Structural Reconstruction of Protein-Protein Complexes Involved in Intracellular Signaling

2016 ◽  
pp. 315-326
Author(s):  
Klára Kirsch ◽  
Péter Sok ◽  
Attila Reményi
Keyword(s):  
Intracellular Signaling ◽  
Protein Complexes

scholarly journals Orchestration of Primary Hemostasis by Platelet and Endothelial Lysosome-Related Organelles

2020 ◽  
Vol 40 (6) ◽  
pp. 1441-1453 ◽  
Author(s):  
Ellie Karampini ◽  
Ruben Bierings ◽  
Jan Voorberg
Keyword(s):  
Endothelial Cells ◽  
Intracellular Signaling ◽  
Protein Complexes ◽  
Biological Properties ◽  
Bleeding Disorders ◽  
Granule Formation ◽  
Primary Hemostasis ◽  
Granule Maturation ◽  
Lysosome Related Organelles ◽  
Von Willebrand

Megakaryocyte-derived platelets and endothelial cells store their hemostatic cargo in α- and δ-granules and Weibel-Palade bodies, respectively. These storage granules belong to the lysosome-related organelles (LROs), a heterogeneous group of organelles that are rapidly released following agonist-induced triggering of intracellular signaling pathways. Following vascular injury, endothelial Weibel-Palade bodies release their content into the vascular lumen and promote the formation of long VWF (von Willebrand factor) strings that form an adhesive platform for platelets. Binding to VWF strings as well as exposed subendothelial collagen activates platelets resulting in the release of α- and δ-granules, which are crucial events in formation of a primary hemostatic plug. Biogenesis and secretion of these LROs are pivotal for the maintenance of proper hemostasis. Several bleeding disorders have been linked to abnormal generation of LROs in megakaryocytes and endothelial cells. Recent reviews have emphasized common pathways in the biogenesis and biological properties of LROs, focusing mainly on melanosomes. Despite many similarities, LROs in platelet and endothelial cells clearly possess distinct properties that allow them to provide a highly coordinated and synergistic contribution to primary hemostasis by sequentially releasing hemostatic cargo. In this brief review, we discuss in depth the known regulators of α- and δ-granules in megakaryocytes/platelets and Weibel-Palade bodies in endothelial cells, starting from transcription factors that have been associated with granule formation to protein complexes that promote granule maturation. In addition, we provide a detailed view on the interplay between platelet and endothelial LROs in controlling hemostasis as well as their dysfunction in LRO related bleeding disorders.

scholarly journals Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1776
Author(s):  
Alicia Landeira-Viñuela ◽  
Paula Díez ◽  
Pablo Juanes-Velasco ◽  
Quentin Lécrevisse ◽  
Alberto Orfao ◽  
...  
Keyword(s):  
B Cell ◽  
Cell Line ◽  
Intracellular Signaling ◽  
Protein Extraction ◽  
Protein Complexes ◽  
B Cell Lymphoma ◽  
Size Exclusion ◽  
Sequencing Analysis ◽  
Affinity Proteomics

Human Proteome Project (HPP) presents a systematic characterization of the protein landscape under different conditions using several complementary-omic techniques (LC-MS/MS proteomics, affinity proteomics, transcriptomics, etc.). In the present study, using a B-cell lymphoma cell line as a model, comprehensive integration of RNA-Seq transcriptomics, MS/MS, and antibody-based affinity proteomics (combined with size-exclusion chromatography) (SEC-MAP) were performed to uncover correlations that could provide insights into protein dynamics at the intracellular level. Here, 5672 unique proteins were systematically identified by MS/MS analysis and subcellular protein extraction strategies (neXtProt release 2020-21, MS/MS data are available via ProteomeXchange with identifier PXD003939). Moreover, RNA deep sequencing analysis of this lymphoma B-cell line identified 19,518 expressed genes and 5707 protein coding genes (mapped to neXtProt). Among these data sets, 162 relevant proteins (targeted by 206 antibodies) were systematically analyzed by the SEC-MAP approach, providing information about PTMs, isoforms, protein complexes, and subcellular localization. Finally, a bioinformatic pipeline has been designed and developed for orthogonal integration of these high-content proteomics and transcriptomics datasets, which might be useful for comprehensive and global characterization of intracellular protein profiles.

