scholarly journals The Human Plasma Membrane Peripherome: Visualization and Analysis of Interactions

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Katerina C. Nastou ◽  
Georgios N. Tsaousis ◽  
Kimon E. Kremizas ◽  
Zoi I. Litou ◽  
Stavros J. Hamodrakas
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Human Plasma ◽  
Noncovalent Interactions ◽  
Interaction Network ◽  
Subcellular Location ◽  
Membrane Function ◽  
Peripheral Membrane Proteins ◽  
Peripheral Proteins ◽  
Approved Drugs

A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with noncovalent interactions. The aim of this study was to construct and analyze the interactions of the human plasma membrane peripheral proteins (peripherome hereinafter). For this purpose, we collected a dataset of peripheral proteins of the human plasma membrane. We also collected a dataset of experimentally verified interactions for these proteins. The interaction network created from this dataset has been visualized using Cytoscape. We grouped the proteins based on their subcellular location and clustered them using the MCL algorithm in order to detect functional modules. Moreover, functional and graph theory based analyses have been performed to assess biological features of the network. Interaction data with drug molecules show that ~10% of peripheral membrane proteins are targets for approved drugs, suggesting their potential implications in disease. In conclusion, we reveal novel features and properties regarding the protein-protein interaction network created by peripheral proteins of the human plasma membrane.

Phosphoinositides in Constitutive Membrane Traffic

2004 ◽  
Vol 84 (3) ◽  
pp. 699-730 ◽  
Author(s):  
Michael G. Roth
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Membrane Traffic ◽  
Spatial Segregation ◽  
Peripheral Membrane Proteins ◽  
Transport Vesicles ◽  
Early Endosomes ◽  
Lipid Kinases ◽  
Phosphatidylinositol 4 ◽  
Different Parts

Proteins that make, consume, and bind to phosphoinositides are important for constitutive membrane traffic. Different phosphoinositides are concentrated in different parts of the central vacuolar pathway, with phosphatidylinositol 4-phosphate predominate on Golgi, phosphatidylinositol 4,5-bisphosphate predominate at the plasma membrane, phosphatidylinositol 3-phosphate the major phosphoinositide on early endosomes, and phosphatidylinositol 3,5-bisphosphate found on late endocytic organelles. This spatial segregation may be the mechanism by which the direction of membrane traffic is controlled. Phosphoinositides increase the affinity of membranes for peripheral membrane proteins that function for sorting protein cargo or for the docking and fusion of transport vesicles. This implies that constitutive membrane traffic may be regulated by the mechanisms that control the activity of the enzymes that produce and consume phosphoinositides. Although the lipid kinases and phosphatases that function in constitutive membrane traffic are beginning to be identified, their regulation is poorly understood.

scholarly journals Membrane Lipid Switches: How Membrane Lipid Structure Influences Protein–Lipid Interactions

2020 ◽  
Author(s):  
Manuel Torres ◽  
Catalina Ana Rosselló ◽  
Paula Fernández García ◽  
Victoria Llado ◽  
Pablo V Escribá
Keyword(s):  
Plasma Membrane ◽  
Membrane Lipids ◽  
Signal Propagation ◽  
Receptor Activation ◽  
Membrane Lipid ◽  
Therapeutic Interventions ◽  
Signaling Proteins ◽  
Peripheral Membrane Proteins ◽  
Signal Cascade ◽  
Peripheral Proteins

Peripheral membrane proteins are required for signal propagation upon ligand-induced receptor activation at the plasma membrane. The translocation of this amphitropic peripheral proteins from or to the plasma membrane enables signal cascade propagation into the cells. This translocation greatly depends on the membrane’s lipid composition and, consequently, regulation of the lipid bilayer emerges as a novel therapeutic strategy. Indeed, relevant changes in membrane lipids can induce massive translocation of peripheral signaling proteins from or to the plasma membrane, which controls how cells behave. We called these changes “lipid switches”, as they alter the cell’s status (e.g., proliferation, differentiation, death, etc.) in response to the modulation of membrane lipids. This discovery enables therapeutic interventions focused on modifying the bilayer’s lipids, an approach known as membrane-lipid therapy (MLT) or melitherapy.

Particle Movement in Heliozoan Axopods Associated with Lateral Displacement of H ighly Ordered Membrane Domains

1976 ◽  
Vol 31 (3-4) ◽  
pp. 190-194 ◽  
Author(s):  
Christian F. Bardele
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Membrane Fusion ◽  
Lateral Displacement ◽  
Freeze Fracture ◽  
Motive Force ◽  
Membrane Domains ◽  
Particle Movement ◽  
Peripheral Membrane Proteins

Abstract Freeze-fracture studies reveal that extrusive organelles displaying saltatory particle movements in centrohelidian axopod are attached to highly ordered domains within the plasma membrane. It is postulated that the motive force for lateral displacement of these membrane domains with the adhering organelle is located immediately underneath the plasma membrane being either part of the peripheral membrane proteins or attached filaments alined parallel to the axopodial micro­ tubules. The attachment domain is interpreted organelle discharge by membrane fusion.

scholarly journals Exomer: a coat complex for transport of select membrane proteins from the trans-Golgi network to the plasma membrane in yeast

2006 ◽  
Vol 174 (7) ◽  
pp. 973-983 ◽  
Author(s):  
Chao-Wen Wang ◽  
Susan Hamamoto ◽  
Lelio Orci ◽  
Randy Schekman
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Cell Surface ◽  
Protein Complex ◽  
Adaptor Protein ◽  
Nucleotide Exchange ◽  
Trans Golgi Network ◽  
Peripheral Proteins ◽  
Golgi Network

