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https://www.readbyqxmd.com/read/28098292/an-andrographolide-derivative-agp-26b-exhibiting-anti-angiogenic-activity-in-huvecs-and-zebrafish-via-blocking-the-vegfa-vegfr2-signaling-pathway
#1
Bin Huang, Yuran Peng, Jingjing Li, Shang Li, Yicheng Sun, Decai Wang, Binrui Yang, Judy Yuet-Wa Chan, Huidong Yu, George Pak-Heng Leung, Maggie Pui-Man Hoi, Guo-Chun Zhou, Simon Ming-Yuen Lee
The aim of this study is to investigate the anti-angiogenic properties of andrographolide derivatives AGP-26a (12β-isomer), AGP-26b (12α-isomer) and AGP-26 (4 : 1 mixture of AGP-26a and AGP-26b) in vitro and in vivo. Human umbilical vein endothelial cells (HUVECs) and the Tg(fli-1a:EGFP)y1 zebrafish model were used to identify the anti-angiogenic activities of AGP-26, AGP-26a, and AGP-26b. The results showed that AGP-26b exhibits the strongest inhibitory effect on VEGF-induced proliferation, migration, invasion and formation of capillary-like structures in HUVECs...
January 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28098256/dopamine-promotes-nmda-receptor-hypofunction-in-the-retina-through-d1-receptor-mediated-csk-activation-src-inhibition-and-decrease-of-glun2b-phosphorylation
#2
Renato Socodato, Felipe N Santiago, Camila C Portugal, Ivan Domith, Thaísa G Encarnação, Erick C Loiola, Ana L M Ventura, Marcelo Cossenza, João B Relvas, Newton G Castro, Roberto Paes-de-Carvalho
Dopamine and glutamate are critical neurotransmitters involved in light-induced synaptic activity in the retina. In brain neurons, dopamine D1 receptors (D1Rs) and the cytosolic protein tyrosine kinase Src can, independently, modulate the behavior of NMDA-type glutamate receptors (NMDARs). Here we studied the interplay between D1Rs, Src and NMDARs in retinal neurons. We reveal that dopamine-mediated D1R stimulation provoked NMDAR hypofunction in retinal neurons by attenuating NMDA-gated currents, by preventing NMDA-elicited calcium mobilization and by decreasing the phosphorylation of NMDAR subunit GluN2B...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096507/de-novo-phosphorylation-and-conformational-opening-of-the-tyrosine-kinase-lck-act-in-concert-to-initiate-t-cell-receptor-signaling
#3
Lars Philipsen, Amarendra V Reddycherla, Roland Hartig, Janine Gumz, Matthias Kästle, Andreas Kritikos, Mateusz P Poltorak, Yury Prokazov, Evgeny Turbin, André Weber, Werner Zuschratter, Burkhart Schraven, Luca Simeoni, Andreas J Müller
The enzymatic activity of the Src family tyrosine kinase p56(Lck) (Lck) is tightly controlled by differential phosphorylation of two tyrosine residues, Tyr(394) and Tyr(505) Phosphorylation of Tyr(394) and the conformational opening of Lck are believed to activate the kinase, whereas Tyr(505) phosphorylation is thought to generate a closed, inactive conformation of Lck. We investigated whether the conformation of Lck and its phosphorylation state act in concert to regulate the initiation of T cell receptor (TCR) signaling...
