The Wide World of Coacervates: From the Sea to Neurodegeneration Astoricchio, Emanuele; Alfano, Caterina; Rajendran, Lawrence ...
Trends in biochemical sciences (Amsterdam. Regular ed.),
August 2020, 2020-08-00, 20200801, Letnik:
45, Številka:
8
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The formation of immiscible liquid phases or coacervates is a phenomenon widely observed in biology. Marine organisms, for instance, use liquid–liquid phase separation (LLPS) as the precursor phase ...to form various fibrillar or crustaceous materials that are essential for surface adhesion. More recently, the importance of LLPS has been realized in the compartmentalization of living cells and in obtaining ordered but dynamic partitions that can be reversed according to necessity. Here, we compare the properties, features, and peculiarities of intracellular and extracellular coacervates, drawing parallels and learning from the differences. A more general view of the phenomenon may in the future inform new studies to allow a better comprehension of its laws.
Coacervates play key roles in various essential biological processes.In marine organisms, extracellular coacervates are important for the creation of strong adhesion that can resist tides and rough seas.Intracellular coacervates have evolved to create resilient but dynamic compartments in the eukaryotic cell.Despite being based on the same physical laws, the two fields have traditionally been kept separated.It is thus in order to compare the commonalities of and differences between intra- and extracellular coacervates.This comparison allows us to learn about the functional requirements that both processes involve and to formulate new hypotheses that can then be tested experimentally.
The Ball and Chain of Polyubiquitin Structures Alfano, Caterina; Faggiano, Serena; Pastore, Annalisa
Trends in biochemical sciences (Amsterdam. Regular ed.),
April 2016, 2016-04-00, 20160401, Letnik:
41, Številka:
4
Journal Article
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Ubiquitylation is a post-translational modification implicated in several different cellular pathways. The possibility of forming chains through covalent crosslinking between any of the seven ...lysines, or the initial methionine, and the C terminus of another moiety provides ubiquitin (Ub) with special flexibility in its function in signalling. Here, we review the knowledge accumulated over the past several years about the functions and structural features of polyUb chains. This analysis reveals the need to understand further the functional role of some of the linkages and the structural code that determines recognition of polyUbs by protein partners.
Ubiquitin (Ub), a small signalling protein, forms chains as a result of covalent linkage between any of the seven lysines or the N-terminal methionine of one subunit and the C terminus of another Ub.
PolyUb chains both with the same or mixed linkages are involved in several cellular functions from proteasomal targeting to protein regulation and have thus acquired an enormous importance in cellular signalling.
PolyUbs exhibit a unique repertoire of conformational states that is dependent on the specific linkages, which have different flexibilities.
Further complexity is added by the interaction of polyUbs with cellular partners, which modulate their structure and functions.
Understanding the structural and functional aspects of the polyUb code continues to offer an important challenge.
Macromolecular crowding ought to stabilize folded forms of proteins, through an excluded volume effect. This explanation has been questioned and observed effects attributed to weak interactions with ...other cell components. Here we show conclusively that protein stability is affected by volume exclusion and that the effect is more pronounced when the crowder's size is closer to that of the protein under study. Accurate evaluation of the volume exclusion effect is made possible by the choice of yeast frataxin, a protein that undergoes cold denaturation above zero degrees, because the unfolded form at low temperature is more expanded than the corresponding one at high temperature. To achieve optimum sensitivity to changes in stability we introduce an empirical parameter derived from the stability curve. The large effect of PEG 20 on cold denaturation can be explained by a change in water activity, according to Privalov's interpretation of cold denaturation.
Networks-based approaches are often used to analyze gene expression data or protein-protein interactions but are not usually applied to study the relationships between different biomarkers. Given the ...clinical need for more comprehensive and integrative biomarkers that can help to identify personalized therapies, the integration of biomarkers of different natures is an emerging trend in the literature. Network analysis can be used to analyze the relationships between different features of a disease; nodes can be disease-related phenotypes, gene expression, mutational events, protein quantification, imaging-derived features and more. Since different biomarkers can exert causal effects between them, describing such interrelationships can be used to better understand the underlying mechanisms of complex diseases. Networks as biomarkers are not yet commonly used, despite being proven to lead to interesting results. Here, we discuss in which ways they have been used to provide novel insights into disease susceptibility, disease development and severity.
ETV6-related thrombocytopenia is an autosomal dominant thrombocytopenia that has been recently identified in a few families and has been suspected to predispose to hematologic malignancies. To gain ...further information on this disorder, we searched for ETV6 mutations in the 130 families with inherited thrombocytopenia of unknown origin from our cohort of 274 consecutive pedigrees with familial thrombocytopenia. We identified 20 patients with ETV6-related thrombocytopenia from seven pedigrees. They have five different ETV6 variants, including three novel mutations affecting the highly conserved E26 transformation-specific domain. The relative frequency of ETV6-related thrombocytopenia was 2.6% in the whole case series and 4.6% among the families with known forms of inherited thrombocytopenia. The degree of thrombocytopenia and bleeding tendency of the patients with ETV6-related thrombocytopenia were mild, but four subjects developed B-cell acute lymphoblastic leukemia during childhood, resulting in a significantly higher incidence of this condition compared to that in the general population. Clinical and laboratory findings did not identify any particular defects that could lead to the suspicion of this disorder from the routine diagnostic workup. However, at variance with most inherited thrombocytopenias, platelets were not enlarged. In vitro studies revealed that the maturation of the patients' megakaryocytes was defective and that the patients have impaired proplatelet formation. Moreover, platelets from patients with ETV6-related thrombocytopenia have reduced ability to spread on fibrinogen. Since the dominant thrombocytopenias due to mutations in RUNX1 and ANKRD26 are also characterized by normal platelet size and predispose to hematologic malignancies, we suggest that screening for ETV6, RUNX1 and ANKRD26 mutations should be performed in all subjects with autosomal dominant thrombocytopenia and normal platelet size.
