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Finding a Target
Published in Nathan Keighley, Miraculous Medicines and the Chemistry of Drug Design, 2020
Other membrane proteins are located within the cytoplasm; attached to the cell membrane by means of covalent bonding with fatty acid chains, while other membrane proteins are entirely exposed to the extracellular medium and are attached to the cell membrane by covalent bonds to specific oligosaccharides. Additional proteins may be bound to these integral membrane proteins by non-covalent interactions and are known as peripheral membrane proteins. These types of proteins have different functions. The transmembrane proteins are often involved in molecular transport across cell membranes. Extrinsic proteins serve as cell signalling receptors.
Biosynthesis and Genetics of Lipopolysaccharide Core
Published in Helmut Brade, Steven M. Opal, Stefanie N. Vogel, David C. Morrison, Endotoxin in Health and Disease, 2020
David E. Heinrichs, Chris Whitfield, Miguel A. Valvano
Synthesis of the carbohydrate backbone of the core OS requires sugar nucleotide precursors. Assembly of the LPS core occurs using a lipid A-based derivative as an acceptor. In fact, in some bacteria the early steps in core assembly (Kdo addition) occur prior to full acylation and completion of lipid A (4). Assembly of the core then proceeds in a processive manner with sequential sugar addition and core extension. A model for the assembly process was first proposed by Rothfield and colleagues (reviewed in Ref. 5) and was revisited more recently by Rick (6). Briefly, the model proposes that sequential addition of sugar residues to the growing LPS core is catalyzed by a series of membrane-associated glycosyltransferases. More recent sequence data predict that most of these enzymes are peripheral membrane proteins. The glycosyltransferases are proposed to be arranged in the proper sequence and located in close proximity to one another, perhaps forming a multienzyme complex. Based on the peripheral membrane-association of the proteins and the cytoplasmic location of the precursors, the assembly of core OS likely occurs at the interface of the cytoplasm and plasma membrane. Growing LPS molecules, situated in the inner leaflet of the plasma membrane with their growing OS chains projecting into the cytoplasm, are suggested to be capable of movement within the fluid membrane. As they pass across the glycosyltransferases, the core OS is extended in a sequential fashion.
Reconstituted Membrane Systems for Assaying Membrane Proteins in Controlled Lipid Environments
Published in Qiu-Xing Jiang, New Techniques for Studying Biomembranes, 2020
Cell membranes play a pivotal role in separating cells from their environments, maintaining cells in an off-equilibrium steady state, detecting and relaying outside signals into the cells by responding to their environments in specific manners. There has been a strong interest in the scientific community because membrane systems, including both membrane proteins and lipids, are fundamentally important for all live cells, and serve as therapeutic targets for human diseases. Membrane proteins generally include both integral membrane proteins that are integrated in a membrane and traverse both leaflets of the bilayer and peripheral membrane proteins that are associated with lipids or proteins in membranes.1,2 Around 20%–30% of identified proteins of the human genome are predicted integral membrane proteins.3–6 Although the total number of integral membrane proteins is increasing over time, determination of the structural basis for their functions still lags behind. In particular, it remains difficult to study quantitatively the effects of membrane lipids on the structure and function of membrane proteins.
Distribution pattern of ZO-1 and claudins in the epididymis of vampire bats
Published in Tissue Barriers, 2020
Mariana M. Castro, Bongki Kim, Patrícia D. Games, Eric Hill, Clóvis Andrade Neves, José Eduardo Serrão, Sylvie Breton, Mariana Machado-Neves
The expression pattern of ZO-1 observed in D. rotundus epididymis is also documented in epididymis of rodents.10,15,19 So far, only young rats exhibited this peripheral membrane protein in lateral plasma membranes of epididymal cells.20 ZO-1, as well as ZO-2 and ZO-3, are scaffolding proteins of TJs that link membrane proteins to the actin cytoskeleton in various epithelia.6 Particularly, 15,reported that ZO-1 exerts a more fundamental role in epididymal TJ dynamics than ZO-2 and ZO-3, being involved in the targeting of Cldns and occludin to the area of TJs, anchoring these transmembrane proteins at the extracellular seal.19,20 In this study, we have tried to label occludin, ZO-2, and ZO-3 in bat epididymis [according to15] with no success, although the conservation level of those TJ proteins is more than 75% between rodents and bats. We may speculate that, differently to the antibodies used here, anti-rat polyclonal antibodies for those proteins did not show enough cross-reactivity for labeling specific proteins in bat tissue.
Quantitative proteomic analysis of trypsin-treated extracellular vesicles to identify the real-vesicular proteins
Published in Journal of Extracellular Vesicles, 2020
Dongsic Choi, Gyeongyun Go, Dae-Kyum Kim, Jaewook Lee, Seon-Min Park, Dolores Di Vizio, Yong Song Gho
When we consider the vesicle architecture, EV proteins could be categorized into three subgroups of intravesicular, plasma membrane (integral, lipid-anchored and peripheral membrane proteins) and extravesicular cargo proteins (extracellular proteins attached on EVs). In this study, by the combination of quantitative proteomic analyses and bioinformatics-based systems biology approaches, we identified trypsin-sensitive and trypsin-resistant vesicular proteins of human colon cancer cell line SW480-derived EVs. Since trypsin could not penetrate through the vesicular membrane, we reason that vesicular proteins that belong to intravesicular cargo subgroup are resistant to the trypsin treatment while some of vesicular cargo subgroups of plasma membrane and extravesicular cargo proteins, and contaminated non-vesicular proteins are sensitive to the trypsin treatment. By applying the label-free quantitative proteomics and protein–protein interaction network analyses of identified trypsin-sensitive and trypsin-resistant vesicular proteins based on their cellular localization, we revealed the candidate real-vesicular proteins and the contaminated non-vesicular proteins.
Surface markers of human embryonic stem cells: a meta analysis of membrane proteomics reports
Published in Expert Review of Proteomics, 2018
Faezeh Shekari, Chia-Li Han, Jaesuk Lee, Mehdi Mirzaei, Vivek Gupta, Paul A. Haynes, Bonghee Lee, Hossein Baharvand, Yu-Ju Chen, Ghasem Hosseini Salekdeh
Since the exact localization of membrane proteins is experimentally difficult to define, we performed a meta analysis of published annotations for membrane proteins using four bioinformatics parameters obtained from protein databases and computation tools: subcellular localization as ‘cell membrane’ from UniProt, subcellular compartment as ‘plasma membrane’ from Gene Ontology (GO: 0005886) [104], prediction of TM helix by TMHMM [62] and signal peptide prediction by SignalP [63] as reported previously [46]. According to these parameters, four protein categories have been described: (1) plasma membrane proteins (PM proteins); (2) probable peripheral membrane proteins (PPM proteins) (3) probable membrane proteins (PMem proteins); and (4) non-membrane proteins (NonMem proteins), which comprised all other proteins. The first three categories can be considered membrane associated proteins (MAPs).