•IDRs exist as diverse and dynamic populations of interchanging structural conformations.•Subsets of these conformations can have distinct functions.•Cell state changes can shift the structural ...properties of IDRs to modulate their function.•The link between the (un)structure and function of IDRs is poorly understood.
After two decades of research, intrinsically disordered regions (IDRs) are established as a widespread phenomenon. The growing understanding of the significant functional role of IDRs has challenged the structure–function paradigm, proving irrefutably that a stably folded structure is not a strict requirement for function. Nonetheless, (un)structure–function relationships remain at the core of IDR-mediated interactions. An IDR can populate a continuously transitioning continuum of structural conformations from fully disordered to stable globular states. In these ensembles, only subsets of conformations are binding competent, with intramolecular IDR contacts serving as important intermolecular binding determinants. Here, we review our current understanding of different types of intramolecular IDR interactions, their effects on IDR complex formation and their modes of biological regulation.
RNA-binding proteins (RBPs) determine RNA fate from synthesis to decay. Employing two complementary protocols for covalent UV crosslinking of RBPs to RNA, we describe a systematic, unbiased, and ...comprehensive approach, termed “interactome capture,” to define the mRNA interactome of proliferating human HeLa cells. We identify 860 proteins that qualify as RBPs by biochemical and statistical criteria, adding more than 300 RBPs to those previously known and shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism, RNA-binding kinases, and RNA-binding architectures. Unexpectedly, we find that many proteins of the HeLa mRNA interactome are highly intrinsically disordered and enriched in short repetitive amino acid motifs. Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings.
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► Interactome capture identifies hundreds of RBPs previously unknown to bind RNA ► Some globular and disordered regions represent unorthodox binding architectures ► Many RNA binders are linked to Mendelian disease ► Metabolic enzymes moonlighting as RBPs
Interactome capture identifies the landscape of mRNA-binding proteins in mammalian cells, revealing new roles for metabolic enzymes and a propensity for globular and unstructured regions to associate with messages.
The anaphase-promoting complex or cyclosome (APC/C) is a ubiquitin ligase that polyubiquitinates specific substrates at precise times in the cell cycle, thereby triggering the events of late mitosis ...in a strict order. The robust substrate specificity of the APC/C prevents the potentially deleterious degradation of non-APC/C substrates and also averts the cell-cycle errors and genomic instability that could result from mistimed degradation of APC/C targets. The APC/C recognizes short linear sequence motifs, or degrons, on its substrates. The specific and timely modification and degradation of APC/C substrates is likely to be modulated by variations in degron sequence and context. We discuss the extensive affinity, specificity, and selectivity determinants encoded in APC/C degrons, and we describe some of the extrinsic mechanisms that control APC/C-substrate recognition. As an archetype for protein motif-driven regulation of cell function, the APC/C-substrate interaction provides insights into the general properties of post-translational regulatory systems.
Davey and Morgan review our current knowledge of the short linear sequence motifs, or degrons, that mediate specific and selective substrate binding to the ubiquitin ligase APC/C, and they discuss how variations in degron features and extrinsic regulation determine the timing of APC/C substrate degradation in mitosis.
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.
A molecular description of functional modules in the cell is the focus of many high-throughput studies in the postgenomic era. A large portion of biomolecular interactions in virtually all cellular ...processes is mediated by compact interaction modules, referred to as peptide motifs. Such motifs are typically less than ten residues in length, occur within intrinsically disordered regions, and are recognized and/or posttranslationally modified by structured domains of the interacting partner. In this review, we suggest that there might be over a million instances of peptide motifs in the human proteome. While this staggering number suggests that peptide motifs are numerous and the most understudied functional module in the cell, it also holds great opportunities for new discoveries.