January 17, 2017: Science Signaling
https://www.readbyqxmd.com/read/28096359/%C3%AE-synuclein-binds-and-sequesters-pike-l-into-lewy-bodies-triggering-dopaminergic-cell-death-via-ampk-hyperactivation
#4
Seong Su Kang, Zhentao Zhang, Xia Liu, Fredric P Manfredsson, Li He, P Michael Iuvone, Xuebing Cao, Yi E Sun, Lingjing Jin, Keqiang Ye
The abnormal aggregation of fibrillar α-synuclein in Lewy bodies plays a critical role in the pathogenesis of Parkinson's disease. However, the molecular mechanisms regulating α-synuclein pathological effects are incompletely understood. Here we show that α-synuclein binds phosphoinositide-3 kinase enhancer L (PIKE-L) in a phosphorylation-dependent manner and sequesters it in Lewy bodies, leading to dopaminergic cell death via AMP-activated protein kinase (AMPK) hyperactivation. α-Synuclein interacts with PIKE-L, an AMPK inhibitory binding partner, and this action is increased by S129 phosphorylation through AMPK and is decreased by Y125 phosphorylation via Src family kinase Fyn...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28092048/using-reciprocal-protein-peptide-array-screening-to-unravel-protein-interaction-networks
#5
Huadong Liu, Courtney Voss, Shawn S C Li
Protein-protein interactions (PPIs) play a central role in almost all cellular processes. Recent technological advances have enabled the elucidation of an incredibly complex PPI network within the cell. However, protein interactions driven by posttranslational modifications (PTMs) such as phosphorylation, which comprises a significant part of the PPI network, have proven difficult to decipher systematically. Herein, we describe a reciprocal protein-peptide array strategy to uncover PPIs mediated by tyrosine phosphorylation and the Src homology 2 (SH2) domain...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092045/sh2-domains-as-affinity-reagents-for-phosphotyrosine-protein-enrichment-and-proteomic-analysis
#6
Mi Ke, Bizhu Chu, Lin Lin, Ruijun Tian
Dynamic tyrosine phosphorylation is a key molecular modulation for many signal transduction events. Because of their low abundance and dynamic nature in cells, the detection and enrichment of phosphotyrosine proteins has long relied on specific antibodies, such as 4G10 and P-Tyr-100. Another well-established approach for phosphotyrosine proteins recognition and enrichment is by their specific binding domains, such as Src homology 2 (SH2) domains. In this chapter, we describe a typical analytical approach for purifying specific SH2 domains, enriching specific phosphotyrosine proteins from activated cells, mass spectrometry analysis, and related data analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092044/high-throughput-quantification-of-sh2-domain-phosphopeptide-interactions-with-cellulose-peptide-conjugate-microarrays
#7
Brett W Engelmann
The Src Homology 2 (SH2) domain family primarily recognizes phosphorylated tyrosine (pY) containing peptide motifs. The relative affinity preferences among competing SH2 domains for phosphopeptide ligands define "specificity space," and underpins many functional pY mediated interactions within signaling networks. The degree of promiscuity exhibited and the dynamic range of affinities supported by individual domains or phosphopeptides is best resolved by a carefully executed and controlled quantitative high-throughput experiment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092043/characterizing-sh2-domain-specificity-and-network-interactions-using-spot-peptide-arrays
#8
Bernard A Liu
Src Homology 2 (SH2) domains are protein interaction modules that recognize and bind tyrosine phosphorylated ligands. Their ability to distinguish binding to over thousands of potential phosphotyrosine (pTyr) ligands within the cell is critical for the fidelity of receptor tyrosine kinase (RTK) signaling. Within humans there are over a hundred SH2 domains with more than several thousand potential ligands across many cell types and cell states. Therefore, defining the specificity of individual SH2 domains is critical for predicting and identifying their physiological ligands...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092037/structural-characterization-of-monomeric-dimeric-state-of-p59-fyn-sh2-domain
#9
Radu Huculeci, Fabien Kieken, Abel Garcia-Pino, Lieven Buts, Nico van Nuland, Tom Lenaerts
Src homology 2 (SH2) domains are key modulators in various signaling pathways allowing the recognition of phosphotyrosine sites of different proteins. Despite the fact that SH2 domains acquire their biological functions in a monomeric state, a multitude of reports have shown their tendency to dimerize. Here, we provide a technical description on how to isolate and characterize by gel filtration, circular dichroism (CD), and nuclear magnetic resonance (NMR) each conformational state of p59(fyn) SH2 domain.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092034/expression-and-purification-of-sh2-domains-using-baculovirus-expression-system
#10
Mari Ogiue-Ikeda, Kazuya Machida
Recombinant proteins expressed in bacteria are sometimes insoluble, aggregated, and incorrectly folded. For those Src homology 2 (SH2) domains that are insoluble in bacteria, baculovirus-insect cell expression systems can be an alternative to produce soluble and functionally active proteins. We describe a protocol for cloning and purification of GST-tagged SH2 domains using the Bac-to-Bac baculovirus expression system.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092033/purification-of-socs-suppressor-of-cytokine-signaling-sh2-domains-for-structural-and-functional-studies
#11
Nicholas P D Liau, Artem Laktyushin, Jeffrey J Babon
