Figure 1 - available via license: CC BY
Content may be subject to copyright.
Structural regions analyzed in this study. The structural regions were defined based on solvent-accessible surface areas measured from protein complex structures. Residues with changes in relative solvent accessible surface area (rASA; see Methods) between the bound and unbound conformations were defined as core residues (red) if rASAs are smaller than 0.25 and rim residues (blue) if rASAs are greater than 0.25 in the bound structures. Buried residues are non-interface residues with rASAs smaller than 0.25 in the unbound structures, and the remainder are surface residues (gray). Because the full-length protein often contains regions without structural data coverage, these structurally undefined sequences were classified as external regions in our analyses.
Source publication
Because proteins are fundamental to most biological processes, many genetic diseases can be traced back to single nucleotide variants (SNVs) that cause changes in protein sequences. However, not all SNVs that result in amino acid substitutions cause disease as each residue is under different structural and functional constraints. Influential studie...
Contexts in source publication
Context 1
... this work, we built on previous studies analyzing the localization of several categories of missense mutations in protein complex structures, but we focused on IDR interactions. Specifically, we analyzed the bias of missense mutations among interface residues as well as buried and surface non-interface residues (Figure 1). Importantly, we separated protein interfaces into core and rim regions because we and others have demonstrated characteristic differences in the two interface regions, including residue composition and SNV enrichment [2,9,46,49]. ...
Context 2
... each interaction pair, relative solvent accessible surface area (rASA) of protein residues were calculated to categorize the residues into protein regions. The SASA of each residue of the protein Figure 1. Structural regions analyzed in this study. ...
Context 3
... the categorized residues were mapped to UniProt sequences [57]. Supplementary Figure S1 provides an overview of the construction process of the interaction structure datasets, as well as the number of structures and proteins involved. The dataset of globular interactions encompasses all interaction pairs, which is justifiable since the dataset of IDR interactions is small in comparison. ...
Context 4
... each of the 15 combined datasets, UniProt sequences lacking either structural data or mutations were removed. In case of overlap between multiple PDB structures, the residue structural label was decided by their priority from highest to lowest: core, rim, buried, surface, and unstructured (external region; see Figure 1). In other words, if a protein residue position was an interface core residue in one structure and a non-interface surface residue in another, the residue will be labeled as an interface core residue in the merged data. ...
Context 5
... the surface and buried regions were defined as residues that are exposed and unexposed to solvent in the unbound state, respectively. The interface region was defined as residues that become more buried upon complex formation, i.e., residues that change in solvent exposure when comparing the complex to the separate protein chains (Figure 1). We further divided the interface region into core and rim, which are the central and peripheral sections of the interface, respectively, because of the differences in sequence and structural characteristics between the two regions [2,9]. ...
Context 6
... Y-axis is centered at one, and ORs > 1 show enrichment while ORs < 1 show depletion. Structural regions are color-coded (see Figure 1). Statistical significance is denoted by asterisks: *p-value < 0.05, **p-value < 0.01, ***p-value < 0.001. ...
Similar publications
Hepatitis E virus (HEV) is one of the causative agents of liver infections. The essential open reading frame 4 (ORF4) encoded protein role in HEV regulation remains undetermined. Intrinsically disordered protein regions (IDPRs)/intrinsically disordered protein (IDPs) in viral proteomes are linked with virus’s pathogenicity and infectivity. Therefor...
Citations
... Finally, it has been recently proposed that disease-associated mutations are prevalently located in the IDRs, and they have been frequently overlooked or annotated as variants of unknown significance [53][54][55] . We specifically examined a recently reported LIN28A variant R192G located in the IDR region in the C-terminal associated with parkinson's disease without a known mechanism 23 . ...
LIN28A is important in somatic reprogramming and pluripotency regulation. Although previous studies addressed that LIN28A can repress let-7 microRNA maturation in the cytoplasm, few focused on its role within the nucleus. Here, we show that the nucleolus-localized LIN28A protein undergoes liquid-liquid phase separation (LLPS) in mouse embryonic stem cells (mESCs) and in vitro. The RNA binding domains (RBD) and intrinsically disordered regions (IDR) of LIN28A contribute to LIN28A and the other nucleolar proteins’ phase-separated condensate establishment. S120A, S200A and R192G mutations in the IDR result in subcellular mislocalization of LIN28A and abnormal nucleolar phase separation. Moreover, we find that the naive-to-primed pluripotency state conversion and the reprogramming are associated with dynamic nucleolar remodeling, which depends on LIN28A’s phase separation capacity, because the LIN28A IDR point mutations abolish its role in regulating nucleolus and in these cell fate decision processes, and an exogenous IDR rescues it. These findings shed light on the nucleolar function in pluripotent stem cell states and on a non-canonical RNA-independent role of LIN28A in phase separation and cell fate decisions.