The extensive intrinsically disordered regions of higher eukaryotic proteomes contain vast numbers of functional interaction modules known as short linear motifs (SLiMs). Here, we present SLiMSearch, ...a motif discovery tool that scans a motif consensus, representing the specificity determinants of a motif-binding domain, against a proteome to discover putative novel motif instances. SLiMSearch applies several distinct and complementary approaches exploiting the common properties of SLiMs to predict novel motifs. Consensus matches are annotated with overlapping sequence annotation, including feature information describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterisation of functional regions. Discriminatory motif attributes such as conservation and accessibility are also calculated. In addition, SLiMSearch provides functional enrichment and evolutionary analysis tools. The enrichment tool analyses GO terms, keywords and interacting partner enrichment to indicate possible motif function. The evolutionary tool evaluates motif taxonomic range and the conservation of motif sequence context. Consensus matches can be filtered based on motif attributes such as accessibility and taxonomic range; or by the localisation, interacting partners or ontology annotation of the peptide-containing protein. SLiMSearch supports a range of species of experimental and therapeutic relevance and is available online at http://slim.ucd.ie/slimsearch/.
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions ...mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein–protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
•Tens of thousands of interactions in the human cell mediated by short linear motifs (SLiMs) are predicted to remain undiscovered.•In recent years, several novel experimental approaches for high-throughput motif discovery have been developed.•These methods will allow the mapping of an underexplored part of the human interactome at amino acid resolution.•Several of the methods also allow affinity data to be quantified for a large number of interactions.•Many of the newly characterized interactions will modulate key regulatory processes.
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure ...predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.
The anaphase-promoting complex or cyclosome (APC/C) is the ubiquitin ligase that regulates mitosis by targeting specific proteins for degradation at specific times under the control of the spindle ...assembly checkpoint (SAC). How the APC/C recognizes its different substrates is a key problem in the control of cell division. Here, we have identified the ABBA motif in cyclin A, BUBR1, BUB1, and Acm1, and we show that it binds to the APC/C coactivator CDC20. The ABBA motif in cyclin A is required for its proper degradation in prometaphase through competing with BUBR1 for the same site on CDC20. Moreover, the ABBA motifs in BUBR1 and BUB1 are necessary for the SAC to work at full strength and to recruit CDC20 to kinetochores. Thus, we have identified a conserved motif integral to the proper control of mitosis that connects APC/C substrate recognition with the SAC.
•The conserved ABBA motif that binds to APC/C coactivators is identified•The ABBA motifs of cyclin A and BUBR1 bind the same site on CDC20•The ABBA motif is required for rapid cyclin A degradation in prometaphase•The ABBA motifs in BUBR1 and BUB1 are required for a fully functional SAC
Di Fiore et al. identify an interaction motif, “ABBA,” common to both BubR1, a spindle assembly checkpoint (SAC) protein, and cyclin A, a mitotic regulator. This motif mediates binding of these proteins to the APC/C activator Cdc20 and is required for SAC function and timely cyclin A degradation.
Abstract
Almost twenty years after its initial release, the Eukaryotic Linear Motif (ELM) resource remains an invaluable source of information for the study of motif-mediated protein-protein ...interactions. ELM provides a comprehensive, regularly updated and well-organised repository of manually curated, experimentally validated short linear motifs (SLiMs). An increasing number of SLiM-mediated interactions are discovered each year and keeping the resource up-to-date continues to be a great challenge. In the current update, 30 novel motif classes have been added and five existing classes have undergone major revisions. The update includes 411 new motif instances mostly focused on cell-cycle regulation, control of the actin cytoskeleton, membrane remodelling and vesicle trafficking pathways, liquid-liquid phase separation and integrin signalling. Many of the newly annotated motif-mediated interactions are targets of pathogenic motif mimicry by viral, bacterial or eukaryotic pathogens, providing invaluable insights into the molecular mechanisms underlying infectious diseases. The current ELM release includes 317 motif classes incorporating 3934 individual motif instances manually curated from 3867 scientific publications. ELM is available at: http://elm.eu.org.
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