Interaction modules that impart specificity to disordered protein

Abstract

Intrinsically disordered regions (IDRs) are especially enriched among proteins that regulate chromatin and transcription. As a result, mechanisms that influence specificity of IDR-driven interactions have emerged as exciting unresolved issues for understanding gene regulation. We review the molecular elements frequently found within IDRs that confer regulatory specificity. In particular, we summarize the differing roles of disordered low-complexity regions (LCRs) and short linear motifs (SLiMs) towards selective nuclear regulation. Examination of IDR-driven interactions highlights SLiMs as organizers of selectivity, with widespread roles in gene regulation and integration of cellular signals. Analysis of recurrent interactions between SLiMs and folded domains suggests diverse avenues for SLiMs to influence phase-separated condensates and highlights opportunities to manipulate these interactions for control of biological activity.

Keywords: composition; condensate; expression; liquid–liquid phase separation; structure.

Figure 1.. Intrinsically disordered regions (IDRs) are enriched among chromatin and transcription regulators.

(A) All UniProt GO terms containing ≥50 human proteins, ranked by mean percent disorder in proteins contained within each term. GO terms related to transcription and chromatin are highlighted in teal and those related to regulation of metabolism and homeostasis in fuchsia. (B) Illustration of resolved (fuchsia) and unresolved (missing) regions in multiprotein complexes resolved by Cryo-EM (PDB accessions 6MZL and 6LTJ). Stokes hydrodynamic volumes of protein are based on molecular weight and sedimentation constants of full complexes, illustrating the large portion of volume made up by unresolved regions. (C) Example full-length structures of chromatin and transcription regulators predicted by AlphaFold2. Disordered regions in depicted structures are artificially constrained into a more compact configuration in AlphaFold2 for illustration purposes. Folded domains are highlighted in fuchsia and IDRs in teal.

Figure 2.. Principal mechanisms by which IDRs selectively contribute to transcription regulation.

Selective roles of IDRs are generally related to the non-mutually exclusive activities that include: regulation of subnuclear localization; organization of switchable protein-protein interactions to influence other proteins or to auto-regulate; acting as degrons or mediating degron masking to regulate protein stability; and/or assisting assembly of oligomeric and higher-order complexes.

Figure 3.. Major functional elements found within the IDRs of chromatin and transcription regulators.

(A) Low-complexity regions (LCRs) form dynamic, non-stoichiometric networks. (B) Short Linear Motifs (SLiMs) mediate selective bipartite interactions with folded domains. IDRs in proteins possess a fluid, non-mutually exclusive spectrum of properties that span from LCR-like to SLiM-like.

Figure 4.. Examples of SLiM interaction scaffolds in chromatin and transcription regulators.

(A) SLiMs (teal surface) are depicted in complexes with their interaction scaffolds (fuchsia ribbon). SLiM-mediated interactions employ recurrent structural configurations (PDB accessions 6ZV4, 7LQT, 1KDX, 1SB0, 3P4F, 5HYN, 2MDJ, 1F8A, 5VKO, 1YVL, 3JUA, 5GN0). (B) Examples of SLiM consensus sequences for SLiM interaction scaffolds. Individual amino acids are represented by their IUPAC codes. X denotes any amino acid, φ represents hydrophobic amino acid; p-prefix indicates phosphorylated amino acid; square brackets represent any one of the amino acids contained within the brackets; subscript n denotes repetition; (COOH) denotes carboxy terminus.