... 33,[37][38][39] As it is common in protein/protein interactions the presence of disordered regions may act as a hub to favor the complexation due to the greater flexibility and structural adaptability. [40][41][42][43] In this contribution we resort to all-atom molecular dynamics (MD) simulations performed on Ail embedded in a lipid bilayer mimicking the composition of the Y. pestis outer membrane, notably involving two dissymmetric leaflet the external one composed of Y. pestis lipopolysaccharides and the internal one composed of 74% PVPG, 21% PPPE, and 5% PVCL2. 44 The initial structure of the bacterial protein has been retrieved from the pdb database (5JV8). ...
Yersinia pestis , the causative agent of plague, is capable to evade human immune system response by recruiting the plasma circulating vitronectin proteins, which acts as a shield and avoids its lysis. Vitronectin recruitment is mediated by its interaction with the bacterial transmembrane protein Ail, protruding from Y. pestis outer membrane. By using all atom long-scale molecular dynamic simulations of Ail embedded in a realistic model of the bacterial membrane, we have shown that vitronectin forms a stable complex, mediated by interactions between the disordered moieties of the two proteins. The main amino acids driving the complexation have also been evidenced, thus favoring the possible rational design of specific peptides which, by inhibiting vitronectin recruitment, could act as original antibacterial agents.
TOC ABSTRACT
... It should be noted that the S96 residue resides in the IDR of STN1 (Fig. 2A). Owing to their conformational flexibility, IDRs are commonly involved in protein-protein interactions 81,82 . As IDRs are rich in polar amino acids, many residues in IDRs are prone to PTMs which may regulate key functions of a protein, for example, interaction with other signaling molecules, protein folding, etc. and consequently, changes protein functions in various biological settings 33,83 . ...
Keeping replication fork stable is essential for safeguarding genome integrity; hence, its protection is highly regulated. The CTC1-STN1-TEN1 (CST) complex protects stalled forks from aberrant MRE11-mediated nascent strand DNA degradation (NSD). However, the activation mechanism for CST at forks is unknown. Here, we report that STN1 is phosphorylated in its intrinsic disordered region. Loss of STN1 phosphorylation reduces the replication stress-induced STN1 localization to stalled forks, elevates NSD, increases MRE11 access to stalled forks, and decreases RAD51 localization at forks, leading to increased genome instability under perturbed DNA replication condition. STN1 is phosphorylated by both the ATR-CHK1 and the calcium-sensing kinase CaMKK2 in response to hydroxyurea/aphidicolin treatment or elevated cytosolic calcium concentration. Cancer-associated STN1 variants impair STN1 phosphorylation, conferring inability of fork protection. Collectively, our study uncovers that CaMKK2 and ATR-CHK1 target STN1 to enable its fork protective function, and suggests an important role of STN1 phosphorylation in cancer development.
... Many disease-causing mutations occur in the core of folded regions of proteins, affecting their structural stability (Wang & Moult, 2001). Other mutations are found on the protein surface and often occur in PPI interfaces (David et al, 2012;David & Sternberg, 2015;Wong et al, 2020). Approximately 10% of missense SNVs have been suggested to have a disruptive impact on PPIs (Fragoza et al, 2019). ...
Whole genome and exome sequencing are reporting on hundreds of thousands of missense mutations. Taking a pan-disease approach, we explored how mutations in the intrinsically disordered regions (IDRs) break or generate short linear motifs. We created a peptide-phage display library tiling peptides overlapping 12,301 disease-associated mutations from the IDRs of the human proteome. The mutations are linked to diverse diseases including cancer, metabolic diseases and neurological diseases. By screening 80 human proteins we found 367 mutation-modulated interactions, with half of the mutations diminishing binding, and half enhancing or creating novel interaction interfaces. The effects of the mutations were confirmed by affinity measurements. In cellular assays, the effects of motif-disruptive mutations were validated, including loss of a nuclear localisation signal in the cell division control protein CDC45 by a mutation associated with Meier-Gorlin syndrome. The study provides a panoramic view of how disease-associated mutations perturb and rewire the motif-based interactome.
... Disease-associated SAVs in IDRs are enriched at interaction interfaces, supporting the view that many mutations in IDRs cause disease by affecting PPIs (Wong et al, 2020). ...
Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employed peptide-based interaction proteomics to investigate 36 disease-causing mutations affecting phosphorylation sites. Our results unveiled significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We found that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments revealed the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering fresh insights into potential molecular mechanisms underlying pathogenesis.
