The suggestion that the native state of many proteins is intrinsically disordered (or, as originally termed, unstructured) is now integral to our general view of protein structure and function. A ...little more than 10 years ago, however, such challenge to the almost dogmatic ‘structure–function paradigm’ was pure heresy due to the overwhelming evidence that structure determines function. A decade of steady progress turned skepticism around: this 10-year recap review outlines the situation a decade ago and the major directions of the breathtaking advance achieved by experimental and computational approaches. I show that the evidence for the generality and importance of this phenomenon is now so insurmountable that it demands the inclusion of ‘unstructural’ biology into mainstream biology and biochemistry textbooks.
Intrinsically unstructured proteins (IUPs) are common in various proteomes and occupy a unique structural and functional niche in which function is directly linked to structural disorder. The ...evidence that these proteins exist without a well-defined folded structure in vitro is compelling, and justifies considering them a separate class within the protein world. In this paper, novel advances in the rapidly advancing field of IUPs are reviewed, with the major attention directed to the evidence of their unfolded character in vivo, the interplay of their residual structure and their various functional modes and the functional benefits their malleable structural state provides. Via all these details, it is demonstrated that in only a couple of years after its conception, the idea of protein disorder has already come of age and transformed our basic concepts of protein structure and function.
The notion that all protein functions are determined through macromolecular interactions is the driving force behind current efforts that aim to solve the structures of all cellular complexes. Recent ...findings, however, demonstrate a significant amount of structural disorder or polymorphism in protein complexes, a phenomenon that has been largely overlooked thus far. It is our view that such disorder can be classified into four mechanistic categories, covering a continuous spectrum of structural states from static to dynamic disorder and from segmental to full disorder. To emphasize its generality and importance, we suggest a generic term, ‘fuzziness’, for this phenomenon. Given the crucial role of protein disorder in protein–protein interactions and in regulatory processes, we envision that fuzziness will become integral to understanding the interactome.
•Intrinsically disordered proteins mostly function by molecular recognition.•Post-translational modifications regulate the interactions of IDPs.•Structural disorder can facilitate allosteric ...regulation.•IDPs are often involved in misfolding and disease.•IDPs can undergo phase transitions to physically organize cell interior.
Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein–protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural–functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as ‘interaction specialists’.
Based on early bioinformatic studies on a handful of species, the frequency of structural disorder of proteins is generally thought to be much higher in eukaryotes than in prokaryotes. To refine this ...view, we present here a comparative prediction study and analysis of 194 fully described eukaryotic proteomes and 87 reference prokaryotes for structural disorder. We found that structural disorder does distinguish eukaryotes from prokaryotes, but its frequency spans a very wide range in the two superkingdoms that largely overlap. The number of disordered binding regions and different Pfam domain types also contribute to distinguish eukaryotes from prokaryotes. Unexpectedly, the highest levels--and highest variability--of predicted disorder is found in protists, i.e. single-celled eukaryotes, often surpassing more complex eukaryote organisms, plants and animals. This trend contrasts with that of the number of domain types, which increases rather monotonously toward more complex organisms. The level of structural disorder appears to be strongly correlated with lifestyle, because some obligate intracellular parasites and endosymbionts have the lowest levels, whereas host-changing parasites have the highest level of predicted disorder. We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established.
Intracellular organelles are either membrane-bound vesicles or membrane-less compartments that are made up of proteins and RNA. These organelles play key biological roles, by compartmentalizing the ...cell to enable spatiotemporal control of biological reactions. Recent studies suggest that membrane-less intracellular compartments are multicomponent viscous liquid droplets that form via phase separation. Proteins that have an intrinsic tendency for being conformationally heterogeneous seem to be the main drivers of liquid-liquid phase separation in the cell. These findings highlight the relevance of classical concepts from the physics of polymeric phase transitions for understanding the assembly of intracellular membrane-less compartments. However, applying these concepts is challenging, given the heteropolymeric nature of protein sequences, the complex intracellular environment, and non-equilibrium features intrinsic to cells. This provides new opportunities for adapting established theories and for the emergence of new physics.
Cellular compartments and organelles organize biological matter. Most well-known organelles are separated by a membrane boundary from their surrounding milieu. There are also many so-called ...membraneless organelles and recent studies suggest that these organelles, which are supramolecular assemblies of proteins and RNA molecules, form via protein phase separation. Recent discoveries have shed light on the molecular properties, formation, regulation, and function of membraneless organelles. A combination of techniques from cell biology, biophysics, physical chemistry, structural biology, and bioinformatics are starting to help establish the molecular principles of an emerging field, thus paving the way for exciting discoveries, including novel therapeutic approaches for the treatment of age-related disorders.
Phase separation is known to play a role in a variety of cellular processes, including formation of classical membraneless organelles, signaling complexes, the cytoskeleton, and numerous other supramolecular assemblies.
The concept of phase separation provides a new framework for our understanding of the functional role of sequence degeneracy (low-complexity) and protein disorder.
Accumulating evidence points to a key role for phase transitions in human diseases associated with protein aggregation, and to the misregulation of membraneless organelles in disease.
Understanding the physical principles and molecular interactions behind protein phase separation could inspire novel biomaterials.
Specific signals (degrons) regulate protein turnover mediated by the ubiquitin-proteasome system. Here we systematically analyse known degrons and propose a tripartite model comprising the following: ...(1) a primary degron (peptide motif) that specifies substrate recognition by cognate E3 ubiquitin ligases, (2) secondary site(s) comprising a single or multiple neighbouring ubiquitinated lysine(s) and (3) a structurally disordered segment that initiates substrate unfolding at the 26S proteasome. Primary degron sequences are conserved among orthologues and occur in structurally disordered regions that undergo E3-induced folding-on-binding. Posttranslational modifications can switch primary degrons into E3-binding-competent states, thereby integrating degradation with signalling pathways. Degradation-linked lysines tend to be located within disordered segments that also initiate substrate degradation by effective proteasomal engagement. Many characterized mutations and alternative isoforms with abrogated degron components are implicated in disease. These effects result from increased protein stability and interactome rewiring. The distributed nature of degrons ensures regulation, specificity and combinatorial control of degradation.
Proteins are the basic functional units of the cell, carrying out myriads of functions essential for life. There are countless reports in molecular cell biology addressing the functioning of proteins ...under physiological and pathological conditions, aiming to understand life at the atomistic-molecular level and thereby being able to develop remedies against diseases. The central theme in most of these studies is that the functional unit under study is the protein itself. Recent rapid progress has radically challenged and extended this protein-function paradigm, by demonstrating that novel function(s) may emerge when proteins form dynamic and non-stoichiometric supramolecular assemblies. There is an increasing number of cases for such collective functions, such as targeting, localization, protection/shielding and filtering effects, as exemplified by signaling complexes and prions, biominerals and mucus, amphibian adhesions and bacterial biofilms, and a broad range of membraneless organelles (bio-condensates) formed by liquid-liquid phase separation in the cell. In this short review, we show that such non-stoichiometric organization may derive from the heterogeneity of the system, a mismatch in valency and/or geometry of the partners, and/or intrinsic structural disorder and multivalency of the component proteins. Either way, the resulting functional features cannot be simply described by, or predicted from, the properties of the isolated single protein(s), as they belong to the collection of proteins.
•Proteins, the basic functional units of the cell often form loosely-associated assemblies in the cell.•In these assemblies the molar ratio of proteins is not well defined, i.e. they lack exact “stoichiometry”.•The function of these assemblies cannot be predicted from that of individual proteins.•Their function pertains to the whole assembly, i.e. it is an emergent property.
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