Intrinsically Disordered Proteins Function Research Articles

How disorder influences order and vice versa – mutual effects in fusion proteins containing an intrinsically disordered and a globular protein

Intrinsically disordered proteins (IDPs) are functional proteins either fully or partly lacking stable secondary and tertiary structure under physiological conditions that are involved in important biological functions, such as regulation and signalling in eukaryotes, prokaryotes and viruses. The function of many IDPs relies upon interactions with partner proteins, often accompanied by conformational changes and disorder-to-order transitions in the unstructured partner. To investigate how disordered and ordered regions interact when fused to one to another within the same protein, we covalently linked the green fluorescent protein to three different, well characterized IDPs and analyzed the conformational properties of the fusion proteins using various biochemical and biophysical approaches. We observed that the overall structure, compactness and stability of the chimeric proteins all differ from what could have been anticipated from the structural features of their isolated components and that they vary as a function of the fused IDP.

Catalytic and chaperone-like functions in an intrinsically disordered protein associated with desiccation tolerance

Intrinsically disordered proteins (IDPs) lack well-defined structure but are widely represented in eukaryotic proteomes. Although the functions of most IDPs are not understood, some have been shown to have molecular recognition and/or regulatory roles where their disordered nature might be advantageous. Anhydrin is an uncharacterized IDP induced by dehydration in an anhydrobiotic nematode, Aphelenchus avenae. We show here that anhydrin is a moonlighting protein with two novel, independent functions relating to desiccation tolerance. First, it has a chaperone-like activity that can reduce desiccation-induced enzyme aggregation and inactivation in vitro. When expressed in a human cell line, anhydrin localizes to the nucleus and reduces the propensity of a polyalanine expansion protein associated with oculopharyngeal muscular dystrophy to form aggregates. This in vivo activity is distinguished by a loose association of anhydrin with its client protein, consistent with a role as a molecular shield. In addition, anhydrin exhibits a second function as an endonuclease whose substrates include supercoiled, linear, and chromatin linker DNA. This nuclease activity could be involved in either repair of desiccation-induced DNA damage incurred during anhydrobiosis or in apoptotic or necrotic processes, for example, but it is particularly unexpected for anhydrin because IDP functions defined to date anticorrelate with enzyme activity. Enzymes usually require precise three-dimensional positioning of residues at the active site, but our results suggest this need not be the case. Anhydrin therefore extends the range of IDP functional categories to include catalysis and highlights the potential for the discovery of new functions in disordered proteomes.

Charge interactions can dominate the dimensions of intrinsically disordered proteins

Many eukaryotic proteins are disordered under physiological conditions, and fold into ordered structures only on binding to their cellular targets. Such intrinsically disordered proteins (IDPs) often contain a large fraction of charged amino acids. Here, we use single-molecule Förster resonance energy transfer to investigate the influence of charged residues on the dimensions of unfolded and intrinsically disordered proteins. We find that, in contrast to the compact unfolded conformations that have been observed for many proteins at low denaturant concentration, IDPs can exhibit a prominent expansion at low ionic strength that correlates with their net charge. Charge-balanced polypeptides, however, can exhibit an additional collapse at low ionic strength, as predicted by polyampholyte theory from the attraction between opposite charges in the chain. The pronounced effect of charges on the dimensions of unfolded proteins has important implications for the cellular functions of IDPs.

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) adopt heterogeneous ensembles of conformations under physiological conditions. Understanding the relationship between amino acid sequence and conformational ensembles of IDPs can help clarify the role of disorder in physiological function. Recent studies revealed that polar IDPs favor collapsed ensembles in water despite the absence of hydrophobic groups--a result that holds for polypeptide backbones as well. By studying highly charged polypeptides, a different archetype of IDPs, we assess how charge content modulates the intrinsic preference of polypeptide backbones for collapsed structures. We characterized conformational ensembles for a set of protamines in aqueous milieus using molecular simulations and fluorescence measurements. Protamines are arginine-rich IDPs involved in the condensation of chromatin during spermatogenesis. Simulations based on the ABSINTH implicit solvation model predict the existence of a globule-to-coil transition, with net charge per residue serving as the discriminating order parameter. The transition is supported by quantitative agreement between simulation and experiment. Local conformational preferences partially explain the observed trends of polymeric properties. Our results lead to the proposal of a schematic protein phase diagram that should enable prediction of polymeric attributes for IDP conformational ensembles using easily calculated physicochemical properties of amino acid sequences. Although sequence composition allows the prediction of polymeric properties, interresidue contact preferences of protamines with similar polymeric attributes suggest that certain details of conformational ensembles depend on the sequence. This provides a plausible mechanism for specificity in the functions of IDPs.