... In periaxin, the mutations disturb protein-protein interactions. In line with this, disease mutations affecting IDRs often cluster at sites of protein-protein interactions [100]. Simulations have additionally suggested that disease mutations may reduce conformational heterogeneity of IDRs, which may in turn affect protein interactions [101]. ...
Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.
... We briefly summarize impact of one of the structural aspects covered by these resources, the intrinsic disorder. Just in 2021, the disorder predictions of the popular IUPred [37 -40], which are available via D 2 P 2 and MobiDB databases, were used to analyze the SARS-CoV-2 proteins [164][165][166][167], link mutations in the intrinsically disordered sequence regions to cancer [168,169], investigate liquid-liquid phase separation [170][171][172], localize disorder across compartments of the human cell [108], and to develop a wide range of predictive tools [173][174][175][176][177][178], among many other applications. Similarly long list of diverse uses can be attributed to the results produced by DisoRDPbind [44][45][46], which covers putative disordered protein/DNA/RNA binding AAs and which are available via DescribePROT. ...
... Moreover, the analysis of components of the ATP-dependent ubiquitin-proteasome degradation system (UPS) revealed the importance of the disorder content and MoRFs of the complex in neurodegenerative disorders and cancers [329]. However, identifying key mutations, PTM sites, and functional motifs in the disordered regions, exploring the evolutionary history of IDPs involved in diseases, understanding the cooperative functioning of ordered and disordered domains, and dissecting the IDPs' interactome are some of the many active research areas involving IDPs/IDRs and diseases [288,[330][331][332][333][334]. ...
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called “Disorder–function paradigm” of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
... In many cases, modular proteins have a hybrid composition. They include structurally well-organized domains connected by intrinsically disordered regions (IDRs), which appear to be crucial elements in the cooperative folding of MDPs and the modulation of protein functions [5][6][7]. As the inherent flexibility of IDRs delivers dynamic cross-domain communication between remote domains, enabling cooperative allosteric regulation in an MDP, the use of cleaved IDRs as stand-alone entities is still questioned [8,9]. ...
Receptor tyrosine kinases (RTKs) are modular membrane proteins possessing both well-folded and disordered domains acting together in ligand-induced activation and regulation of post-transduction processes that tightly couple extracellular and cytoplasmic events. They ensure the fine-turning control of signal transmission by signal transduction. Deregulation of RTK KIT, including overexpression and gain of function mutations, has been detected in several human cancers. In this paper, we analysed by in silico techniques the Kinase Insert Domain (KID), a key platform of KIT transduction processes, as a generic macrocycle (KIDGC), a cleaved isolated polypeptide (KIDC), and a natively fused TKD domain (KIDD). We assumed that these KID species have similar structural and dynamic characteristics indicating the intrinsically disordered nature of this domain. This finding means that both polypeptides, cyclic KIDGC and linear KIDC, are valid models of KID integrated into the RTK KIT and will be helpful for further computational and empirical studies of post-transduction KIT events.
... In this regard, it is known that frustrated surface regions can create hubs for the interaction network 42,43 and that polymorphic and pathogenic variations involving residues located on structurally exposed regions often cause a rewiring of a protein interactome. 44,45 Thus, we analyzed the interactome of the two AGT1 isoforms by co-immunoprecipitation coupled with quantitative mass spectrometry (IP-MS). Selected clones of HEK293 cells expressing AGT-Ma or AGT-Mi did not show any gross changes in morphology or viability as compared to control cells. ...
The conformational landscape of a protein is constantly expanded by genetic variations that have a minimal impact on the function(s) while causing subtle effects on protein structure. The wider the conformational space sampled by these variants, the higher the probabilities to adapt to changes in environmental conditions. However, the probability that a single mutation may result in a pathogenic phenotype also increases. Here we present a paradigmatic example of how protein evolution balances structural stability and dynamics to maximize protein adaptability and preserve protein fitness. We took advantage of known genetic variations of human alanine:glyoxylate aminotransferase (AGT1), which is present as a common major allelic form (AGT‐Ma) and a minor polymorphic form (AGT‐Mi) expressed in 20% of Caucasian population. By integrating crystallographic studies and molecular dynamics simulations, we show that AGT‐Ma is endowed with structurally unstable (frustrated) regions, which become disordered in AGT‐Mi. An in‐depth biochemical characterization of variants from an anticonsensus library, encompassing the frustrated regions, correlates this plasticity to a fitness window defined by AGT‐Ma and AGT‐Mi. Finally, co‐immunoprecipitation analysis suggests that structural frustration in AGT1 could favor additional functions related to protein–protein interactions. These results expand our understanding of protein structural evolution by establishing that naturally occurring genetic variations tip the balance between stability and frustration to maximize the ensemble of conformations falling within a well‐defined fitness window, thus expanding the adaptability potential of the protein.
