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Molecular & Cellular Proteomics: MCP

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https://www.readbyqxmd.com/read/28637836/bacterial-cellulose-shifts-transcriptome-and-proteome-of-cultured-endothelial-cells-towards-native-differentiation
#1
Gerhard Feil, Ralf Horres, Julia Schulte, Andreas F Mack, Svenja Petzoldt, Caroline Arnold, Chen Meng, Lukas Jost, Jochen Boxleitner, Nicole Kiessling-Wolf, Ender Serbest, Dominic Helm, Bernhard Kuster, Isabel Hartmann, Thomas Korff, Hannes Hahne
Preserving the native phenotype of primary cells in vitro is a complex challenge. Recently, hydrogel-based cellular matrices have evolved as alternatives to conventional cell culture techniques. We developed a bacterial cellulose-based aqueous gel-like biomaterial, dubbed Xellulin, which mimics a cellular microenvironment and seems to maintain the native phenotype of cultured and primary cells. When applied to human umbilical vein endothelial cells (HUVEC), it allowed the continuous cultivation of cell monolayers for more than one year without degradation or dedifferentiation...
June 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28630087/paucimannose-rich-n-glycosylation-of-spatiotemporally-regulated-human-neutrophil-elastase-modulates-its-immune-functions
#2
Ian Loke, Ole Østergaard, Niels H H Heegaard, Nicolle H Packer, Morten Thaysen-Andersen
Human neutrophil elastase (HNE) is an important N-glycosylated serine protease in the innate immune system, but the structure and immune-modulating functions of HNE N-glycosylation remain undescribed. Herein, LC-MS/MS-based glycan, glycopeptide and glycoprotein profiling were utilised to first determine the heterogeneous N-glycosylation of HNE purified from neutrophil lysates and then from isolated neutrophil granules of healthy individuals. The spatiotemporal expression of HNE during neutrophil activation and the biological importance of its N-glycosylation were also investigated using immunoblotting, cell surface capture, native MS, receptor interaction, protease inhibition, and bacteria growth assays...
June 19, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28611094/agonist-specific-protein-interactomes-of-glucocorticoid-and-androgen-receptor-as-revealed-by-proximity-mapping
#3
Joanna K Lempiäinen, Einari A Niskanen, Kaisa-Mari Vuoti, Riikka E Lampinen, Helka Göös, Markku Varjosalo, Jorma J Palvimo
Glucocorticoid receptor (GR) and androgen receptor (AR) are steroid-inducible transcription factors (TFs). GR and AR are central regulators of various metabolic, homeostatic and differentiation processes and hence important therapeutic targets, especially in inflammation and prostate cancer, respectively. Hormone binding to these steroid receptors (SRs) leads to DNA binding and activation or repression of their target genes with the aid of interacting proteins, coregulators. However, protein interactomes of these important drug targets have remained poorly defined...
June 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28606917/quantitative-temporal-viromics-of-an-inducible-hiv-1-model-yields-insight-to-global-host-targets-and-phospho-dynamics-associated-with-vpr
#4
John D Lapek, Mary K Lewinski, Jacob M Wozniak, John Guatelli, David J Gonzalez
The mechanisms by which human immunodeficiency virus (HIV) circumvents and coopts cellular machinery to replicate and persist in cells are not fully understood. HIV accessory proteins play key roles in the HIV life cycle by altering host pathways that are often dependent on post-translational modifications (PTMs). Thus, the identification of HIV accessory protein host targets and their PTM status is critical to fully understand how HIV invades, avoids detection and replicates to spread infection. To date, a comprehensive characterization of HIV accessory protein host targets and modulation of their PTM status does not exist...
June 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28576849/proteome-wide-identification-of-glycosylation-dependent-interactors-of-galectin-1-and-galectin-3-on-mesenchymal-retinal-pigment-epithelial-cells
#5
Jara Obermann, Claudia S Priglinger, Juliane Merl-Pham, Arie Geerlof, Sigfried Priglinger, Magdalena Götz, Stefanie M Hauck
Identification of interactors is a major goal in cell biology. Not only protein-protein but also protein-carbohydrate interactions are of high relevance for signal transduction in biological systems. Here we aim to identify novel interacting binding partners for the β-galactoside-binding proteins Galectin-1 (Gal-1) and Galectin-3 (Gal-3) relevant in the context of the eye disease proliferative vitreoretinopathy (PVR). PVR is one of the most common failures after retinal detachment surgeries and is characterized by the migration, adhesion and epithelial-to-mesenchymal transition (EMT) of retinal pigment epithelial cells (RPE) and the subsequent formation of sub- and epiretinal fibrocellular membranes...