scholarly journals Expression of Cytoskeleton Actin in Cancer and Metastasis

2019 ◽  
Vol 2 (1) ◽  
pp. 19-22
Author(s):  
Sabeera Afzal ◽  
Hina Sadaf ◽  
Qurat-ul-ain Fatima
Keyword(s):  
Intracellular Signaling ◽  
Binding Proteins ◽  
Protein Complexes ◽  
Eukaryotic Cell ◽  
Actin Binding ◽  
Actin Binding Proteins ◽  
Homologous Protein ◽  
Exact Shape ◽  
Syndrome Protein ◽  
G Protein Coupled

Cytoskeleton in Eukaryotic cell is very important for cell to keep the exact shape and supports the plasma membrane and give the mechanical support to cell. Actin is a type of cytoskeleton that is involved in several functions. Actin filaments are made up of indistinguishable actin binding proteins which is set in a lengthy curved chain which performs important function of body. Expresion of some actin binding proteins are regulated during carcinogenesis and metastasis, these proteins include Arp2/3 (Actin related protein 2 and 3 complex), fascin and the tropomyosin’s, WASP/WAVE (Wiskott-Aldrich syndrome protein/WASP and Verprolin homologous protein) complexes. The expansion of cancer cells from the primary tumor to other tissues and the organs is called metastasis. The connection amongst the hyperactivated signaling pathways plays a very important role in the development of metastatic. GPCRs (G Protein Coupled Receptors) through β-arrs (β-arrestins) act as a intracellular signaling particles. In tumor cells the increased and decreased expression of these actin binding proteins are involved in progression of different types of cancer and metastasis. For further insight we have to understand what is actin and the function of actin binding proteins.

scholarly journals Growth hormone and erythropoietin differentially activate DNA-binding proteins by tyrosine phosphorylation.

1994 ◽  
Vol 14 (3) ◽  
pp. 2113-2118 ◽  
Author(s):  
D S Finbloom ◽  
E F Petricoin ◽  
R H Hackett ◽  
M David ◽  
G M Feldman ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Dna Binding ◽  
Tyrosine Phosphorylation ◽  
Tyrosine Kinases ◽  
Intracellular Signaling ◽  
Protein Complexes ◽  
Early Response ◽  
Receptor Clustering ◽  
Intracellular Signaling Pathway ◽  
Transcription Complexes

Binding of growth hormone (GH) and erythropoietin (EPO) to their respective receptors results in receptor clustering and activation of tyrosine kinases that initiate a cascade of events resulting not only in the rapid tyrosine phosphorylation of several proteins but also in the induction of early-response genes. In this report, we show that GH and EPO induce the tyrosine phosphorylation of cellular proteins with molecular masses of 93 kDa and of 91 and 84 kDa, respectively, and that these proteins form DNA-binding complexes which recognize an enhancer that has features in common with several rapidly induced genes such as c-fos. Assembly of the protein complexes required tyrosine phosphorylation, which occurred within minutes after addition of ligand. The activated complexes translocated from the cytoplasm to the nucleus. The protein activated by GH is antigenically similar to p91, a protein common to several transcription complexes that are activated by interferons and other cytokines. In contrast, the proteins activated by EPO are distinct from p91. These findings establish the outlines for a cytokine-induced intracellular signaling pathway, which begins with ligand-induced receptor clustering that activates one or more tyrosine kinases. These data are the first to demonstrate that GH- and EPO-activated tyrosine-phosphorylated proteins can specifically recognize a well-defined enhancer and therefore provide a mechanism for rapidly transducing signals from the membrane to the nucleus.

scholarly journals Cadherin signaling: keeping cells in touch

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 550 ◽  
Author(s):  
Olga Klezovitch ◽  
Valeri Vasioukhin
Keyword(s):  
Cell Adhesion ◽  
Signaling Pathways ◽  
Cell Body ◽  
Intracellular Signaling ◽  
Protein Complexes ◽  
Adhesion Protein ◽  
The Past ◽  
Intracellular Signaling Pathways ◽  
Mechanical Linkage ◽  
Cell Cell

Cadherin-catenin complexes are critical for the assembly of cell-cell adhesion structures known as adherens junctions. In addition to the mechanical linkage of neighboring cells to each other, these cell-cell adhesion protein complexes have recently emerged as important sensors and transmitters of the extracellular cues inside the cell body and into the nucleus. In the past few years, multiple studies have identified a connection between the cadherin-catenin protein complexes and major intracellular signaling pathways. Those studies are the main focus of this review.

