For a review on IDP - membrane interactions Contents Introduction IDPs - characteristics, occurrence, functions Membrane - nature and types, where all do they occur, composition Protein Interactions - inside, with membrane from inside and outside IDP - membrane interactions Experimental and computational methods to study Database Membrane curvature and formation Membrane contact sites Fuzzy association Disordered boundary membrane dynamics and transport Autophagy Signalling Other functions? Evolutionary perspective Importance in diseases Introduction IDPs - characteristics, occurrence, functions Intrinsically Disordered Proteins (IDPs) and Intrinsically Disordered Protein Regions (IDPRs) were first mentioned more than twenty years ago [10]. The presence of disorder and its functional importance was noted almost 50 years before [11]. Now IDPs and IDRs are an accepted reality [5,6,7,8] which typically exhibit characteristics that distinguish them from their ordered counterparts. These proteins or protein regions are defined by their amino acid sequences, which have a combination of relatively high net charge and low mean hydropathy [10]. Generally, IDPs/IDPRs contain fewer order-promoting residues ( Trp, Cys, Tyr, Ile, Phe,Val, Asn, Leu) and have a higher proportion of disorder-promoting residues (Arg,Pro,Gln,Gly,Glu,Ser,Ala,Lys) [1]. IDPs/IDPRs commonly contain repeats within their amino acid sequences. These repeats contribute to the reduced informational content of their sequences compared to ordered regions or proteins. They occupy a different free energy landscape which is relatively flat lacking a deep minimum [1]. Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) can be found across all three superkingdoms and in their viruses [13]. Their prevalence tends to increase proportionally with the complexity of the organism. Notably, only a small percentage of proteins with known crystal structures in the Protein Data Bank (PDB) (https://www.rcsb.org/) lack any disordered regions. IDPs and IDRs undergo induced folding and become structured upon binding to specific partners, such as proteins, nucleic acids, or small molecules. The current understanding is that IDPs and IDRs are not rare anomalies but rather widespread and common. Even if a protein is entirely free of intrinsically disordered regions in its mature state—an uncommon scenario—it still encounters various forms of disorder (intrinsic, extrinsic, or induced) throughout its functional life, from synthesis to degradation [9]. Intrinsic disorder plays a crucial role in protein function, providing flexibility, adaptability, and the ability to interact with multiple partners. Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) undergo induced conformational changes in response to their environment, enabling them to bind different partners and perform molecular recognition functions [10,7,5]. The distinct disordered parts of protein molecules can respond differently to similar environmental cues, adding complexity to these heterogeneous entities. The heteropolymeric nature of IDPs/IDRs means they are not completely unstructured, but often contain transiently populated elements of secondary structure that serve as targets for their interaction partners, facilitating binding in a kinetically efficient manner. IDPs/IDRs are promiscuous binders that form static, semi-static, and dynamic complexes with various partners through multiple binding scenarios. As a result, IDPs are involved in a diverse range of functions, including biogenesis of assemblages, intracellular communication, tethering, preventing overcrowding, protein degradation, molecular assembly, chaperone activity, effector roles, scavenging, metal sponging, molecular recognition, signalling, gene regulation, protein modification, and entropic chain activities [2,4,6,7,8,12,1]. The presence of disorder in proteins is not a limitation but rather an evolutionary advantage [14], enabling them to perform diverse functions and adapt to changing cellular environments. Membrane - nature and types, where all do they occur, composition Protein Interactions - inside, with membrane from inside and outside IDP - membrane interactions Experimental and computational methods to study Database Membrane curvature and formation Membrane contact sites Fuzzy association Disordered boundary membrane dynamics and transport Autophagy Signalling Other functions? Evolutionary perspective Importance in diseases References Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics Review by uversky on IDPs that says Micrometer-Scale Signaling Zones at the Membrane Surface: Although the aforementioned liquid-liquid and liquid-gel phase transitions were described in threedimensional solutions, it was pointed out that the dynamic interactions between the multivalent cytoplasmic tails of transmembrane proteins and their multivalent binding partners can trigger the formation of large (at least micron-sized) two-dimensional protein clusters on the membrane surface [217]. This possibility was illustrated by the system that included the phosphorylated cytoplasmic domain of Nephrin and its intracellular targets, Nck and N-WASP [217]. Although in a three-dimensional solution, these three proteins phase separated into dynamic micron sized liquid droplets when critical