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Anchor proteins

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https://www.readbyqxmd.com/read/29349619/1h-15n-and-13c-chemical-shift-assignments-of-the-micelle-immersed-fat-c-terminal-fatc-domains-of-the-human-protein-kinases-ataxia-telangiectasia-mutated-atm-and-dna-dependent-protein-kinase-catalytic-subunit-dna-pkcs-fused-to-the-b1-domain-of-streptococcal
#1
Munirah S Abd Rahim, Lisa A M Sommer, Anja Wacker, Martin Schaad, Sonja A Dames
FAT C-terminal (FATC) is a circa 33 residue-long domain. It controls the kinase functionality in phosphatidylinositol-3 kinase-related kinases (PIKKs). Recent NMR- and CD-monitored interaction studies indicated that the FATC domains of all PIKKs can interact with membrane mimetics albeit with different preferences for membrane properties such as surface charge and curvature. Thus they may generally act as membrane anchoring unit. Here, we present the 1H, 15N, and 13C chemical shift assignments of the DPC micelle immersed FATC domains of the human PIKKs ataxia-telangiectasia mutated (ATM, residues 3024-3056) and DNA protein kinase catalytic subunit (DNA-PKcs, residues 4096-4128), both fused to the 56 residue long B1 domain of Streptococcal protein G (GB1)...
January 18, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29349451/on-the-turn-inducing-properties-of-asparagine-the-structuring-role-of-the-amide-side-chain-from-isolated-model-peptides-to-crystallized-proteins
#2
S Habka, W Y Sohn, V Vaquero-Vara, M Géléoc, B Tardivel, V Brenner, E Gloaguen, M Mons
Asparagine (Asn) is a powerful turn-inducer residue, with a large propensity to occupy the second position in the central region of β-turns of proteins. The present work aims at investigating the role of a local anchoring between the Asn side chain and the main chain in this remarkable property. For this purpose, the H-bonding patterns of an asparagine residue in an isolated protein chain fragment forming a γ- or a β-turn have been determined using IR/UV double resonance gas phase spectroscopy on laser-desorbed, jet-cooled short models in conjunction with relevant quantum chemistry calculations...
January 19, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29345911/role-of-glycanation-and-convertase-maturation-of-the-soluble-glypican-3-in-inhibiting-proliferation-of-hepatocellular-carcinoma-cells
#3
Ahmad Saad, Benjamin Liet, Gilles Joucla, Xavier Santarelli, Justine Charpentier, Stéphane Claverol, Christophe F Grosset, Véronique Trézéguet
Glypican 3 (GPC3) is a complex heparan sulfate proteoglycan associated with the outer surface of the plasma membrane by a glycosyl-phosphatidylinositol anchor (GPI). It is also N-glycosylated and processed by a furine-like convertase. GPC3 has numerous biological functions. While undetectable in normal liver tissue, it is abnormally and highly overexpressed in hepatocellular carcinoma (HCC). Interestingly, proliferation of HCC cells such as HepG2 and HuH7 is inhibited when they express a soluble form of GPC3 after lentiviral transduction...
January 18, 2018: Biochemistry
https://www.readbyqxmd.com/read/29345720/effects-of-nicotine-administration-in-rats-on-mmp2-and-vegf-levels-in-periodontal-membrane
#4
Buşra Deveci, Buket Ayna, İbrahim Halil Tacir, Engin Deveci, Mehmet Cudi Tuncer, Ayşegül Pala
Nicotine is associated with increased incidence of periodontal disease and poor response to therapy. This article aimed at identifying the expression of Matrix metalloproteinases-2 (MMP2) and Vascular endothelial growth factor (VEGF) proteins on extracellular matrix, fibrous distribution and angiogenetic development in periodontitis caused by nicotine effects on periodontal membrane. In this experimental study, the groups were divided into nicotine and control groups. While the nicotine groups in rats (n=6) were administered 2mg/kg Nicotine sulphate for 28 days, the control group in rats (n=6) were only administered 1,5 ml physiologic saline solution subcutaneously for 28 days...
