物理化学学报 >> 2005, Vol. 21 >> Issue (05): 499-503.doi: 10.3866/PKU.WHXB20050508

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泉生热袍菌结构基因组的选靶研究

裴剑锋; 来鲁华   

  1. 北京大学化学与分子工程学院, 分子动态与稳态结构国家重点实验室，北京  100871； 北京大学理论生物学中心，北京  100871
  • 收稿日期:2004-09-29 修回日期:2004-12-01 发布日期:2005-05-15
  • 通讯作者: 来鲁华 E-mail:lhlai@pku.edu.cn

Protein Target Selection for Structural Genomics of Thermoanaerobacter Tengcongensis

PEI Jian-Feng; LAI Lu-Hua   

  1. State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing   100871;  Center for Theoretical Biology, Peking University, Beijing   100871
  • Received:2004-09-29 Revised:2004-12-01 Published:2005-05-15
  • Contact: LAI Lu-Hua E-mail:lhlai@pku.edu.cn

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摘要： 对泉生热袍菌进行了结构基因组的选靶研究，从泉生热袍菌的蛋白组中挑选了20个蛋白质作为第一批进行结构测定的目标，以发现新的蛋白质折叠模式. 选靶研究主要使用了BLAST搜索， PSI-BLAST搜索和ProtoNet数据库搜索等方法. 另外，还用PredictProtein程序对选中的蛋白质进行了二级结构和外形预测. 选中的20个蛋白质中有8个被克隆、表达和纯化，其中2个得到了单晶并收集了X衍射数据. 实验结果和最近一些文献报道的结果表明，挑选的一些蛋白质具有新的折叠模式，表明了这种选靶策略的有效性.

关键词: 泉生热袍菌, 结构基因组, 选靶, 蛋白质结构, BLAST, PSI-BLAST, ProtoNet

Abstract: 20 proteins were selected from Thermoanaerobacter tengcongensis proteome as the pilot group of targets for a structural genomics project which aims to fish for proteins with new folds and important biological functions. BLASTP, PSI-BLAST and TBLASTN searches were performed against pdb, nr and est-human databases, respectively, in order to find proteins that are least homologous to PDB proteins and most homologous to human proteins. Transmembrane protein predicting programs were used to classify membrane and soluble proteins. The selection was then made with further considerations on functions and parameters such as molecular weight and cysteine ratio. A validation made by the ProtoNet protein sequence hierarchical classification database showed that 95% of our target proteins locate in clusters that have no structures solved. Secondary structures and shapes of the target proteins predicted by PredictProtein program provided useful information for the experimental efforts. 8 selected proteins were cloned, expressed and purified, of which 2 were crystallized. Our experimental results and some recently published results show that some of our selected proteins bear new fold.

Key words: Thermoanaerobacter tengcongensis, Structural genomics, Target selection, Protein structure, BLAST, PSI-BLAST, ProtoNet