MobiDB: intrinsically disordered proteins in 2021

Abstract

The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users.

Light-triggered and phosphorylation-dependent 14-3-3 association with NONPHOTOTROPIC HYPOCOTYL 3 is required for hypocotyl phototropism

“…Since both the N-and C-terminal domain of NPH3 are predicted to be intrinsically disordered (Fig. S1, [25]), the corresponding truncated versions were analyzed by yeast two hybrid assays. While NPH3 lacking the N-terminal 54 residues (NPH3DN54, still comprising the BTB domain) was capable of 14-3-3 binding, deletion of the C-terminal 51 residues (NPH3DC51, still comprising the CC domain) abolished 14-3-3 association, suggesting that the 14-3-3 binding site localizes downstream of the CC domain (Fig.…”

Interplay between disordered regions in RNAs and proteins modulates interactions within stress granules and processing bodies

“…We retrieved from BioGRID [39] all binary protein-protein interactions (PPIs) involving proteins located in SGs and PBs (Materials and Methods and Supplementary Table 2) [48] and, as a control, an equal amount of PPI with interactors that were not found therein (extracted multiple times, Supplementary Figure 5). In this analysis, we measured the amount of disorder available using MobiDB [49] (mean disHL disorder score for each pair) (Figure 3A and Supplementary Figure 5 and 6 ). In addition, we also measured the amount of disorder of single condensates and non-condensates proteins (Supplementary Figure 7).…”

“…Based on the increased amount of single-stranded regions in enriched RNAs and their capacity to form a larger number of interactions with proteins, we expected an increased amount of disorder in RBPs. To test this hypothesis, we analyzed the least and most structured RNAs (data from DMS measured in vivo) [36] in SGs and PBs and measured the disorder content (disHL score from MobiDB) of the interacting proteins [49] (Materials and Methods). In this analysis we focused on proteins that bind to RNA as predicted by catRAPID and for which the eCLIP interactome is available [32].…”

“…Information about human protein disorder predictions were retrieved from MobiDB database (version 4.0) [49], from which we selected the predictions obtained with DisEMBL tool with hot loops threshold (DisHL) [56]…”

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

“…For proteins without regular stable structures, the Issue offers a trio of databases. The main innovations at the returning database MobiDB ( 31 ) cover functional annotations relating to disordered regions; regions undergoing a disorder to order transition on binding, predicted linear interaction motifs, post-translational modifications and regions implicated in phase separation. PED ( 32 ), also publishing an update, covers experimentally characterized structural ensembles of disordered regions and proteins.…”