Intrinsically disordered proteins play diverse roles in cell signaling

Abstract

Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca²⁺ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered.

Keywords: Cell signal amplification; Differentiation; Integration; Propagation; Specificity.

Fig. 1

When binding a partner protein, intrinsically disordered regions can adopt multiple unstructured or structurally ambiguous topologies to form fuzzy complexes (A), fold to create stable secondary/tertiary structure (B) or adopt an unstructured yet static conformation (C)

Fig. 2

Intrinsic disorder predisposition of human glucocorticoid receptor (UniProt ID: P04150) evaluated by PONDR® VSL2 [179], PONDR® VL3 [180], PONDR® VLXT [6], PONDR® FIT [181], IUPred2A_long and IUPred2A_short [181, 182]. Mean disorder score is shown as well. Positions of the N-terminal domain (residues 1–420), DNA binding domain (residues 420–485), a hinge region (residues 486–527), and ligand binding domain (residues 528–777) are shown as red, cyan, blue and lime shaded areas. Clearly, the N-terminal domain and a hinge region are mostly disordered

Fig. 3

The function of the glucocorticoid receptor is regulated in part by its intrinsically disordered C-terminal tail. A The GR tail interacts with chaperones in the cytoplasm in the unliganded state. B Alternative splicing and post-translational modifications impact these interactions

Fig. 4

Disorder can occur at any step of the Wnt cell signaling pathway. A A schematic of signaling components in the core canonical Wnt signaling pathway, showing the inactive state on the left and the active state on the right. The cell membrane is indicated by an arc and the nucleus by a light blue oval. Wnt signaling is able to control many processes by employing different variants of many proteins involved in Wnt signaling, which exist due to gene duplication, alternative splicing, and PTMs [258]. Consequently, a protein was marked as disordered (using a starburst) if the sequence off any variant, not post-translationally modified, was identified as intrinsically disordered in the literature. Wnt [258], Fz [268], LRP [268], Dsh/Dvl [264, 265], APC, CK1, Axin, GSK3 [269], β-catenin [269, 270], TCF/LEF [271], Groucho [272] all can include intrinsic disorder. B Analysis of 117 proteins involved in Wnt signaling based on disorder score and percent of disordered residues. Large values of each parameter indicate increasing disorder. Color blocks indicate regions in which are mostly ordered (blue and light blue), moderately disordered (pink), or mostly disordered (red). If the two parameters agree, the corresponding part of background is dark (blue or pink), whereas light blue and light pink reflect areas in which only one of these criteria applies. It is noteworthy that no Wnt pathway proteins are very structured (dark blue) and only two proteins can be considered mostly disordered. The remaining 115 proteins are either moderately disordered or highly disordered

Fig. 5

Alternative splicing and PTMs, localized in intrinsically disordered regions, direct differential CXCR4 signaling. Predicted disorder identified by PONDR-FIT is depicted on a heat map (lower left), with red and blue indicating predicted disorder and order, respectively. A crystal structure of the structured regions (28–303 residues, PDB ID: 3OE9) is shown as a blue ribbon. Alternative splicing regulates receptor function by generating three tissue-specific isoforms by replacing the first five residues at the disordered N-terminus with other sequences of varying length. Multiple PTMs regulate different aspects of CXCR4 function: sulfation of Y7, Y12, and Y21 modulates receptor-ligand binding and dimerization [300], and glycosylation of N11 plays a role in masking the coreceptor functional activity [301]. Likewise, phosphorylation of Y157 is required for activation of the G_i-independent JAK2/STAT3 pathway [302]. Consequently, combinations of C-terminal PTMs are associated with three different biological processes: phosphorylation of S339 in G protein-coupled receptor kinase 6 (GRK6) and possibly GRK2 phosphorylation (two residues from S346-S348 and S351-S352) lead to receptor-arrestin3 binding, G protein uncoupling, and subsequent receptor desensitization. In contrast, phosphorylation of GRK3 (at the same regions as GRK2, but probably different residues), and GRK6 (S330 and S339) result in arrestin2 recruitment and subsequent ERK1/2 activation [303]. In addition, protein kinase C (PKC) and GRK6 phosphorylation (S324 or S325, S330 respectively) initiate degradation modulated by ubiquitination of K327, K331, and K333 [303, 304]. Adapted from Zhou et al. [39]