Expanding the Landscape of Amyloid Sequences with CARs-DB: A Database of Polar Amyloidogenic Peptides from Disordered Proteins.

Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura

Methods in molecular biology (Clifton, N.J.) 2024

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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/ . © 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Citation

Carlos Pintado-Grima, Oriol Bárcenas, Salvador Ventura. Expanding the Landscape of Amyloid Sequences with CARs-DB: A Database of Polar Amyloidogenic Peptides from Disordered Proteins. Methods in molecular biology (Clifton, N.J.). 2024;2714:171-185