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Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations

Acta Pharmacologica Sinica 2004年第12期25卷 146-152页

作者： xiao-hui cai, Qing ZHANG, da-fu ding2 key laboratory of proteomics, institute of biochemistry and cell biology, shanghai institutes for biological sciences, chinese academy of sciences, graduate school of the chinese academy of sciences, shanghai 200031, china 中科院上海生命科学院 Key Laboratory of Proteomics CAS 上海 200031

AIM: To model the three-dimensional structure and investigatethe interaction mechanism ofthe proprotein convertase furin/kexin and their inhibitors (eglin c mutants). METHODS: The three-dimensional complex structures of furin/ kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition con- stants to find the correlation between them. RESULTS: High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostaticenergies of interaction showeda linear correlation to the experimental inhibition constants. CONCLUSION: The modeled structures give good explanations of the specificity of eglin c mutants to furin/ kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge- charge interactions in the binding of furin/kexin and their inhibitors.

关键词： furin kexin eglin c drug design electrostatic mutation

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Searching for Potential Drug Targets in Two-component and Phosphorelay Signal-transduction Systems using Three-dimensional Cluster Analysis

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Acta Biochimica et Biophysica Sinica 2005年第5期37卷 293-302页

作者： xiao-hui cai Qing ZHANG shuo-yong shi da-fu ding key laboratory of Proteonmics,institute of biochemistry and cell biology,Stanghai institutes for biological sciences, chinese academy of sciences,graduate school of the chinese academy of sciences, shanghai 200031,china key laboratory of proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China

Two-component and phosphorelay signal transduction systems are central components in thevirulence and antimicrobial resistance responses of a number of bacterial and fungal pathogens;in somecases,these systems are essential for bacterial growth and ***,we analyze in detail the conservedsurface residue clusters in the phosphotransferase domain of histidine kinases and the regulatory domain ofresponse regulators by using complex structure-based three-dimensional cluster *** also investigatethe protein-protein interactions that these residue clusters participate *** Spo0B-Spo0F complex structurewas used as the reference structure,and the multiple aligned sequences of phosphotransferases and responseregulators were paired *** results show that a contiguous conserved residue cluster isformed around the active site,which crosses the interface of histidine kinases and response *** residue clusters of phosphotransferase and the regulatory domains are directly involved in thefunctional implementation of two-component signal transduction systems and are good targets for thedevelopment of novel antimicrobial agents.

关键词： two-component system phosphorelay histidine kinase response regulator three-dimensional cluster analysis

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Identification and Categorization of Horizontally Transferred Genes in Prokaryotic Genomes

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Acta Biochimica et Biophysica Sinica 2005年第8期37卷 561-566页

作者： shuo-yong shi~1 xiao-hui cai~1 and da-fu ding~(1,2*) key laboratory of proteomics.institute of biochemistry and cell biology.shanghai institutes for biological sciences,chinese academy of sciences,graduate school of the chinese academy of sciences.shanghai 200031,china ~2 school of Life Science & Technology.shanghai Jiaotong University.shanghai 200030.china key laboratory of proteomics Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Graduate School of the Chinese Academy of SciencesShanghai 200031 China school of Life Science & Technology Shanghai Jiaotong UniversityShanghai 200030 China

Horizontal gene transfer(HGT),a process through which genomes acquire genetic materialsfrom distantly related organisms,is believed to be one of the major forces in prokaryotic genome ***,systematic investigation is still scarce to clarify two basic issues about HGT:(1) what types ofgenes are transferred:and(2)what influence HGT events over the organization and evolution of ***-scale investigations of these two issues will advance the systematical understanding ofHGT in the context of prokaryotic genome *** investigated 82 genomes,we constructed anHGT database across broad evolutionary *** identified four function categories containing a highproportion of horizontally transferred genes:cell envelope,energy metabolism,regulatory functions,andtransport/binding *** biased function distribution indicates that HGT is not completely random;instead,it is under high selective pressure,required by function restraints in ***,wemapped the transferred genes onto the connectivity structure map of organism-specific pathways listed inKyoto Encyclopedia of Genes and Genomes(KEGG).Our results suggest that recruitment of transferredgenes into pathways is also selectively constrained because of the tuned interaction between original *** organization structures still conserve well through evolution even with the recruitment ofhorizontally transferred ***,in pathways whose organization were significantly affected byHGT events,the operon-like arrangement of transferred genes was found to be *** resultssuggest that operon plays an essential and directional role in the integration of alien genes into pathways.

关键词： genome evolution horizontal gene transfer function and pathway analysis

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从酵母表达时间序列估计基因调控网络

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生物化学与生物物理学报 2003年第8期35卷 707-716页

作者：徐肖江王连水丁达夫中国科学院上海生命科学研究院生物化学与细胞生物学研究所蛋白质组学重点实验室中国科学院上海生命科学研究院生物化学与细胞生物学研究所蛋白质组学重点实验室上海200031

基因调控网络是生命功能在基因表达层面上的展现。用组合线性调控模型、调控元件识别和基因聚类等方法 ,从基因组表达谱解读酵母在细胞周期与环境胁迫中的基因调控网络。结果表明 ,细胞在不同环境条件下会调整基因调控网络。在适应的环... 详细信息

基因调控网络是生命功能在基因表达层面上的展现。用组合线性调控模型、调控元件识别和基因聚类等方法 ,从基因组表达谱解读酵母在细胞周期与环境胁迫中的基因调控网络。结果表明 ,细胞在不同环境条件下会调整基因调控网络。在适应的环境下 ,起主要作用的是细胞生长和增殖有关的基因调控网络 ;而在响应环境胁迫时 ,细胞会再规划调控网络 ,抑制细胞生长和增殖相关的基因 ,诱导跟适应性糖类代谢与结构修复相关的基因 ,还可能启动减数分裂产生孢子。分别从细胞周期和环境胁迫响应相关基因中 ,搜索到转录因子Mcm1结合位点TT CC T GGAAA ,和dal82在尿囊素代谢途径相关基因上的结合位点TGAAAAWTTT。从而 ,从酵母表达时间序列估计基因调控网络是可行的 ,与至今已知的实验观察相当吻合

关键词：基因调控网络基因组表达时间序列细胞周期环境胁迫

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