Src Homology 2 (SH2) domains are protein domains which have a high binding affinity for specific amino acid sequences containing a phosphorylated tyrosine residue. The Suppressors of Cytokine Signaling (SOCS) proteins use an SH2 domain to bind to components of certain cytokine signaling pathways to downregulate the signaling cascade. The recombinantly produced SH2 domains of various SOCS proteins have been used to undertake structural and functional studies elucidating the method of how such targeting occurs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092031/expression-and-production-of-sh2-domain-proteins
#12
Bernard A Liu, Mari Ogiue-Ikeda, Kazuya Machida
The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092030/proteomic-clustering-analysis-of-sh2-domain-datasets
#13
Karl Jablonowski
Proteomic clustering analysis provides a means of identifying relationships and visualizing those relationships in an extremely complex field of study with many interacting parts. With recent high-throughput studies of Src Homology 2 (SH2) domains, many and varied datasets are being amassed. A strategy for analyzing patterns between these large datasets is required to transform the information into knowledge. The methods for creating neighbor-joining phylogenetic trees, pairs scatter plots, and two-dimensional hierarchical clustering heatmaps are just a few of the diverse methods available to a proteomic researcher...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092029/an-efficient-semi-supervised-learning-approach-to-predict-sh2-domain-mediated-interactions
#14
Kousik Kundu, Rolf Backofen
Src homology 2 (SH2) domain is an important subclass of modular protein domains that plays an indispensable role in several biological processes in eukaryotes. SH2 domains specifically bind to the phosphotyrosine residue of their binding peptides to facilitate various molecular functions. For determining the subtle binding specificities of SH2 domains, it is very important to understand the intriguing mechanisms by which these domains recognize their target peptides in a complex cellular environment. There are several attempts have been made to predict SH2-peptide interactions using high-throughput data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092027/classification-and-lineage-tracing-of-sh2-domains-throughout-eukaryotes
#15
Bernard A Liu
Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092026/hidden-markov-models-for-protein-domain-homology-identification-and-analysis
#16
Karl Jablonowski
Protein domain identification and analysis are cornerstones of modern proteomics. The tools available to protein domain researchers avail a variety of approaches to understanding large protein domain families. Hidden Markov Models (HMM) form the basis for identifying and categorizing evolutionarily linked protein domains. Here I describe the use of HMM models for predicting and identifying Src Homology 2 (SH2) domains within the proteome.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092024/introduction-history-of-sh2-domains-and-their-applications
#17
Bernard A Liu, Kazuya Machida
The Src Homology 2 (SH2) domain is the prototypical protein interaction module that lies at the heart of phosphotyrosine signaling. Since its serendipitous discovery, there has been a tremendous advancement in technologies and an array of techniques available for studying SH2 domains and phosphotyrosine signaling. In this chapter, we provide a glimpse of the history of SH2 domains and describe many of the tools and techniques that have been developed along the way and discuss future directions for SH2 domain studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28090410/retrospective-analysis-of-heavy-metal-contamination-in-rhode-island-based-on-old-and-new-herbarium-specimens
#18
Sofia M Rudin, David W Murray, Timothy J S Whitfeld
PREMISE OF THE STUDY: Herbarium specimens may provide a record of past environmental conditions, including heavy metal pollution. To explore this potential, we compared concentrations of copper, lead, and zinc in historical and new collections from four sites in Rhode Island, USA. METHODS: We compared historical specimens (1846 to 1916) to congener specimens collected in 2015 at three former industrial sites in Providence, Rhode Island, and one nonindustrial site on Block Island...
January 2017: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28090274/the-role-of-m2000-as-an-anti-inflammatory-agent-in-toll-like-receptor-2-microrna-155-pathway
#19
Fatemeh Pourgholi, Mahsa Hajivalili, Rasoul Razavi, Shadi Esmaeili, Behzad Baradaran, Ali Akbar Movasaghpour, Sanam Sadreddini, Hamidreza Goodarzynejad, Abbas Mirshafiey, Mehdi Yousefi
BACKGROUND: M2000 is a newly designed and safe Non-Steroidal Anti-Inflammatory Drug (NSAID). The aim of this study was to assess the effects of M2000 on expression levels of Suppressor of Cytokine Signaling-1 (SOCS-1) and Src Homology-2 domain-containing inositol-5'-phosphatase 1 (SHIP1) proteins via Toll-Like Receptor (TLR) 2/microRNA-155 pathway. METHODS: HEK293 TLR2 cell line and Peripheral Blood Mononuclear Cells (PBMCs) were treated by different concentrations of M2000 in MTT assay...
January 2017: Avicenna Journal of Medical Biotechnology
https://www.readbyqxmd.com/read/28088327/cftr-impairment-upregulates-c-src-activity-through-il-1%C3%AE-autocrine-signaling
#20
María Macarena Massip-Copiz, Mariángeles Clauzure, Ángel Gabriel Valdivieso, Tomás Antonio Santa-Coloma
Cystic Fibrosis (CF) is a disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Previously, we found several genes showing a differential expression in CFDE cells (epithelial cells derived from a CF patient). One corresponded to c-Src; its expression and activity was found increased in CFDE cells, acting as a signaling molecule between the CFTR activity and MUC1 overexpression. Here we report that bronchial IB3-1 cells (CF cells) also showed increased c-Src activity compared to 'CFTR-corrected' S9 cells...
January 11, 2017: Archives of Biochemistry and Biophysics
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