High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder

Abstract

Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein–protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/

Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions

“…Next we used the programs ANCHOR [17], DisoRDPbind [18] and JPred4 [22] to analyze full-length protein sequences to predict the ability of the selected IDRs to form folded structures (Table 2). The ANCHOR program analyzes amino acid sequence to predict short regions (that we term Anchor regions) within or flanking IDRs that likely stabilize the IDR in an ordered state upon binding.…”

“…DisoRDPbind predicts RNA, DNA, and protein binding regions within IDRs based on amino acid content, sequence complexity, predicted structure and disorder, and sequence alignments [18]. Of the known MoRFs that we selected, all are predicted to contain Anchor regions; however, only GRIM is predicted by DisoRDPbind to contain a protein-binding site (Table 2).…”

“…These sequences were analyzed with IsUnstruct (http://bioinfo.protres.ru/IsUnstruct/) [19], PONDR-FIT (http://www.disprot.org/metapredictor.php) [20], and IUPred (http://iupred.enzim.hu) [21] to predict whether the selected peptide sequences were intrinsically disordered (Table 2). The sequences were also analyzed with ANCHOR (http://anchor.enzim.hu) [17] and DisoRDPbind (http://biomine-ws.ece.ualberta.ca/DisoRDPbind/index.php) [18] to predict whether the selected IDRs were likely to undergo binding-associated structure stabilization (Table 2). Finally, these sequences were analyzed with Jpred4 (http://www.compbio.dundee.ac.uk/jpred/) [22] to predict secondary structure.…”

“…However, binding partners remain unknown for most IDRs, complicating experimental elucidation of structural transitions within IDRs. We hypothesized that it would be possible to identify α-MoRFs by bioinformatics analyses using programs such as ANCHOR [17] and DisoRDPbind [18] combined with experimental evaluation of chemically-induced structural transitions.…”

“…We first performed a bioinformatics analysis using the programs IsUnstruct [19], PONDR-FIT [20] and IUPred [21] to predict IDRs, then used the programs ANCHOR [17] and DisoRDPbind [18] to identify IDRs that are likely to be stabilized in ordered structures upon binding. JPred4 [22] was used to predict potential secondary structure.…”