faecalis. Diversity indices for nirK and nirS sequences were not related to any single geochemical characteristic, but results suggested that the diversity of nirK genes was inversely proportional to the diversity of nirS. Principal component analysis (PCA) of the sites based on geochemistry grouped the samples by low, moderate and high nitrate but PCA of the unique operational taxonomic units (OTUs) distributions grouped the samples differently. Many of the sequences were not closely related to previously observed genes and some phylogenetically related sequences were obtained from similar samples. The results indicated that the contaminated groundwater contained novel nirK and nirS sequences, functional diversity of both genes changed in relation to the contaminant gradient, but the nirK and nirS functional diversity was affected differently.     

Breaking and re-forming the disulfide bond at the high-potential,respiratory-type Rieske [2Fe-2S] center of thermus thermophilus: characterization of the sulfhydryl state by protein-film voltammetry

A disulfide bond, adjacent to the [2Fe-2S] cluster, is conserved in all high-potential Rieske proteins from the respiratory and photosynthetic cytochrome bc(1) and b(6)f complexes but is absent from the low-potential, bacterial dioxygenase Rieske proteins. The role of the disulfide is unclear, since cysteine mutants have resulted in only apoprotein. The high stability of the soluble Thermus thermophilus Rieske protein permits chemical reduction of the disulfide bond and characterization of the sulfhydryl (dithiol) form by protein-film voltammetry. The effect of disulfide reduction on the cluster potential is small (DeltaE(0)' 相似文献   

人突变appE基因在转基因鼠体内的表达及血清脂质变化

为了研究人突变ａｐｏＥ７基因在血脂代谢中的作用．采用微注射的方法建立了人ａｐｏＥ７转基因鼠,三个首建鼠（ｔｇ１,ｔｇ２,ｔｇ３）整合目的基因的拷贝数相差２倍左右,其血中表达的人ａｐｏＥ７的水平也不相同,低水平表达的ｔｇ１为１．２６ｍｇ／ｄｌ,高水平表达的首建鼠ｔｇ３血清中ａｐｏＥ７浓度可高达２１．１ｍｇ／ｄｌ．异常ａｐｏＥ基因的表达导致了转基因鼠血清甘油三酯和胆固醇明显升高,为对照的１．５～３倍．高密度脂蛋白ＨＤＬ降低,低密度脂蛋白ＬＤＬ和极低密度脂蛋白ＶＬＤＬ升高．经２０ｍｍｏｌ／ＬＺｎＳＯ４诱导后,Ｆ１代Ｔｇ３鼠系血清甘油三酯（ＴＧ）水平高达４４４ｍｇ／ｄｌ,胆固醇（ＴＣ）高达２３４ｍｇ／ｄ１．ＨＤＬ升高和ＬＤＬ／ＶＬＤＬ降低十分明显,表现了高脂血症的指征．     

天花粉蛋白R122G突变体的构建及活性研究

天花粉蛋白Ｒ１２２Ｇ突变体的构建及活性研究袁惠东１柯一保孔梅柯欣永夏其昌１张祖传１聂慧玲＊（中国科学院上海细胞生物学研究所,上海２０００３１;１中国科学院上海生物化学研究所,上海２０００３１）关键词天花粉蛋白;突变体;ＲＮＡＮ－糖苷酶天花粉蛋白（ｔｒ...