January 18, 2018: Folia Morphologica (Warsz)
https://www.readbyqxmd.com/read/29344147/systematic-analysis-of-the-molecular-mechanism-of-microrna-124-in-hepatoblastoma-cells
#5
Guiming Wang, Hong Liu, Zhigang Wei, Hongyan Jia, Yu Liu, Jiansheng Liu
The present study aimed to identify the molecular mechanisms of microRNA-124 (miRNA-124/miR-124) in hepatoblastoma. The GSE6207 microarray dataset, obtained from the Gene Expression Omnibus database, included samples extracted from HepG2 cells transfected with miR-124 duplex (the experimental group) or negative control (the control group) at 4, 8, 16, 24, 32, 72 and 120 h after transfection. Differentially expressed genes (DEGs) were screened between the two groups. miR-124 activity was inferred based on the expression of its target genes...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29342145/the-gram-negative-bacterial-periplasm-size-matters
#6
Samuel I Miller, Nina R Salama
Gram-negative bacteria are surrounded by two membrane bilayers separated by a space termed the periplasm. The periplasm is a multipurpose compartment separate from the cytoplasm whose distinct reducing environment allows more efficient and diverse mechanisms of protein oxidation, folding, and quality control. The periplasm also contains structural elements and important environmental sensing modules, and it allows complex nanomachines to span the cell envelope. Recent work indicates that the size or intermembrane distance of the periplasm is controlled by periplasmic lipoproteins that anchor the outer membrane to the periplasmic peptidoglycan polymer...
January 2018: PLoS Biology
https://www.readbyqxmd.com/read/29342139/structure-and-mutagenesis-reveal-essential-capsid-protein-interactions-for-kshv-replication
#7
Xinghong Dai, Danyang Gong, Hanyoung Lim, Jonathan Jih, Ting-Ting Wu, Ren Sun, Z Hong Zhou
Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma, a cancer that commonly affects patients with AIDS and which is endemic in sub-Saharan Africa. The KSHV capsid is highly pressurized by its double-stranded DNA genome, as are the capsids of the eight other human herpesviruses. Capsid assembly and genome packaging of herpesviruses are prone to interruption and can therefore be targeted for the structure-guided development of antiviral agents. However, herpesvirus capsids-comprising nearly 3,000 proteins and over 1,300 Å in diameter-present a formidable challenge to atomic structure determination and functional mapping of molecular interactions...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29341608/molecular-dynamics-pinpoint-the-global-fluorine-effect-in-balanoids-binding-to-pkc%C3%AE%C2%B5-and-pka
#8
Ari Hardianto, Fei Liu, Shoba Ranganathan
(-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with little selectivity. While PKA is known as a tumour promoter, PKC isozymes can be tumour promoters or suppressors. In particular, PKCε is frequently involved in tumorigenesis and a potential target for anticancer drugs. We recently reported that stereospecific fluorination of balanol yielded a balanoid with enhanced selectivity for PKCε over other PKC isozymes and PKA, although the global fluorine effect behind the selectivity enhancement is not fully understood...
January 17, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29341226/molecular-details-of-spontaneous-insertion-and-interaction-of-hcv-non-structure-3-protease-protein-domain-with-pip2-containing-membrane
#9
Huynh Minh Hung, Tran Dieu Hang, Minh Tho Nguyen
Hepatitis C virus (HCV), known as the leading cause of liver cirrhosis, viral hepatitis and hepatocellular carcinoma, has been affecting more than 150 million people globally. The HCV non-structure 3 (NS3) protease protein domain plays a key role in HCV replication and pathogenesis; and is currently a primary target for HCV antiviral therapy. Through unbiased molecular dynamics simulations which take advantage of the novel highly mobile membrane mimetic model, we constructed the membrane-bound state of the protein domain at the atomic level...
January 17, 2018: Proteins
https://www.readbyqxmd.com/read/29340478/the-long-and-successful-journey-of-electrochemically-active-amino-acids-from-fundamental-adsorption-studies-to-potential-surface-engineering-tools
#10
André H B Dourado, Fabián C Pastrián, Susana I Córdoba DE Torresi
Proteins have been the subject of electrochemical studies. It is possible to apply electrochemical techniques to obtain information about their structure due to the presence of five electroactive amino acids that can be oriented to the outside of the peptidic chain. These amino acids are L-Tryptophan (L-Trp), L-Tyrosine (L-Tyr), L-Histidine (L-His), L-Methionine (L-Met) and L-Cysteine (L-Cys); their electrochemical behavior being subject of extensive research, but it is still controversial. No spectroscopic investigations have been reported on L-Trp, and due to the short life time of the intermediates, ex situ techniques cannot be employed, leading to a never-ending discussion about possible intermediates...
