keyword
MENU ▼
Read by QxMD icon Read
search

interactome

keyword
https://www.readbyqxmd.com/read/27913189/construction-and-analysis-of-a-human-testis-sperm-enriched-interaction-network-unraveling-the-ppp1cc2-interactome
#1
Joana Vieira Silva, Sooyeon Yoon, Pieter-Jan De Bock, Alexander V Goltsev, Kris Gevaert, José Fernando F Mendes, Margarida Fardilha
BACKGROUND: Phosphoprotein phosphatase 1 catalytic subunit gamma 2 (PPP1CC2), a PPP1CC tissue-specific alternative splice restricted to testicular germ cells and spermatozoa, is essential for spermatogenesis and spermatozoa motility. The key to understand PPP1CC2 regulation lies on the characterization of its interacting partners. METHODS: We construct a testis/sperm-enriched protein interaction network and analyzed the topological properties and biological context of the network...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27912098/characterization-of-hippo-pathway-components-by-gene-inactivation
#2
Steven W Plouffe, Zhipeng Meng, Kimberly C Lin, Brian Lin, Audrey W Hong, Justin V Chun, Kun-Liang Guan
The Hippo pathway is important for regulating tissue homeostasis, and its dysregulation has been implicated in human cancer. However, it is not well understood how the Hippo pathway becomes dysregulated because few mutations in core Hippo pathway components have been identified. Therefore, much work in the Hippo field has focused on identifying upstream regulators, and a complex Hippo interactome has been identified. Nevertheless, it is not always clear which components are the most physiologically relevant in regulating YAP/TAZ...
December 1, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27911722/dawn-of-the-in-vivo-rna-structurome-and-interactome
#3
REVIEW
Chun Kit Kwok
RNA is one of the most fascinating biomolecules in living systems given its structural versatility to fold into elaborate architectures for important biological functions such as gene regulation, catalysis, and information storage. Knowledge of RNA structures and interactions can provide deep insights into their functional roles in vivo For decades, RNA structural studies have been conducted on a transcript-by-transcript basis. The advent of next-generation sequencing (NGS) has enabled the development of transcriptome-wide structural probing methods to profile the global landscape of RNA structures and interactions, also known as the RNA structurome and interactome, which transformed our understanding of the RNA structure-function relationship on a transcriptomic scale...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911326/localization-and-processing-of%C3%A2-the%C3%A2-amyloid-%C3%AE-protein-precursor-in%C3%A2-mitochondria-associated-membranes
#4
Dolores Del Prete, Jan M Suski, Bénédicte Oulès, Delphine Debayle, Anne Sophie Gay, Sandra Lacas-Gervais, Renaud Bussiere, Charlotte Bauer, Paolo Pinton, Patrizia Paterlini-Bréchot, Mariusz R Wieckowski, Frédéric Checler, Mounia Chami
Alteration of mitochondria-associated membranes (MAMs) has been proposed to contribute to the pathogenesis of Alzheimer's disease (AD). We studied herein the subcellular distribution, the processing, and the protein interactome of the amyloid-β protein precursor (AβPP) and its proteolytic products in MAMs. We reveal that AβPP and its catabolites are present in MAMs in cellular models overexpressing wild type AβPP or AβPP harboring the double Swedish or London familial AD mutations, and in brains of transgenic mice model of AD...
November 26, 2016: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/27908592/activation-of-gpr30-stimulates-gtp-binding-of-g%C3%AE-i1-protein-to-sustain-activation-of-erk1-2-in-inhibition-of-prostate-cancer-cell-growth-and-modulates-metastatic-properties
#5
Kin-Mang Lau, Fanny Man-Ting Ma, Jenny Tian Xia, Queeny Kwan Yi Chan, Chi-Fai Ng, Ka-Fai To
Previously, we reported that GPR30 activation by the receptor-specific, non-estrogenic ligand G-1 inhibited in vitro and in vivo growth of prostate cancer (PCa) cells via sustained Erk1/2 activation. Mechanism underlying the sustained Erk1/2 activation for PCa cell growth inhibition remains unclear. Here we report that G-1, through GPR30, activated Gαi1 proteins to sustain Erk1/2 activation but failed to activate adenylyl cyclase (AC) for cAMP production in PCa cells. The chemical-induced activation of AC-cAMP-PKA signaling attenuated Erk1/2 activity and blocked the cell growth inhibitory effects of G-1...