June 2, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28576848/identification-of-fc-gamma-receptor-glycoforms-that-produce-differential-binding-kinetics-for-rituximab
#6
Jerrard M Hayes, Asa Frostell, Robert Karlsson, Steffen Müller, Silvia Millan-Martin, Martin Pauers, Franziska Reuss, Eoin Cosgrave, Cecilia Anneren, Gavin P Davey, Pauline M Rudd
Fc gamma receptors (FcyR) bind the Fc region of antibodies and therefore play a prominent role in antibody-dependent cell-based immune responses such as ADCC, CDC and ADCP. The immune effector cell activity is directly linked to a productive molecular engagement of FcyRs where both the protein and glycan moiety of antibody and receptor can affect the interaction and in the present study we focus on the role of the FcyR glycans in this interaction. We provide a complete description of the glycan composition of Chinese hamster ovary (CHO) expressed human Fcy receptors RI (CD64), RIIa Arg131/His131 (CD32a), RIIb (CD32b) and RIIIa Phe158/Val158 (CD16a) and analyze the role of the glycans in the binding mechanism with IgG...
June 2, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28572092/cyld-deubiquitinase-is-necessary-for-proper-ubiquitination-and-degradation-of-the-epidermal-growth-factor-receptor
#7
Virginia Sanchez-Quiles, Vyacheslav Akimov, Nerea Osinalde, Chiara Francavilla, Michele Puglia, Inigo Barrio-Hernandez, Irina Kratchmarova, Jesper V Olsen, Blagoy Blagoev
Cylindromatosis tumor suppressor protein (CYLD) is deubiquitinase, best known as an essential negative regulator of the NFkB pathway. Previous studies have suggested an involvement of CYLD in epidermal growth factor (EGF)-dependent signal transduction as well, as it was found enriched within the tyrosine-phosphorylated complexes in cells stimulated with the growth factor. EGF receptor (EGFR) signaling participates in central cellular processes and its tight regulation, partly through ubiquitination cascades, is decisive for a balanced cellular homeostasis...
June 1, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28572091/the-ser-thr-protein-kinase-protein-protein-interaction-map-of-m-tuberculosis
#8
Fan-Lin Wu, Yin Liu, He-Wei Jiang, Yi-Zhao Luan, Hai-Nan Zhang, Xiang He, Zhao-Wei Xu, Jing-Li Hou, Li-Yun Ji, Zhi Xie, Daniel M Czajkowsky, Wei Yan, Jiao-Yu Deng, Li-Jun Bi, Xian-En Zhang, Sheng-Ce Tao
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions...
June 1, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28550167/prediction-of-response-to-sorafenib-in-hepatocellular-carcinoma-a-marker-panel-by-multiple-reaction-monitoring-mass-spectrometry
#9
Hyunsoo Kim, Su Jong Yu, Injun Yeo, Young Youn Cho, Dong Hyeon Lee, Yuri Cho, Eun Ju Cho, Jeong-Hoon Lee, Yoon Jun Kim, Sungyoung Lee, Jongsoo Jun, Taesung Park, Jung-Hwan Yoon, Youngsoo Kim
Sorafenib is the only standard treatment for unresectable hepatocellular carcinoma (HCC), but it provides modest survival benefits over placebo, necessitating predictive biomarkers of the response to sorafenib. Serum samples were obtained from 115 consecutive patients with HCC before sorafenib treatment and analyzed by multiple reaction monitoring-mass spectrometry (MRM-MS) and ELISA to quantify candidate biomarkers. We verified a triple-marker panel to be predictive of the response to sorafenib by MRM-MS, comprising CD5 antigen-like (CD5L), immunoglobulin J (IGJ), and galectin-3-binding protein (LGALS3BP), in HCC patients...
May 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28550166/lysine-acetylome-analysis-reveals-photosystem-ii-manganese-stabilizing-protein-acetylation-is-involved-in-negative-regulation-of-oxygen-evolution-in-model-cyanobacterium-synechococcus-sp-pcc-7002
#10
Zhuo Chen, Guiying Zhang, Mingkun Yang, Tao Li, Feng Ge, Jindong Zhao
Nϵ-Acetylation of lysine residues represents a frequently occurring post-translational modification widespread in bacteria that plays vital roles in regulating bacterial physiology and metabolism. However, the role of lysine acetylation in cyanobacteria remains unclear, presenting a hurdle to in-depth functional study of this post-translational modification. Here, we report the lysine acetylome of Synechococcus sp. PCC 7002 (hereafter Synechococcus) using peptide prefractionation, immunoaffinity enrichment, and coupling with high-precision liquid chromatography-tandem mass spectrometry analysis...