January 11, 2018: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29340240/refining-amino-acid-hydrophobicity-for-dynamics-simulation-of-membrane-proteins
#11
Ronald D Hills
Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues...
2018: PeerJ
https://www.readbyqxmd.com/read/29339492/cytocapsular-tubes-conduct-cell-translocation
#12
Tingfang Yi, Gerhard Wagner
Cell locomotion is essential for multicellular organism embryo development, organ homeostasis, tissue regeneration, immune responses, and tumor metastasis. Here we report that single mammalian cells can generate two extracellular membranous compartments: cytocapsulae and cytocapsular tubes. Cells migrate in cytocapsulae and engender cytocapsular tubes, which exhibit pleiotropic biological functions and provide tubular routes for directed cell transportation. Ultrastructural analysis by electron microscope revealed that nanoprotrusions surround and anchor cytocapsular tubes in place...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339490/structural-basis-of-sterol-recognition-and-nonvesicular-transport-by-lipid-transfer-proteins-anchored-at-membrane-contact-sites
#13
Junsen Tong, Mohammad Kawsar Manik, Young Jun Im
Membrane contact sites (MCSs) in eukaryotic cells are hotspots for lipid exchange, which is essential for many biological functions, including regulation of membrane properties and protein trafficking. Lipid transfer proteins anchored at membrane contact sites (LAMs) contain sterol-specific lipid transfer domains [StARkin domain (SD)] and multiple targeting modules to specific membrane organelles. Elucidating the structural mechanisms of targeting and ligand recognition by LAMs is important for understanding the interorganelle communication and exchange at MCSs...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29335250/akap1-regulates-vascular-function-and-endothelial-cells-behavior
#14
Gabriele Giacomo Schiattarella, Fabio Cattaneo, Albino Carrizzo, Roberta Paolillo, Nicola Boccella, Mariateresa Ambrosio, Antonio Damato, Gianluigi Pironti, Anna Franzone, Giusi Russo, Fabio Magliulo, Marinella Pirozzi, Marianna Storto, Michele Madonna, Giuseppe Gargiulo, Valentina Trimarco, Laura Rinaldi, Massimiliano De Lucia, Corrado Garbi, Antonio Feliciello, Giovanni Esposito, Carmine Vecchione, Cinzia Perrino
MitoAKAPs (mitochondrial A kinase anchoring proteins), encoded by the Akap1 gene, regulate multiple cellular processes governing mitochondrial homeostasis and cell viability. Although mitochondrial alterations have been associated to endothelial dysfunction, the role of mitoAKAPs in the vasculature is currently unknown. To test this, postischemic neovascularization, vascular function, and arterial blood pressure were analyzed in Akap1 knockout mice (Akap1-/- ) and their wild-type (wt) littermates. Primary cultures of aortic endothelial cells (ECs) were also obtained from Akap1-/- and wt mice, and ECs migration, proliferation, survival, and capillary-like network formation were analyzed under different experimental conditions...
January 15, 2018: Hypertension
https://www.readbyqxmd.com/read/29334736/hydration-behavior-along-the-folding-pathways-of-trpzip4-trpzip5-and-trpzip6
#15
Madhulika Gupta, Prabir Khatua, Charusita Chakravarty, Sanjoy Bandyopadhyay
The microscopic properties of water confined within different segments of Trpzip4 (TZ4), Trpzip5 (TZ5) and Trzpip6 (TZ6) have been compared for all the states characterized along their folding pathways. In particular, structural ordering, energetics, and dynamics of water have been examined as the peptide unfolds along the free energy landscape. It is observed that the structuring of tetrahedral network as well as translational and rotational motions of hydration waters confined within the strands and the turn regions are very different, revealing motional heterogeneity in small 16-residue trpzips...
January 15, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29331981/variant-in-c-terminal-region-of-intestinal-alkaline-phosphatase-associated-with-benign-familial-hyperphosphatasaemia
#16
Takayuki Ishige, Sakae Itoga, Emi Utsuno, Motoi Nishimura, Masaharu Yoshikawa, Naoya Kato, Kazuyuki Matsushita, Osamu Yokosuka, Fumio Nomura
BACKGROUND: A genetic diagnosis has been rarely performed in benign familial hyperphosphatasaemia, and molecular mechanism largely remains unclear. OBJECTIVES: We encountered a case with benign familial hyperphosphatasaemia of intestinal alkaline phosphatase (IAP). To elucidate the molecular mechanism, we performed ALPI gene sequencing and in vitro protein expression analysis. METHODS: ALPI gene was sequenced by long-range PCR and massively parallel sequencing...
