Intrinsically Disordered Proteins in Cellular Signaling and Regulation

Intrinsically Disordered Proteins in Cellular Signaling and Regulation

2015 January ; 16(1): 18–29. | Peter E. Wright and H. Jane Dyson
Intrinsically disordered proteins (IDPs) are crucial components of cellular signaling machinery, enabling the same polypeptide to engage in diverse interactions with different outcomes. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and facilitating tissue-specific signaling. They participate in the assembly of signaling complexes and the dynamic self-assembly of membrane-less organelles. Experimental, computational, and bioinformatic approaches have advanced the understanding of disordered regions in proteins, revealing their widespread role in biological processes. The abundance and functional significance of protein disorder in eukaryotes were largely unrecognized until the mid-1990s. Experimental studies and bioinformatics revealed that regions of disorder are common in eukaryotic proteins, especially those involved in cellular regulation and signaling. IDPs are characterized by biased amino acid composition, low sequence complexity, and a low content of bulky hydrophobic amino acids. These proteins cannot fold into stable, well-defined structures but fluctuate rapidly between various conformations, covering a continuum of conformational space. IDPs frequently act as hubs in protein interaction networks, playing central roles in regulating signaling pathways and cellular processes such as transcription, translation, and the cell cycle. Their abundance is tightly regulated to ensure precise signaling, and mutations in IDPs or changes in their cellular abundance are associated with diseases. Recent findings show that many proteins with low-complexity or prion-like sequences can promote phase separation to form membrane-less organelles, contributing to their compartmentalization. The physical characteristics of IDPs allow for exquisite control over cellular signaling processes, including rapid association and dissociation, high specificity, and efficient utilization of conserved sequence motifs. IDPs often contain multiple conserved sequence motifs that mediate binding to nucleic acids or other proteins, and these motifs exhibit structural polymorphism, adopting different structures on different targets. The presence of pre-formed secondary structural elements in IDPs can influence the binding process, but experimental evidence is mixed. IDPs can form "fuzzy" complexes with their targets, where some regions remain disordered even after binding. These dynamic interactions can enhance target binding affinity, mediate pathway crosstalk, and modulate allosteric interactions. IDPs and their disordered regions play a central role in higher-order signaling assemblies, such as signalosomes, which amplify signals, reduce noise, and provide spatial and temporal control over signaling. Alternative splicing, which leads to distinct protein isoforms in different cell types and tissues, also involves IDPs and disordered regions. Future perspectives include the structural characterization of full-length IDPs, the role of IDPs in phase separation and membrane-less organelle assembly, and the potential of IDPs as therapeutic targets.Intrinsically disordered proteins (IDPs) are crucial components of cellular signaling machinery, enabling the same polypeptide to engage in diverse interactions with different outcomes. IDPs are subject to combinatorial post-translational modifications and alternative splicing, adding complexity to regulatory networks and facilitating tissue-specific signaling. They participate in the assembly of signaling complexes and the dynamic self-assembly of membrane-less organelles. Experimental, computational, and bioinformatic approaches have advanced the understanding of disordered regions in proteins, revealing their widespread role in biological processes. The abundance and functional significance of protein disorder in eukaryotes were largely unrecognized until the mid-1990s. Experimental studies and bioinformatics revealed that regions of disorder are common in eukaryotic proteins, especially those involved in cellular regulation and signaling. IDPs are characterized by biased amino acid composition, low sequence complexity, and a low content of bulky hydrophobic amino acids. These proteins cannot fold into stable, well-defined structures but fluctuate rapidly between various conformations, covering a continuum of conformational space. IDPs frequently act as hubs in protein interaction networks, playing central roles in regulating signaling pathways and cellular processes such as transcription, translation, and the cell cycle. Their abundance is tightly regulated to ensure precise signaling, and mutations in IDPs or changes in their cellular abundance are associated with diseases. Recent findings show that many proteins with low-complexity or prion-like sequences can promote phase separation to form membrane-less organelles, contributing to their compartmentalization. The physical characteristics of IDPs allow for exquisite control over cellular signaling processes, including rapid association and dissociation, high specificity, and efficient utilization of conserved sequence motifs. IDPs often contain multiple conserved sequence motifs that mediate binding to nucleic acids or other proteins, and these motifs exhibit structural polymorphism, adopting different structures on different targets. The presence of pre-formed secondary structural elements in IDPs can influence the binding process, but experimental evidence is mixed. IDPs can form "fuzzy" complexes with their targets, where some regions remain disordered even after binding. These dynamic interactions can enhance target binding affinity, mediate pathway crosstalk, and modulate allosteric interactions. IDPs and their disordered regions play a central role in higher-order signaling assemblies, such as signalosomes, which amplify signals, reduce noise, and provide spatial and temporal control over signaling. Alternative splicing, which leads to distinct protein isoforms in different cell types and tissues, also involves IDPs and disordered regions. Future perspectives include the structural characterization of full-length IDPs, the role of IDPs in phase separation and membrane-less organelle assembly, and the potential of IDPs as therapeutic targets.
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