protein concentration (that depended on the valency and affinity of interacting species) in solution was achieved [197], attachment of phosphorylated Nephrin to supported lipid bilayers of DOPC in the presence of Nck and N-WASP resulted in the formation at membranes of the micron-sized concentrated puncta containing all three proteins [217]. Furthermore, these phaseseparated two-dimensional protein clusters were able to successfully promote actin filament assembly via the Arp2/3 complex recruited to the membrane through binding N-WASP, and were themselves remodeled by the resultant filament network [217]. These observations suggest that the multivalent protein interactions leading to phase separation can be responsible for regulation and control of some signaling pathways via generation of spatially organized micron-scale protein clusters [217]. These observations indicated that multivalency-induced polymerization and phase separation can occur in three-dimensional solutions and in two-dimensional systems. Importantly, computational analysis revealed that all three members of this system contain high levels of intrinsic disorder. In fact, more than 60% of residues in the Cterminal cytoplasmic tail of human Nephrin (PMID: O60500, amino acids 1077–1241) are predicted to be disordered. In one study, a rat neural Wiskott-Aldrich syndrome protein (N-WASP, PMID: O08816) construct containing residues 183–193 fused to 273–501 was predicted to be completely disordered. Finally, more than 35% of human cytoplasmic protein NCK1 (PMID: P16333) with C139S, C232A, C266S, and C340S mutations are predicted to be disordered as well. The disordered boundary of the cell: emerging properties of membrane-bound intrinsically disordered proteins We define the disordered boundary of the cell (DBC) as the system formed by membrane tethered intrinsically disordered protein regions, dynamically coupled to the underlying membrane. The emerging properties of the DBC makes it a global system of study, which cannot be understood from the individual properties of their components. Similarly, the properties of lipid bilayers cannot be understood from just the sum of the properties of individual lipid molecules. The highly anisotropic confined environment, restricting the position and orientation of interacting sites, is affecting the properties of individual disordered proteins. In fact, the collective effect caused by high concentrations of disordered proteins extend beyond the sum of individual effects. Examples of emerging properties of the DBC include enhanced protein-protein interactions, protein-driven phase separations, Zcompartmentalization, and protein modulated electrostatics. Fuzzy Association of an Intrinsically Disordered Protein with Acidic Membranes https://pubs.acs.org/doi/10.1021/jacsau.0c00039?ref=pdf Many physiological and pathophysiological processes, including Mycobacterium tuberculosis (Mtb) cell division, may involve fuzzy membrane association by proteins via intrinsically disordered regions. The fuzziness is extreme when the conformation and pose of the bound protein and the composition of the proximal lipids are all highly dynamic. Here, we tackled the challenge in characterizing the extreme fuzzy membrane association of the disordered, cytoplasmic N-terminal region (NT) of ChiZ, an Mtb divisome protein, by combining solution and solid-state NMR spectroscopy and molecular dynamics simulations. While membrane-associated NT does not gain any secondary structure, its interactions with lipids are not random, but formed largely by Arg residues predominantly in the second, conserved half of the NT sequence. As NT frolics on the membrane, lipids quickly redistribute, with acidic lipids, relative to zwitterionic lipids, preferentially taking up Arg-proximal positions. The asymmetric engagement of NT arises partly from competition between acidic lipids and acidic residues, all in the first half of NT, for Arg interactions. This asymmetry is accentuated by membrane insertion of the downstream transmembrane helix. This type of semispecific molecular recognition may be a general mechanism by which disordered proteins target membranes. Intrinsically disordered protein regions at membrane contact sites https://www.sciencedirect.com/science/article/abs/pii/S1388198121001487 Membrane contact sites (MCS) are regions of close apposition between membranebound organelles. Proteins that occupy MCS display various domain organisation. Among them, lipid transfer proteins (LTPs) frequently contain both structured domains as well as regions of intrinsic disorder. In this review, we discuss the various roles of intrinsically disordered protein regions (IDPRs) in LTPs as well as in other proteins that are associated with organelle contact sites. We distinguish the following functions: (i) to act as flexible tethers between two membranes; (ii) to act as entropic barriers to prevent protein crowding and regulate membrane tethering geometry; (iii) to define the action range of catalytic domains. These functions are added to other functions of IDPRs in membrane environments, such as mediating protein-protein and protein-membrane interactions. We suggest that the overall efficiency and fidelity of contact sites might require fine coordination between all these IDPR activities.