scholarly journals A novel locally c-di-GMP-controlled exopolysaccharide synthase required for N4 phage infection of E. coli

2021 ◽  
Author(s):  
Eike H. Junkermeier ◽  
Regine Hengge
Keyword(s):  
Intracellular Signaling ◽  
Extracellular Polymeric Substances ◽  
Protein Complexes ◽  
Receptor System ◽  
Systematic Screening ◽  
E Coli ◽  
Diguanylate Cyclases ◽  
K 12 ◽  
Major Target ◽  
N4 Phage

A major target of c-di-GMP signaling is the production of biofilm-associated extracellular polymeric substances (EPS), which in Escherichia coli K-12 include amyloid curli fibres, phosphoethanolamine-modified (pEtN-)cellulose and poly-N-acetyl-glucosamine (PGA). However, the characterized c-di-GMP-binding effector systems are largely outnumbered by the 12 diguanylate cyclases (DGCs) and 13 phosphodiesterases (PDEs), which synthetize and degrade c-di-GMP, respectively. E. coli possesses a single protein with a potentially c-di-GMP-binding MshEN domain, NfrB, which together with the outer membrane protein NfrA is known to serve as a receptor system for phage N4. Here, we show that NfrB not only binds c-di-GMP with high affinity, but as a novel c-di-GMP-controlled glycosyltransferase synthesizes a secreted EPS, which can impede motility and is required as an initial receptor for phage N4 infection. In addition, a systematic screening of the 12 DGCs of E. coli K-12 revealed that specifically DgcJ is required for the infection with phage N4 and interacts directly with NfrB. This is in line with local signaling models, where specific DGCs and/or PDEs form protein complexes with particular c-di-GMP effector/target systems. Our findings thus provide further evidence that intracellular signaling pathways, which all use the same diffusible second messenger, can act in parallel in a highly specific manner.

Phase 1 clinical trial of KOS-953 + bortezomib (BZ) in relapsed refractory multiple myeloma (MM)

2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 3066-3066 ◽  
Author(s):  
A. Chanan-Khan ◽  
P. Richardson ◽  
M. Alsina ◽  
S. Lonial ◽  
A. Krishnan ◽  
...  
Keyword(s):  
Dose Escalation ◽  
Intracellular Signaling ◽  
Protein Complexes ◽  
Phase 1 ◽  
Single Agent ◽  
Proteasome Inhibition ◽  
20S Proteasome ◽  
Predicted Values ◽  
Grade 3

3066 Background: KOS-953 (17-AAG in Cremophor) inhibits HSP90 chaperone function, resulting in disruption of protein complexes and proteasomal degradation. Single-agent 17-AAG is active in relapsed/refractory MM patients (pts) (ASH 2005 A#361), with a recommended dose ≥ 275 mg/m2. In vitro, BZ + KOS-953 show additive cytotoxicity of myeloma cells. Objectives: Define phase 2 dose of BZ+KOS-953 in pts with relapsed refractory MM. Determine PK of KOS-953 and its active metabolite. Evaluate proteasome inhibition in whole blood lysates and explore changes in intracellular signaling proteins in pt PBMCs and MM cells. Methods: Pts received BZ as IV bolus followed by 1-hour infusion KOS-953 twice weekly for 2 out of 3 weeks. Dose escalation occurred in a step-wise manner. PK and collection of surrogates are performed following the 1st and 4th infusion. Pts assessed for response by EBMT criteria. Results: 20 pts were enrolled in 4 cohorts: BZ+KOS-953 (mg/m2): 0.7+100 (n=3); 1.0+100 (n=3); 1.0+150 (n=8); and 1.3+150 (n=6), receiving a total of 103+ cycles (median 5 cycles; range <1 - 17). Demographics: 10F/10M; median age/KPS 64y/90; median # of prior regimens 4 (range 2–16); 75% prior BZ (5 with ≥2 prior BZ); 95% prior thalidomide; 15% prior lenalidomide; 70% prior SCT(s). DLT observed in Cohort 2 (n=1 grade 4 hepatotoxicity in a setting of congestive heart failure secondary to cardiac amyloidosis) and in Cohort 3 (n=1 pancreatitis). Other Grade 3–4 toxicity (1 each): thrombocytopenia with Herpes Zoster recurrence and pneumonia; septic thrombophlebitis. Drug-related toxicity (mild-to-moderate): diarrhea (n=8), fatigue (n=8), constipation (n=7), neuropathy (n=7), ↑AST (n=5), muscle cramps (n=5) and rash (n=4). PK similar to single-agent trial; stationary kinetics noted upon twice weekly dosing. 20S proteasome function (1.3 mg/m2, end of infusion): 50% decrease (similar to predicted values). Response was seen in 6 out of 12 BZ-refractory patients (1 nCR, 5 MR) and 3 out of 4 BZ-naïve pts (1 nCR, 2 MR). Conclusions: Dose escalation continues with no additive toxicity or PK interactions to date. Similar inhibition of the 20S proteasome is observed compared to BZ alone. Encouraging activity is seen in both BZ-naïve and BZ-refractory heavily pre-treated MM pts. [Table: see text]