Intrinsically disordered chaperones in plants and animalsThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

Intrinsically disordered proteins (IDPs) are widespread in eukaryotes and fulfill important functions associated with signaling and regulation. Recent evidence points to a special and thus largely disrespected functional capacity of IDPs--that they can assist the folding of other proteins and prevent their aggregation, i.e., that they can act as chaperones. In this paper, we survey current information available on this phenomenon, with particular focus on (i) the structure and function of IDPs in general, (ii) disordered chaperones in plants, (iii) disordered chaperones in other organisms spanning from insects to mammals, (iv) the possible mechanisms of action of disordered chaperones, and (v) the possibility of two-faced (Janus) chaperone activity of disordered chaperones, which can assist the folding of both RNA and protein substrates. The evidence is most conclusive in the case of plant stress proteins, such as late embryogenesis abundant (LEA) proteins or dehydrins. We will show that the cellular function of LEA proteins in mitigating the damage caused by stress is clear; nevertheless, experiments carried out in vivo must be extended and the molecular mechanism of the action of IDP chaperones also requires clarification. Using these details, we chart out how far the field has progressed only to emphasize the long road ahead before chaperone function can be firmly established as part of the physiological mechanistic arsenal of the emerging group of IDPs.

Limitations of Induced Folding in Molecular Recognition by Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) exist and function without well-defined three-dimensional structures, thus they defy the classical structure-function paradigm. These proteins are common in proteomes, and they carry out essential functions often related to signalling and regulation of transcription. Herein, the experimental evidence for their lack of structure and the major functional benefits that structural disorder confers, are surveyed. It is shown that IDPs often function by molecular recognition, in which either short motifs, or domain-sized disordered segments are used for partner recognition. In both cases, the binding segment undergoes induced folding and it attains an ordered structure. This folding-upon-binding scenario suggests that the function of IDPs can be interpreted in terms of the static structural view of the classical paradigm. New developments in the field, however, suggest that folding upon binding is limited, and many IDPs preserve a significant level of disorder in the bound state, a phenomenon termed fuzziness. In addition, IDPs may structurally adapt to different partners with different functional outcomes, resulting in promiscuity in function termed moonlighting. It is suggested that a new model describing the structure-function relationship of IDPs has to encompass such structural and functional promiscuity inherent in the disordered state of IDPs.

Intrinsic disorder in proteins associated with neurodegenerative diseases

Neurodegenerative diseases constitute a set of pathological conditions originating from the slow, irreversible and systematic cell loss within the various regions of the brain and/or the spinal cord. Neurodegenerative diseases are proteinopathies associated with misbehavior and disarrangement of a specific protein, affecting its processing, functioning, and/or folding. Many proteins associated with human neurodegenerative diseases are intrinsically disordered; i.e., they lack stable tertiary and/or secondary structure under physiological conditions in vitro. Intrinsically disordered proteins (IDPs) have broad presentation in nature. Functionally, they complement ordered proteins, being typically involved in regulation, signaling and control. Structures and functions of IDPs are intensively modulated by alternative splicing and posttranslational modifications. It is recognized now that nanoimaging offers a set of tools to analyze protein misfolding and self-assembly via monitoring the aggregation process, to visualize protein aggregates, and to analyze properties of these aggregates. The major goals of this review are to show the interconnections between intrinsic disorder and human neurodegenerative diseases and to overview a recent progress in development of novel nanoimaging tools to follow protein aggregation.

Structural Rationale for the Coupled Binding and Unfolding of the c-Myc Oncoprotein by Small Molecules

The basic-helix-loop-helix-leucine-zipper domains of the c-Myc oncoprotein and its obligate partner Max are intrinsically disordered (ID) monomers that undergo coupled folding and binding upon heterodimerization. We have identified the binding sites and determined the structural means by which two unrelated small molecules, 10058-F4 and 10074-G5, bind c-Myc and stabilize the ID monomer over the highly ordered c-Myc-Max heterodimer. In solution, the molecules bind to distinct regions of c-Myc and thus limit its ability to interact with Max and assume a more rigid and defined conformation. The identification of multiple, specific binding sites on an ID domain suggests that small molecules may provide a general means for manipulating the structure and function of ID proteins, such as c-Myc.

Intrinsically Disordered Proteins in Human Diseases: Introducing the D2Concept

Intrinsically disordered proteins (IDPs) lack stable tertiary and/or secondary structures under physiological conditions in vitro. They are highly abundant in nature and their functional repertoire complements the functions of ordered proteins. IDPs are involved in regulation, signaling, and control, where binding to multiple partners and high-specificity/low-affinity interactions play a crucial role. Functions of IDPs are tuned via alternative splicing and posttranslational modifications. Intrinsic disorder is a unique structural feature that enables IDPs to participate in both one-to-many and many-to-one signaling. Numerous IDPs are associated with human diseases, including cancer, cardiovascular disease, amyloidoses, neurodegenerative diseases, and diabetes. Overall, intriguing interconnections among intrinsic disorder, cell signaling, and human diseases suggest that protein conformational diseases may result not only from protein misfolding, but also from misidentification, missignaling, and unnatural or nonnative folding. IDPs, such as alpha-synuclein, tau protein, p53, and BRCA1, are attractive targets for drugs modulating protein-protein interactions. From these and other examples, novel strategies for drug discovery based on IDPs have been developed. To summarize work in this area, we are introducing the D2 (disorder in disorders) concept.