November 28, 2016: Experimental Cell Research
https://www.readbyqxmd.com/read/27903633/an-e2-guided-e3-screen-identifies-the-rnf17-ube2u-pair-as-regulator-of-the-riddle-syndrome-protein-rnf168
#6
Yingying Guo, Liwei An, Hoi-Man Ng, Shirley M H Sy, Michael S Y Huen
Protein ubiquitination has emerged as pivotal regulatory reactions that promote cellular responses to DNA damage. With a goal to delineate the DNA damage signal transduction cascade, we systematically analysed the human E2 ubiquitin and ubiquitin-like conjugating enzymes for their ability to mobilise the DNA damage marker 53BP1 onto IR-induced DNA double-strand breaks (DSBs). RNAi-based screen identified UBE2U as a candidate regulator of chromatin responses at DSBs. Further mining of the UBE2U interactome uncovered its cognate E3 RNF17 as a novel factor that, via the Riddle syndrome protein RNF168, enforces DNA damage responses...
November 30, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27900575/glycosaminoglycanomics-where-we-are
#7
Sylvie Ricard-Blum, Frédérique Lisacek
Glycosaminoglycans regulate numerous physiopathological processes such as development, angiogenesis, innate immunity, cancer and neurodegenerative diseases. Cell surface GAGs are involved in cell-cell and cell-matrix interactions, cell adhesion and signaling, and host-pathogen interactions. GAGs contribute to the assembly of the extracellular matrix and heparan sulfate chains are able to sequester growth factors in the ECM. Their biological activities are regulated by their interactions with proteins. The structural heterogeneity of GAGs, mostly due to chemical modifications occurring during and after their synthesis, makes the development of analytical techniques for their profiling in cells, tissues, and biological fluids, and of computational tools for mining GAG-protein interaction data very challenging...
November 30, 2016: Glycoconjugate Journal
https://www.readbyqxmd.com/read/27899679/atpid-a-genome-scale-resource-for-genotype-phenotype-associations-in-arabidopsis
#8
Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi
AtPID (Arabidopsis thaliana Protein Interactome Database, available at http://www.megabionet.org/atpid) is an integrated database resource for protein interaction network and functional annotation. In the past few years, we collected 5564 mutants with significant morphological alterations and manually curated them to 167 plant ontology (PO) morphology categories. These single/multiple-gene mutants were indexed and linked to 3919 genes. After integrated these genotype-phenotype associations with the comprehensive protein interaction network in AtPID, we developed a Naïve Bayes method and predicted 4457 novel high confidence gene-PO pairs with 1369 genes as the complement...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899617/epigenetic-and-genetic-deregulation-in-cancer-target-distinct-signaling-pathway-domains
#9
Yang Gao, Andrew E Teschendorff
Cancer is characterized by both genetic and epigenetic alterations. While cancer driver mutations and copy-number alterations have been studied at a systems-level, relatively little is known about the systems-level patterns exhibited by their epigenetic counterparts. Here we perform a pan-cancer wide systems-level analysis, mapping candidate cancer-driver DNA methylation (DNAm) alterations onto a human interactome. We demonstrate that functional DNAm alterations in cancer tend to map to nodes of lower connectivity and inter-connectivity, compared to the corresponding alterations at the genomic level...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899274/systematic-identification-of-hepatitis-e-virus-orf2-interactome-reveals-that-tmem134-engages-in-orf2-mediated-nf-%C3%AE%C2%BAb-pathway
#10
Yabin Tian, Weijin Huang, Jun Yang, Zhiheng Wen, Yansheng Geng, Chenyan Zhao, Heqiu Zhang, Youchun Wang
Hepatitis E virus (HEV) is the causative agent of acute hepatitis E. Open reading frame 2 (ORF2) encodes the capsid protein of HEV, which is the main structural protein and may participate, together with the host factors, in viral entry and egress. However, it is still not clear which host proteins are involved in the interaction with ORF2 and what the functions of these ORF2-interacting proteins are. In this study, we have applied a split-ubiquitin yeast two-hybrid screening approach in combination with the pull-down and coimmunoprecipitation assays, identified and validated multiple interacting partners of ORF2 of genotype 1 and 4, which have diverse biological functions...
