淀粉样蛋白生成序列的边界：PDB \_Amyloid Collection中平行β折叠的前缀分析
On the Border of the Amyloidogenic Sequences: Prefix Analysis of the Parallel Beta Sheets in the PDB\_Amyloid Collection
摘要：
蛋白质数据库（PDB）今天包含超过153，000个生物大分子三维结构的条目。使用这个存储库的丰富资源，可以为不同的应用程序识别具有特定的、有趣的属性的子集。我们的研究小组准备了一份自动更新的淀粉样蛋白和可能的淀粉样蛋白生成分子列表，PDB\_Amyloid collection，可在地址\url{http://pitgroup.org/amyloid}免费获得。该资源专门应用空间结构的几何特性来识别淀粉样蛋白。在本贡献中，我们分析了开始（即，前缀）序列，并鉴定这些长度为5的前缀序列在整个PDB数据集中的进一步出现。我们已经以这种方式鉴定了许多蛋白质，其正常或不正常功能涉及淀粉样蛋白形成、结构错误折叠或抗凝血特性，仅仅通过包含这些前缀：包括与主要组织相容性复合体MHC-1和MHC-2结合的T细胞受体（TCR）; p53肿瘤抑制蛋白;分枝杆菌RNA聚合酶转录起始复合体;人桥接整合蛋白BIN-1;和蜱抗凝肽TAP。
英文摘要：
The Protein Data Bank (PDB) today contains more than 153,000 entries with the 3-dimensional structures of biological macromolecules. Using the rich resources of this repository, it is possible identifying subsets with specific, interesting properties for different applications. Our research group prepared an automatically updated list of amyloid- and probably amyloidogenic molecules, the PDB\_Amyloid collection, which is freely available at the address \url{http://pitgroup.org/amyloid}. This resource applies exclusively the geometric properties of the steric structures for identifying amyloids. In the present contribution, we analyze the starting (i.e., prefix) subsequences of the characteristic, parallel beta-sheets of the structures in the PDB\_Amyloid collection, and identify further appearances of these length-5 prefix subsequences in the whole PDB data set. We have identified this way numerous proteins, whose normal or irregular functions involve amyloid formation, structural misfolding, or anti-coagulant properties, simply by containing these prefixes: including the T-cell receptor (TCR), bound with the major histocompatibility complexes MHC-1 and MHC-2; the p53 tumor suppressor protein; a mycobacterial RNA polymerase transcription initialization complex; the human bridging integrator protein BIN-1; and the tick anti-coagulant peptide TAP.
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