Folded proteins have a defined three-dimensional structure determined solely by its primary sequence. This principle occupies a central place in biology and is a direct predecessor of the so-called “structure-function” paradigm which suggests that a well-defined 3D structure encodes a specific function and therefore, by extrapolation, a well-defined structure is a necessity for functionality. biological.1. There is substantial evidence for this dogma, based on the ever-increasing number of structures in the Protein Data Bank (PDB). For example, striking structural similarity of enzymes and often correspondence of structural imprints with the evolution of molecular function support this dogma2,3. Say no to plagiarism. Get a tailor-made essay on “Why Violent Video Games Should Not Be Banned”? Get the original essay However, there is growing evidence that a significant number of proteins remain unfolded under physiological conditions4,5,6,7. Such proteins adopt a multitude of rapidly converting structures instead of one predominant structure unlike folded proteins. Such proteins or such regions in a protein are thus respectively called intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs)8,9. For the sake of simplicity, I will refer to IDRs and IDPs as IDPs from now on. After the Human Genome Project, advanced protein structure prediction algorithms10,11,12 quickly led to the realization that a large portion of human proteins contain disordered regions of up to approximately 40%13. Protein synthesis is an energy-expensive process for a living cell14 and the discussions above indeed lead us to ask if functionality was solely a consequence of structure, why would a cell expend its resources to synthesize IDPs ; suggesting that there must be "a method to the madness". Eukaryotes/complex life forms have been shown to exhibit significantly greater disorder in their proteome compared to elementary organisms such as bacteria which typically contain less than 10% disordered proteins15. This indicates that IDPs could be crucial for several complex functionalities required for cellular function16. As we will see below, an IDP has certain sequence peculiarities that encode disorder and, therefore, function. Therefore, IDPs escape the classical structure-function paradigm and an alternative paradigm must be invoked to understand IDP function where sequence codes for disorder which codes for function 17 (Fig. 1.1). Folded proteins have certain sequence features that help them achieve a folded globular structure. These sequence features include a certain fraction of hydrophobic residues that favor the formation of a collapsed state where hydrophobic side chains are buried and allow the formation of secondary structural elements. There is also some extent to which folded proteins can tolerate unbalanced charge residues, as these cause the protein to expand due to electrostatics. A comprehensive analysis of the footage of many people displaced by Uversky et. al. showed a clear trend in the sequence composition of IDPs, IDPs consistently have more unbalanced charges and fewer hydrophobic residues compared to folded proteins18. This analysis even led to an empirical relationship that leads to a clear separation of sequence space into folded and unfolded regions.(Fig. 1.2). This suggests the presence of a threshold in terms of average hydrophobicity relative to average net charge, after which proteins no longer manage to fold18. IDPs are known to bind to several biological targets. The binding interactions of IDPs are classified into two categories: 1) folding-binding coupling and 2) fuzzy complex formation (Fig. 1.3) 19,20,21,22,23. Coupled folding-binding mechanisms involve a folding transition of the IDP where, in the bound state, the IDP adopts a folded structure. In such a binding mechanism, the binding partner provides structure-forming interactions that the IDP otherwise lacks, allowing it to adopt a folded structure in the context of the bound complex. The coupled folding-binding mechanisms are also available in two versions; induced fit and conformational selection24. In the case of an induced adjustment mechanism, the disordered ensemble as a whole can bind the partner and the folding transition occurs after binding. In contrast, for conformational selection, a minor conformation prone to binding in the disordered ensemble and exhibiting significant resemblance to the bound state is selected. set of structures in equilibrium by the binding partner. This causes equilibrium to be re-established, again producing competent conformers which re-bind to the partner and the process continues to populate the bound state. Thus, for conformational selection, folding or structural transition occurs primarily before the binding event. Fuzzy complexes form when the disordered ensemble retains its disorder after partner binding, without undergoing significant conformational changes. In many cases, this involves multivalent interactions between IDPs and partner proteins, where several small binding epitopes on the IDP serve as anchor