November 27, 2016: Virus Research
https://www.readbyqxmd.com/read/27896772/characterization-of-a-protein-interactome-by-co-immunoprecipitation-and-shotgun-mass-spectrometry
#11
Giuseppina Maccarrone, Juan Jose Bonfiglio, Susana Silberstein, Christoph W Turck, Daniel Martins-de-Souza
Identifying the partners of a given protein (the interactome) may provide leads about the protein's function and the molecular mechanisms in which it is involved. One of the alternative strategies used to characterize protein interactomes consists of co-immunoprecipitation (co-IP) followed by shotgun mass spectrometry. This enables the isolation and identification of a protein target in its native state and its interactome from cells or tissue lysates under physiological conditions. In this chapter, we describe a co-IP protocol for interactome studies that uses an antibody against a protein of interest bound to protein A/G plus agarose beads to isolate a protein complex...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27893735/computational-discovery-of-putative-leads-for-drug-repositioning-through-drug-target-interaction-prediction
#12
Edgar D Coelho, Joel P Arrais, José Luís Oliveira
De novo experimental drug discovery is an expensive and time-consuming task. It requires the identification of drug-target interactions (DTIs) towards targets of biological interest, either to inhibit or enhance a specific molecular function. Dedicated computational models for protein simulation and DTI prediction are crucial for speed and to reduce the costs associated with DTI identification. In this paper we present a computational pipeline that enables the discovery of putative leads for drug repositioning that can be applied to any microbial proteome, as long as the interactome of interest is at least partially known...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27883084/nucleoside-diphosphate-kinase-of-p-gingivalis-is-secreted-from-epithelial-cells-in-the-absence-of-a-leader-sequence-through-a-pannexin-1-interactome
#13
Kalina Atanasova, Jungnam Lee, JoAnn Roberts, Kyulim Lee, David M Ojcius, Özlem Yilmaz
Nucleoside-diphosphate-kinases (NDKs) are leaderless, multifunctional enzymes. The mode(s) of NDK secretion is currently undefined, while extracellular translocation of bacterial NDKs is critical for avoidance of host pathogen clearance by opportunistic pathogens such as Porphyromonas gingivalis. P. gingivalis-NDK during infection inhibits extracellular-ATP (eATP)/P2X7-receptor mediated cell death in gingival epithelial cells (GECs) via eATP hydrolysis. Furthermore, depletion of pannexin-1-hemichannel (PNX1) coupled with P2X7-receptor blocks the infection-induced eATP release in GECs, and P...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27881680/structures-and-short-linear-motif-of-disordered-transcription-factor-regions-provide-clues-to-the-interactome-of-the-cellular-hub-radical-induced-cell-death1
#14
Charlotte O'Shea, Lasse Staby, Sidsel Krogh Bendsen, Frederik Grønbæk Tidemand, Andreas Redsted, Martin Willemoës, Birthe B Kragelund, Karen Skriver
Intrinsically disordered protein regions (IDRs) lack a well-defined three-dimensional structure, but often facilitate key protein functions. Some interactions between IDRs and folded protein domains rely on short linear motifs (SLiMs). These motifs are challenging to identify, but once found can point to larger networks of interactions, such as with proteins that serve as hubs for essential cellular functions. The stress-associated plant protein Radical-Induced Cell Death1 (RCD1) is one such hub, interacting with many transcription factors via their flexible IDRs...
November 23, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27880917/phenotypic-and-interaction-profiling-of-the-human-phosphatases-identifies-diverse-mitotic-regulators
#15
Nicole St-Denis, Gagan D Gupta, Zhen Yuan Lin, Beatriz Gonzalez-Badillo, Amanda O Veri, James D R Knight, Dushyandi Rajendran, Amber L Couzens, Ko W Currie, Johnny M Tkach, Sally W T Cheung, Laurence Pelletier, Anne-Claude Gingras
Reversible phosphorylation is a fundamental regulatory mechanism, intricately coordinated by kinases and phosphatases, two classes of enzymes widely disrupted in human disease. To better understand the functions of the relatively understudied phosphatases, we have used complementary affinity purification and proximity-based interaction proteomics approaches to generate a physical interactome for 140 human proteins harboring phosphatase catalytic domains. We identified 1,335 high-confidence interactions (1,104 previously unreported), implicating these phosphatases in the regulation of a variety of cellular processes...