Abstract In 2019, the novel SARS-CoV-2 coronavirus emerged in China, causing the pneumonia named COVID-19. At the beginning, all research efforts were focused on the spike (S) glycoprotein. However, ...it became evident that the nucleocapsid (N) protein is pivotal in viral replication, genome packaging and evasion of the immune system, is highly immunogenic, which makes it another compelling target for antibody development alongside the spike protein. This study focused on the construction of single chain fragments variable (scFvs) libraries from SARS-CoV-2-infected patients to establish a valuable, immortalized and extensive antibodies source. We used the Intracellular Antibody Capture Technology to select a panel of scFvs against the SARS-CoV-2 N protein. The whole panel of scFv was expressed and characterized both as intrabodies and recombinant proteins. ScFvs were then divided into 2 subgroups: those that exhibited high binding activity to N protein when expressed in yeast or in mammalian cells as intrabodies, and those purified as recombinant proteins, displaying affinity for recombinant N protein in the nanomolar range. This panel of scFvs against the N protein represents a novel platform for research and potential diagnostic applications.
Congenital amegakaryocytic thrombocytopenia (CAMT) is an inherited disorder characterized at birth by thrombocytopenia with reduced megakaryocytes, which evolves into generalized bone marrow aplasia ...during childhood. Although CAMT is genetically heterogeneous, mutations of MPL, the gene encoding for the receptor of thrombopoietin (THPO), are the only known disease‐causing alterations. We identified a family with three children affected with CAMT caused by a homozygous mutation (p.R119C) of the THPO gene. Functional studies showed that p.R119C affects not only ability of the cytokine to stimulate MPL but also its release, which is consistent with the relatively low serum THPO levels measured in patients. In all the three affected children, treatment with the THPO‐mimetic romiplostim induced trilineage hematological responses, remission of bleeding and infections, and transfusion independence, which were maintained after up to 6.5 years of observation. Recognizing patients with THPO mutations among those with juvenile bone marrow failure is essential to provide them with appropriate substitutive therapy and prevent the use of invasive and unnecessary treatments, such as hematopoietic stem cell transplantation or immunosuppression.
Synopsis
Congenital amegakaryocytic thrombocytopenia (CAMT) is a fatal inherited juvenile bone marrow failure syndrome, unless children are treated with hematopoietic stem cell transplantation (HSCT). The only known cause of CAMT is mutations in the MPL gene. A novel THPO mutation is here described.
We identified a family affected with CAMT that is caused by a novel homozygous missense mutation (p.R119C) in THPO, the gene encoding for thrombopoietin (THPO).
Functional studies in vitro showed that p.R119C significantly impairs secretion of THPO, consistent with the relatively low serum THPO levels measured in patients.
The mutation also affects interaction of THPO with MPL, resulting in defective signalling downstream of the receptor, which is reduced by about 50% compared with wild‐type THPO.
In three affected children, administration of the THPO‐mimetic romiplostim induced sustained trilineage improvement of blood counts and remission of bleeding and infections, maintained after an up to 6.5‐year follow‐up.
THPO mutations must be considered in patients presenting with the phenotype of CAMT: recognition of this disorder (disease variant) is essential to avoid unnecessary HSCT and give appropriate substitutive therapy with MPL agonists.
Congenital amegakaryocytic thrombocytopenia (CAMT) is a fatal inherited juvenile bone marrow failure syndrome, unless children are treated with hematopoietic stem cell transplantation (HSCT). The only known cause of CAMT is mutations in the MPL gene. A novel THPO mutation is here described.
Hormonal contraceptives (HCs) have been shown to be safe and effective when used correctly and consistently, however, as other classes of drugs, they are also associated with adverse health outcomes. ...In this study, we aim to explain the occurrence of common and unexpected HCs side effects (SEs) integrating drug-target, drug-SE and protein-protein interaction (PPI) public databases. We created a tripartite network that includes three types of vertices: SEs, drugs, and targets. The three layers are linked by means of the inter-layer associations drug-target and drug-SE, whereas only the target layer is characterized also by intra-layer links (PPIs). We exploited the drug-mediated association SE-target to identify the side effect modules defined as a network connected component composed of target proteins plus the proteins needed to connect them. We found that module proteins are associated with diseases/phenotypes and/or KEGG pathways related to the SEs. In particular, in many cases, targets are not enriched in SE features, whereas investigating their neighborhood (here defined as the proteins that allow the targets' connection) we found SE-related pathways. These results show that HCs action can perturb the targets’ neighborhood inducing unwanted reaction and that the proposed approach can help to understand how, and through which molecular mechanisms, side effects can occur. The approach is general in its nature: it can be applied to other drugs categories providing a support in identifying a subject-specific therapy that takes into account comorbidities and lifestyle to reduce or avoid the most undesired side effects.
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