Growth hormone and erythropoietin differentially activate DNA-binding proteins by tyrosine phosphorylation

1994 ◽  
Vol 14 (3) ◽  
pp. 2113-2118
Author(s):  
D S Finbloom ◽  
E F Petricoin ◽  
R H Hackett ◽  
M David ◽  
G M Feldman ◽  
...  
Keyword(s):  
Growth Hormone ◽  
Dna Binding ◽  
Tyrosine Phosphorylation ◽  
Tyrosine Kinases ◽  
Intracellular Signaling ◽  
Protein Complexes ◽  
Early Response ◽  
Receptor Clustering ◽  
Intracellular Signaling Pathway ◽  
Transcription Complexes

Binding of growth hormone (GH) and erythropoietin (EPO) to their respective receptors results in receptor clustering and activation of tyrosine kinases that initiate a cascade of events resulting not only in the rapid tyrosine phosphorylation of several proteins but also in the induction of early-response genes. In this report, we show that GH and EPO induce the tyrosine phosphorylation of cellular proteins with molecular masses of 93 kDa and of 91 and 84 kDa, respectively, and that these proteins form DNA-binding complexes which recognize an enhancer that has features in common with several rapidly induced genes such as c-fos. Assembly of the protein complexes required tyrosine phosphorylation, which occurred within minutes after addition of ligand. The activated complexes translocated from the cytoplasm to the nucleus. The protein activated by GH is antigenically similar to p91, a protein common to several transcription complexes that are activated by interferons and other cytokines. In contrast, the proteins activated by EPO are distinct from p91. These findings establish the outlines for a cytokine-induced intracellular signaling pathway, which begins with ligand-induced receptor clustering that activates one or more tyrosine kinases. These data are the first to demonstrate that GH- and EPO-activated tyrosine-phosphorylated proteins can specifically recognize a well-defined enhancer and therefore provide a mechanism for rapidly transducing signals from the membrane to the nucleus.

Electron Microscopy and image analysis of nucleo-protein complexes

1994 ◽  
Vol 52 ◽  
pp. 88-89
Author(s):  
E. H. Egelman ◽  
X. Yu
Keyword(s):  
Electron Microscopy ◽  
Image Analysis ◽  
Normal Cell ◽  
Genetic Recombination ◽  
Protein Complexes ◽  
Chromosomal Rearrangements ◽  
Reca Protein ◽  
E Coli ◽  
Helical Polymer ◽  
Specific Protease

The RecA protein of E. coli has been shown to mediate genetic recombination, regulate its own synthesis, control the expression of other genes, act as a specific protease, form a helical polymer and have an ATPase activity, among other observed properties. The unusual filament formed by the RecA protein on DNA has not previously been shown to exist outside of bacteria. Within this filament, the 36 Å pitch of B-form DNA is extended to about 95 Å, the pitch of the RecA helix. We have now establishedthat similar nucleo-protein complexes are formed by bacteriophage and yeast proteins, and availableevidence suggests that this structure is universal across all of biology, including humans. Thus, understanding the function of the RecA protein will reveal basic mechanisms, in existence inall organisms, that are at the foundation of general genetic recombination and repair.Recombination at this moment is assuming an importance far greater than just pure biology. The association between chromosomal rearrangements and neoplasms has become stronger and stronger, and these rearrangements are most likely products of the recombinatory apparatus of the normal cell. Further, damage to DNA appears to be a major cause of cancer.

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