CARs-DB: A Database of Cryptic Amyloidogenic Regions in Intrinsically Disordered Proteins

Abstract

Proteome-wide analyses suggest that most globular proteins contain at least one amyloidogenic region, whereas these aggregation-prone segments are thought to be underrepresented in intrinsically disordered proteins (IDPs). In recent work, we reported that intrinsically disordered regions (IDRs) indeed sustain a significant amyloid load in the form of cryptic amyloidogenic regions (CARs). CARs are widespread in IDRs, but they are necessarily exposed to solvent, and thus they should be more polar and have a milder aggregation potential than conventional amyloid regions protected inside globular proteins. CARs are connected with IDPs function and, in particular, with the establishment of protein-protein interactions through their IDRs. However, their presence also appears associated with pathologies like cancer or Alzheimer’s disease. Given the relevance of CARs for both IDPs function and malfunction, we developed CARs-DB, a database containing precomputed predictions for all CARs present in the IDPs deposited in the DisProt database. This web tool allows for the fast and comprehensive exploration of previously unnoticed amyloidogenic regions embedded within IDRs sequences and might turn helpful in identifying disordered interacting regions. It contains >8,900 unique CARs identified in a total of 1711 IDRs. CARs-DB is freely available for users and can be accessed at http://carsdb.ppmclab.com. To validate CARs-DB, we demonstrate that two previously undescribed CARs selected from the database display full amyloidogenic potential. Overall, CARs-DB allows easy access to a previously unexplored amyloid sequence space.

Exploring cryptic amyloidogenic regions in prion-like proteins from plants

“…Regarding the molecular functions of pCARs, significant enrichments were found for regulative processes, especially for nucleic acids, including DNA, RNA and mRNA binding, but also protein binding ( Figure 5 ; Supplementary Table 1 ). This is interesting, as CARs have already been described to mediate key PPIs in IDPs ( Santos et al., 2021 ; Pintado-Grima et al., 2022a ). It is not surprising that, provided the previously proposed regulatory function of CARs, pCARs are found enriched in biological activities of gene expression, transcription, and translation.…”

“…The concept of CARs has been gaining strength by means of the continuous experimental validation of predicted segments of hydrophilic nature that form amyloid fibrils in vitro ( Santos et al., 2021 ; Pintado-Grima et al., 2022a ). Our goal is to increase the body of evidence on the intrinsic amyloidogenic potential of these sequences, when they are disconnected from their interpCARs regions.…”

“…PLAAC searches protein sequences to identify probable prion subsequences exploiting a hidden-Markov model (HMM) algorithm using the selected background probabilities. pCARs longer than six residues were obtained from PrLDs by applying the Waltz algorithm at thresholds 73.5, 80, and 85, as optimized in our original study of CARs ( Santos et al., 2021 ) and CARs-DB ( Pintado-Grima et al., 2022a ) to account for polar amyloidogenic regions. The Waltz algorithm ( Maurer-Stroh et al., 2010 ) explores the sequence determinants of amyloid structure using position-specific scoring matrices derived from analyzing a database of short amyloid-forming and non-forming sequences.…”

“…In fact, CARs consistently overlap with interacting motifs in IDPs. We collected these predictions in a comprehensive database named CARs-DB ( Pintado-Grima et al., 2022a ).…”

Confident protein datasets for liquid-liquid phase separation studies

“…While hydrophobic aggregation-prone regions in IDRs are traditionally considered deleterious due to their likelihood to nucleate toxic amyloid formation [47,48], cryptic amyloidogenic regions of a polar nature are widespread in both IDRs and PrLDs [36,49]. These regions endorse disordered proteins with a self-assembly potential to establish interactions while minimizing the risk of pathogenic aggregation.…”