Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain.
Methods Mol Biol. 2024;2714:171-185. doi: 10.1007/978-1-0716-3441-7_10.
Several databases collecting amyloidogenic regions have been released to provide information on protein sequences able to form amyloid fibrils. However, most of these resources are built with data from experiments that detect highly hydrophobic stretches located within transiently exposed protein segments. We recently demonstrated that cryptic amyloidogenic regions (CARs) of polar nature have the potential to form amyloid fibrils in vitro. Given the underrepresentation of these types of sequences in current amyloid databases, we developed CARs-DB, the first repository that collects thousands of predicted CARs from intrinsically disordered regions. This protocol chapter describes how to use CARs-DB to search for sequences of interest that might be connected to disease or functional protein-protein interactions. In addition, we provide study cases to illustrate the database's features to users. The CARs-DB is readily accessible at http://carsdb.ppmclab.com/ .
已经发布了几个收集淀粉样蛋白区域的数据库，以提供能够形成淀粉样纤维的蛋白质序列的信息。然而，这些资源中的大多数都是基于实验数据构建的，这些实验检测到位于瞬态暴露的蛋白质片段中的高度疏水序列。我们最近证明，具有极性的隐匿性淀粉样蛋白区域（CARs）有可能在体外形成淀粉样纤维。鉴于目前淀粉样蛋白数据库中这些类型的序列代表性不足，我们开发了 CARs-DB，这是第一个从无序区域中收集数千个预测 CARs 的存储库。本章描述了如何使用 CARs-DB 搜索可能与疾病或功能性蛋白质-蛋白质相互作用有关的感兴趣序列。此外，我们还为用户提供了案例研究来说明数据库的功能。CARs-DB 可在 http://carsdb.ppmclab.com/ 上轻松访问。