January 13, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29331638/comparative-analysis-of-membrane-protein-structure-databases
#17
REVIEW
Kentaro Shimizu, Wei Cao, Gull Saad, Michiru Shoji, Tohru Terada
BACKGROUND: Membrane proteins play important roles in cell survival and cell communication, as they function as transporters, receptors, anchors and enzymes. They are also potential targets for drugs that block receptors or inhibit enzymes related to diseases. Although the number of known structures of membrane proteins is still small relative to the size of the proteome as a whole, many new membrane protein structures have been determined recently. SCOPE OF THE ARTICLE: We compared and analyzed the widely used membrane protein databases, mpstruc, Orientations of Proteins in Membranes(OPM), and PDBTM, as well as the extended dataset of mpstruc based on sequence similarity, the PDB structures whose classification field indicates that they are "membrane proteins" and the proteins with Structural Classification of Proteins (SCOP) class-f domains...
January 10, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29330115/pediatric-onset-evans-syndrome-heterogeneous-presentation-and-high-frequency-of-monogenic-disorders-including-lrba-and-ctla4-mutations
#18
Caroline Besnard, Eva Levy, Nathalie Aladjidi, Marie-Claude Stolzenberg, Aude Magerus-Chatinet, Olivier Alibeu, Patrick Nitschke, Stéphane Blanche, Olivier Hermine, Eric Jeziorski, Judith Landman-Parker, Guy Leverger, Nizar Mahlaoui, Gérard Michel, Isabelle Pellier, Felipe Suarez, Isabelle Thuret, Geneviève de Saint-Basile, Capucine Picard, Alain Fischer, Bénédicte Neven, Frédéric Rieux-Laucat, Pierre Quartier
Evans syndrome (ES) is defined by the combination of autoimmune hemolytic anemia and immune thrombocytopenia. Clinical presentation includes manifestations of immune dysregulation, found in primary immune deficiencies, autoimmune lymphoproliferative syndrome with FAS (ALPS-FAS), Cytotoxic T Lymphocyte Antigen-4 (CTLA-4) and Lipopolysaccharide-Responsive vesicle trafficking Beige-like and Anchor protein (LRBA) defects. We report the clinical history and genetic results of 18 children with ES after excluding ALPS-FAS...
January 9, 2018: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/29329602/abatacept-used-in-combination-with-non-methotrexate-disease-modifying-antirheumatic-drugs-a-descriptive-analysis-of-data-from-interventional-trials-and-the-real-world-setting
#19
Rieke Alten, Harald Burkhardt, Eugen Feist, Klaus Krüger, Juergen Rech, Andrea Rubbert-Roth, Reinhard E Voll, Yedid Elbez, Christiane Rauch
BACKGROUND: Methotrexate (MTX) remains the anchor drug in rheumatoid arthritis (RA) treatment, but is poorly tolerated or contraindicated in some patients. There is a wealth of data supporting the use of abatacept in combination with MTX, but data on alternative conventional synthetic disease-modifying antirheumatic drug (csDMARD) combinations with abatacept are scarce. METHODS: In this post-hoc exploratory analysis, efficacy and safety data were extracted from abatacept RA studies in which combination with csDMARDs other than MTX was permitted: three interventional trials (ATTAIN, ASSURE, and ARRIVE) and one real-world study (ACTION)...
January 2, 2018: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/29329339/accessibility-and-contribution-to-glucan-masking-of-natural-and-genetically-tagged-versions-of-yeast-wall-protein-1-of-candida-albicans
#20
Bruce L Granger
Yeast wall protein 1 (Ywp1) is an abundant glycoprotein of the cell wall of the yeast form of Candida albicans, the most prevalent fungal pathogen of humans. Antibodies that bind to the polypeptide backbone of isolated Ywp1 show little binding to intact yeast cells, presumably because the Ywp1 epitopes are masked by the polysaccharides of the mannoproteins that form the outer layer of the cell wall. Rare cells do exhibit much greater anti-Ywp1 binding, however, and one of these was isolated and characterized...
2018: PloS One
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