Ayeast plasma membrane protein, Chs3p, transits to the mother–bud neck from a reservoir comprising the trans-Golgi network (TGN) and endosomal system. Two TGN/endosomal peripheral proteins, Chs5p and Chs6p, and three Chs6p paralogues form a complex that is required for the TGN to cell surface transport of Chs3p. The role of these peripheral proteins has not been clear, and we now provide evidence that they create a coat complex required for the capture of membrane proteins en route to the cell surface. Sec7p, a Golgi protein required for general membrane traffic and functioning as a nucleotide exchange factor for the guanosine triphosphate (GTP)–binding protein Arf1p, is required to recruit Chs5p to the TGN surface in vivo. Recombinant forms of Chs5p, Chs6p, and the Chs6p paralogues expressed in baculovirus form a complex of approximately 1 MD that binds synthetic liposomes in a reaction requiring acidic phospholipids, Arf1p, and the nonhydrolyzable GTPγS. The complex remains bound to liposomes centrifuged on a sucrose density gradient. Thin section electron microscopy reveals a spiky coat structure on liposomes incubated with the full complex, Arf1p, and GTPγS. We termed the novel coat exomer for its role in exocytosis from the TGN to the cell surface. Unlike other coats (e.g., coat protein complex I, II, and clathrin/adaptor protein complex), the exomer does not form buds or vesicles on liposomes.

Changes Occur in Plasma Membrane Turnover when K562 Leukemia Cells are Induced to Differentiate

1982 ◽  
Vol 40 ◽  
pp. 286-287
Author(s):  
L. M. Marshall
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Intracellular Transport ◽  
Parent Cell ◽  
Membrane Turnover ◽  
Coated Pits ◽  
Surface Distribution ◽  
Specific Proteins ◽  
Erythroleukemic Cell ◽  
Specific Membrane

A human erythroleukemic cell line, metabolically blocked in a late stage of erythropoiesis, becomes capable of differentiation along the normal pathway when grown in the presence of hemin. This process is characterized by hemoglobin synthesis followed by rearrangement of the plasma membrane proteins and culminates in asymmetrical cytokinesis in the absence of nuclear division. A reticulocyte-like cell buds from the nucleus-containing parent cell after erythrocyte specific membrane proteins have been sequestered into its membrane. In this process the parent cell faces two obstacles. First, to organize its erythrocyte specific proteins at one pole of the cell for inclusion in the reticulocyte; second, to reduce or abolish membrane protein turnover since hemoglobin is virtually the only protein being synthesized at this stage. A means of achieving redistribution and cessation of turnover could involve movement of membrane proteins by a directional lipid flow. Generation of a lipid flow towards one pole and accumulation of erythrocyte-specific membrane proteins could be achieved by clathrin coated pits which are implicated in membrane endocytosis, intracellular transport and turnover. In non-differentiating cells, membrane proteins are turned over and are random in surface distribution. If, however, the erythrocyte specific proteins in differentiating cells were excluded from endocytosing coated pits, not only would their turnover cease, but they would also tend to drift towards and collect at the site of endocytosis. This hypothesis requires that different protein species are endocytosed by the coated vesicles in non-differentiating than by differentiating cells.

Discovering Therapeutic Protein Targets for Bladder Cancer Using Proteomic Data Analysis

2020 ◽  
Vol 13 (2) ◽  
pp. 150-172 ◽  
Author(s):  
Samira Bahrami ◽  
Bahram Kazemi ◽  
Hakimeh Zali ◽  
Peter C. Black ◽  
Abbas Basiri ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Gene Ontology ◽  
Monoclonal Antibodies ◽  
Membrane Proteins ◽  
Growth Factor Receptor ◽  
Subcellular Location ◽  
Cancer Tissue ◽  
Heat Shock Protein 60 ◽  
Absolute Quantitation ◽  
Muscle Invasive

Background: Bladder cancer accounts for almost 54% of urinary system cancer and is the second most frequent cause of death in genitourinary malignancies after prostate cancer. About 70% of bladder tumors are non-muscle-invasive, and the rest are muscle-invasive. Recurrence of the tumor is the common feature of bladder cancer. Chemotherapy is a conventional treatment for MIBC, but it cannot improve the survival rate of these patients sufficiently. Therefore, researchers must develop new therapies. Antibody-based therapy is one of the most important strategies for the treatment of solid tumors. Selecting a suitable target is the most critical step for this strategy. Objective: The aim of this study is to detect therapeutic cell surface antigen targets in bladder cancer using data obtained by proteomic studies. Methods: Isobaric tag for relative and absolute quantitation (iTRAQ) analysis had identified 131 overexpressed proteins in baldder cancer tissue and reverse-phase proteomic array (RPPA) analysis had been done for 343 tumor tissues and 208 antibodies. All identified proteins from two studies (131+208 proteins) were collected and duplicates were removed (331 unique proteins). Gene ontology study was performed using gene ontology (GO) and protein analysis through evolutionary relationships (PANTHER) databases. The Human Protein Atlas database was used to search the protein class and subcellular location of membrane proteins obtained from the PANTHER analysis. Results: Membrane proteins that could be suitable therapeutic targets for bladder cancer were selected. These included: Epidermal growth factor receptor (EGFR), Her2, Kinase insert domain receptor (KDR), Heat shock protein 60 (HSP60), HSP90, Transferrin receptor (TFRC), Activin A Receptor Like Type 1 (ACVRL1), and cadherin 2 (CDH2). Monoclonal antibodies against these proteins or their inhibitors were used for the treatment of different cancers in preclinical and clinical trials. Conclusion: These monoclonal antibodies and inhibitor molecules and also their combination can be used for the treatment of bladder cancer.

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