May 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28550165/the-clasp2-protein-interaction-network-in-adipocytes-links-clip2-to-agap3-clasp2-to-g2l1-mark2-and-soga1-and-identifies-soga1-as-a-microtubule-associated-protein
#11
Rikke Kruse, James Krantz, Natalie Barker, Richard Coletta, Ruslan Rafikov, Moulun Luo, Kurt Hoejlund, Lawrence J Mandarino, Paul R Langlais
CLASP2 is a microtubule-associated protein that undergoes insulin-stimulated phosphorylation and co-localization with reorganized actin and GLUT4 at the plasma membrane. To gain insight to the role of CLASP2 in this system, we developed and successfully executed a streamlined interactome approach and built a CLASP2 protein network in 3T3-L1 adipocytes. Using two different commercially available antibodies for CLASP2 and an antibody for epitope-tagged, overexpressed CLASP2, we performed multiple affinity purification coupled with mass spectrometry (AP-MS) experiments in combination with label-free quantitative proteomics and analyzed the data with the bioinformatics tool Significance Analysis of Interactome (SAINT)...
May 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28546465/quantitative-mass-spectrometry-analysis-of-pd-l1-protein-expression-n-glycosylation-and-expression-stoichiometry-with-pd-1-and-pd-l2-in-human-melanoma
#12
Carlos A Morales-Betanzos, Hyoungjoo Lee, Paula I Gonzalez-Ericsson, Justin M Balko, Douglas B Johnson, Lisa J Zimmerman, Daniel C Liebler
Quantitative assessment of key proteins that control the tumor-immune interface is one of the most formidable analytical challenges in immunotherapeutics. We developed a targeted mass spectrometry (MS) platform to quantify programmed cell death-1 (PD-1), programmed cell death 1 ligand 1 (PD-L1), and programmed cell death 1 ligand 2 (PD-L2) at fmol/microgram protein levels in formalin fixed, paraffin-embedded sections from 22 human melanomas. PD-L1 abundance ranged 50-fold, from approximately 0.03 to 1.5 fmol/microgram protein and the PRM data were largely concordant with total PD-L1-positive cell content, as analyzed by immunohistochemistry (IHC) with the E1L3N antibody...
May 25, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28539327/quantitative-phospho-proteomic-analysis-of-tnf%C3%AE-nf%C3%AE%C2%BAb-signaling-reveals-a-role-for-ripk1-phosphorylation-in-suppressing-necrotic-cell-death
#13
Firaz Mohideen, Joao Paolo, Alban Ordureau, Steve P Gygi, J Wade Harper
TNFα is a potent inducer of inflammation due to its ability to promote gene expression, in part via the NFκB pathway. Moreover, in some contexts, TNFα promotes Caspase-dependent apoptosis or RIPK1/RIPK3/MLKL-dependent necrosis. Engagement of the TNF Receptor Signaling Complex (TNF-RSC), which contains multiple kinase activities, promotes phosphorylation of several downstream components, including TAK1, IKKα/IKKβ, IκBα, and NFκB. However, immediate downstream phosphorylation events occurring in response to TNFα signaling are poorly understood at a proteome-wide level...
May 24, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28539326/systematic-evaluation-of-protein-reduction-and-alkylation-reveals-massive-unspecific-side-effects-by-iodine-containing-reagents
#14
Torsten Müller, Dominic Winter
Reduction and alkylation of cysteine residues is part of virtually any proteomics workflow. Despite its frequent use, up to date no systematic investigation of the impact of different conditions on the outcome of proteomics studies has been performed. In this study, we compared common reduction reagents (dithiothreitol, tris-(2-carboxyethyl)-phosphine, and beta-mercaptoethanol) and alkylation reagents (iodoacetamide, iodoacetic acid, acrylamide, and chloroacetamide). Using in-gel digests as well as SAX fractionated in-solution digests of cytosolic fractions of HeLa cells, we evaluated 13 different reduction and alkylation conditions resulting in considerably varying identification rates...
May 24, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28515314/the-mzidentml-data-standard-version-1-2-supporting-advances-in-proteome-informatics
#15
Juan Antonio Vizcaíno, Gerhard Mayer, Simon R Perkins, Harald Barsnes, Marc Vaudel, Yasset Perez-Riverol, Tobias Ternent, Julian Uszkoreit, Martin Eisenacher, Lutz Fischer, Juri Rappsilber, Eugen Netz, Mathias Walzer, Oliver Kohlbacher, Alexander Leitner, Robert J Chalkley, Fawaz Ghali, Salvador Martínez-Bartolomé, Eric W Deutsch, Andrew R Jones
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012 - capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (i) scores associated with localization of modifications on peptides; (ii) statistics performed at the level of peptides; (iii) identification of cross-linked peptides; and (iv) support for proteogenomics approaches...