November 22, 2016: Cell Reports
https://www.readbyqxmd.com/read/27872612/systems-biomedicine-of-rabies-delineates-the-affected-signaling-pathways
#16
Sadegh Azimzadeh Jamalkandi, Sayed-Hamidreza Mozhgani, Hamid Gholami Pourbadie, Mehdi Mirzaie, Farshid Noorbakhsh, Behrouz Vaziri, Alireza Gholami, Naser Ansari-Pour, Mohieddin Jafari
The prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27872148/proteomics-screen-identifies-class-i-rab11-fips-as-key-regulators-of-cytokinesis
#17
Carl Laflamme, Jacob A Galan, Khaled Ben El Kadhi, Antoine Méant, Carlos Zeledon, Sébastien Carréno, Philippe P Roux, Gregory Emery
The 14-3-3 protein family orchestrates a complex network of molecular interactions that regulates various biological processes. Owing to their role in regulating the cell cycle and protein trafficking, 14-3-3 proteins are prevalent in human diseases, such as cancer, diabetes and neurodegeneration. 14-3-3 proteins are expressed in all eukaryotic cells, suggesting that they mediate their biological functions through evolutionarily conserved protein interactions. To identify these core 14-3-3 client proteins, we used an affinity-based proteomics approach to characterize and compare the human and Drosophila 14-3-3 interactome...
November 21, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27870635/alternative-exon-usage-creates-novel-transcript-variants-of-tumor-suppressor-shrew-1-gene-with-differential-tissue-expression-profile
#18
Petra A B Klemmt, Eduard Resch, Isabell Smyrek, Knut Engels, Ernst H K Stelzer, Anna Starzinski-Powitz
Shrew-1, also called AJAP1, is a transmembrane protein associated with E-cadherin-mediated adherence junctions and a putative tumor suppressor. Apart from its interaction with β-catenin and involvement in E-cadherin internalization, little structure or function information exists. Here we explored shrew-1 expression during postnatal differentiation of mammary gland as a model system. Immunohistological analyses with antibodies against either the extracellular or the cytoplasmic domains of shrew-1 consistently revealed the expression of full-length shrew-1 in myoepithelial cells, but only part of it in luminal cells...
November 15, 2016: Biology Open
https://www.readbyqxmd.com/read/27866222/the-cytoskeletal-protein-septin-11-is-associated-with-human-obesity-and-is-involved-in-adipocyte-lipid-storage-and-metabolism
#19
Natalia Moreno-Castellanos, Amaia Rodríguez, Yoana Rabanal-Ruiz, Alejandro Fernández-Vega, José López-Miranda, Rafael Vázquez-Martínez, Gema Frühbeck, María M Malagón
AIMS/HYPOTHESIS: Septins are newly identified members of the cytoskeleton that have been proposed as biomarkers of a number of diseases. However, septins have not been characterised in adipose tissue and their relationship with obesity and insulin resistance remains unknown. Herein, we characterised a member of this family, septin 11 (SEPT11), in human adipose tissue and analysed its potential involvement in the regulation of adipocyte metabolism. METHODS: Gene and protein expression levels of SEPT11 were analysed in human adipose tissue...
November 19, 2016: Diabetologia
https://www.readbyqxmd.com/read/27863249/lineage-specific-genome-architecture-links-enhancers-and-non-coding-disease-variants-to-target-gene-promoters
#20
Biola M Javierre, Oliver S Burren, Steven P Wilder, Roman Kreuzhuber, Steven M Hill, Sven Sewitz, Jonathan Cairns, Steven W Wingett, Csilla Várnai, Michiel J Thiecke, Frances Burden, Samantha Farrow, Antony J Cutler, Karola Rehnström, Kate Downes, Luigi Grassi, Myrto Kostadima, Paula Freire-Pritchett, Fan Wang, Hendrik G Stunnenberg, John A Todd, Daniel R Zerbino, Oliver Stegle, Willem H Ouwehand, Mattia Frontini, Chris Wallace, Mikhail Spivakov, Peter Fraser
Long-range interactions between regulatory elements and gene promoters play key roles in transcriptional regulation. The vast majority of interactions are uncharted, constituting a major missing link in understanding genome control. Here, we use promoter capture Hi-C to identify interacting regions of 31,253 promoters in 17 human primary hematopoietic cell types. We show that promoter interactions are highly cell type specific and enriched for links between active promoters and epigenetically marked enhancers...
November 17, 2016: Cell
keyword
keyword
2225
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"