points with the binding partner 25,26. IDPs often contain short linear motifs (SLiMs) 27,28 that serve as target-binding epitopes and multiple copies of these SLiMs may be present, allowing the IDP to engage in multivalent interactions with the partner ; such multivalency leads to an overall increase in binding affinity, but at the same time the small size of the epitopes allows binding without any major conformational changes of the disordered ensemble. It is now clear that IDPs act as key players in cellular regulation and function. . It is therefore fair to say that IDPs constitute a cornerstone of eukaryotic cell biology as we know it. Sequence analysis reveals a very high content of long-disordered regions in proteins involved in transcription regulation, such as transcription factors, transcription co-activators and trans-activators, and chromosomal proteins such as linker histones29, 30.31. Disordered regions play many roles in such cases32. IDPs can constitute linker regions between recognition motifs/domains in molecules acting as molecular centers and facilitate allosteric interactions between distant sites. A classic example is CBP/p300 which harbors multiple sites for the transcription factor separated by IDP33s. Such scaffolding offers the possibility of allosteric and cooperative interactions. Interestingly, several of the transcription factors that bind CBP/p300 are also disordered themselves33. IDPs, due to their promiscuous binding behavior, may also themselves act as nodal points in regulatory pathways and encode regulatory and signaling functions; a great examplebeing the transcription factor p53 which forms a disordered core having approximately 700 binding partners34. IDPs with large surface areas are likely to undergo post-translational modifications, which proves to be an easy way to achieve dynamic regulation. Such regulatory mechanisms are widely observed in IDPs functioning at all stages of transcription regulation, ranging from phosphorylation-regulated transcription factors such as p53 to the dynamic regulation of linker histones via post-translational modifications in their messy tails. The chemistry of IDPs in solution, such as collapse, scaling and phase behavior, can be explained to a large extent, based on the basic principles of polymer physics37. Thus, like polymers in solution, IDPs can undergo liquid-liquid phase separation forming a concentrated phase surrounded by a dilute phase (Fig. 1.4)38. In recent years, the discovery that many cellular organelles such as stress granules, P-bodies, nucleoli, Cajal bodies, etc. are formed by liquid-liquid phase separation, often caused by IDPs, has led to new fundamental insights into cellular organization. In fact, it is also assumed that the permeability of the nuclear pore complex (NPC) is formed by phase-separated IDPs (discussed in more detail in the following sections)39,40,41,42,43,44. IDPs play a crucial role in cellular organization by forming different membraneless organelles, at different physiological signals via liquid-liquid phase separation, which serve as crucibles for several biochemical reactions that would otherwise not be achievable in dilute concentrations.1.2 Transport nucleocytoplasmic and nuclear pore complex1.2.1 The nuclear pore complex: structure, function and nucleocytoplasmic transport pathwayThe cornerstone of eukaryotic cell biology is the compartmentalization of cellular components. A eukaryotic cell is primarily compartmentalized into two components: the nucleus, which is a double-membrane enclosure that houses DNA/genetic information, surrounded by the cytosol, which constitutes an aqueous medium containing essential biomolecules necessary for cellular function. The transport of molecules from the cytoplasm to the nucleus and vice versa is crucial for cellular homeostasis. The nuclear envelope is decorated with several nuclear pore complexes (NPCs), which are giant macromolecular complexes that serve as the sole conduit for the transport of molecules across the nuclear envelope between the nucleus and the cytoplasm. The NPC, with a size of 120 MDa, is the largest. macromolecular complex in the eukaryotic cell. For a long time, the NPC was known in the literature to have a ring-shaped architecture with apparent 8-fold rotational symmetry46. Recent developments in cryo-EM have resulted in the visualization of NPC structure in unprecedented detail47,48,49. The basic framework of the NPC structure includes three rings: the inner ring, the nuclear ring, and the cytoplasmic ring. The inner ring lies at the junction of the outer and inner nuclear membranes and anchors the nuclear and cytoplasmic rings to the nuclear and cytoplasmic sides, respectively. The nuclear and cytoplasmic rings bear extensions called cytoplasmic filaments and nuclear basket, respectively. The NPC structure is made up of 30 different proteins called nucleoporins (Nups) which are present in several copies; the copy numbers always being a multiple of 847.48. A striking feature of all NPC cryo-EM boards is its large central hole, approximately.