May 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28512230/differential-proteomic-analysis-of-gender-dependent-hepatic-tumorigenesis-in-hras12v-transgenic-mice
#16
Zhuona Rong, Tingting Fan, Huiling Li, Juan Li, Kangwei Wang, Xinxin Wang, Jianyi Dong, Jun Chen, Fujin Wang, Jingyu Wang, Aiguo Wang
Male prevalence is an outstanding characteristic of hepatocellular carcinoma (HCC), and the underlying mechanisms for this have remained largely unknown. In the present study, Hras12V transgenic mice, in which hepatocyte-specific expression of the ras oncogene induces male-biased hepatic tumorigenesis, were studied, and altered proteins were detected by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). Protein samples from hepatic tumor tissues (T) and peri-tumor tissues (P) of transgenic males and females and the corresponding normal liver tissues (Wt) of non-transgenic males and females were subjected to pairwise comparisons based on proteomic analysis...
May 16, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28501802/stability-of-proteins-in-dried-blood-spot-biobanks
#17
Johan Björkesten, Stefan Enroth, Qiujin Shen, Lotta Wik, David Hougaard, Arieh Cohen, Lene Sörensen, Vilmantas Giedraitis, Martin Ingelsson, Anders Larsson, Masood Kamali-Moghaddam, Ulf Landegren
An important motivation for the construction of biobanks is to discover biomarkers that identify diseases at early, potentially curable stages. This will require biobanks from large numbers of individuals, preferably sampled repeatedly, where the samples are collected and stored under conditions that preserve potential biomarkers. Dried blood samples are attractive for biobanking because of the ease and low cost of collection and storage. Here we have investigated their suitability for protein measurements...
May 13, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28500030/translating-divergent-environmental-stresses-into-a-common-proteome-response-through-hik33-in-a-model-cyanobacterium
#18
Haitao Ge, Longfa Fang, Xiahe Huang, Jinlong Wang, Weiyang Chen, Ye Liu, Yuanya Zhang, Xiaorong Wang, Wu Xu, Qingfang He, Yingchun Wang
The histidine kinase Hik33 plays important roles in mediating cyanobacterial response to divergent types of abiotic stresses including cold, salt, high light (HL), and osmotic stresses. However, how these functions are regulated by Hik33 remains to be addressed. Using a hik33-deficient strain (Δhik33) of Synechocystis sp. PCC 6803 (Synechocystis) and quantitative proteomics, we found that Hik33 depletion induces differential protein expression highly similar to that induced by divergent types of stresses. This typically includes downregulation of proteins in photosynthesis and carbon assimilation that are necessary for cell propagation, and upregulation of heat shock proteins, chaperons, and proteases that are important for cell survival...
May 12, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28490445/serological-epithelial-component-proteins-identify-intestinal-complications-in-crohn-s-disease
#19
Yunki Y Yau, Rupert Wl Leong, Aviv Pudipeddi, Diane Redmond, Valerie C Wasinger
Crohns Disease (CD) is a relapsing inflammation of the gastrointestinal tract that affects a young working age population and is increasing in developing countries. Half of all sufferers will experience stricturing or fistulizing intestinal complications that require extensive surgical interventions and neither genes nor clinical risk factors can predict this debilitating natural history. We applied discovery and verification phase studies as part of an NCI-FDA modelled biomarker pipeline to identify differences in the low-mass (<25kDa) blood-serum proteome between CD behavioural phenotypes...
May 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28483926/some-gram-negative-lipoproteins-keep-their-surface-topology-when-transplanted-from-one-species-to-another-and-deliver-foreign-polypeptides-to-the-bacterial-surface
#20
Laura Fantappiè, Carmela Irene, Micaela De Santis, Alessandro Armini, Assunta Gagliardi, Michele Tomasi, Matteo Parri, Valeria Cafardi, Serena Bonomi, Luisa Ganfini, Francesca Zerbini, Ilaria Zanella, Chiara Carnemolla, Luca Bini, Alberto Grandi, Guido Grandi
In Gram-negative bacteria, outer membrane-associated lipoproteins can either face the periplasm or protrude out of the bacterial surface. The mechanisms involved in lipoprotein transport through the outer membrane are not fully elucidated. Some lipoproteins reach the surface by using species-specific transport machinery. By contrast, a still poorly characterized group of lipoproteins appears to always cross the outer membrane, even when transplanted from one organism to another. To investigate such lipoproteins, we tested the expression and compartmentalization in E...
May 8, 2017: Molecular & Cellular Proteomics: MCP
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