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https://www.readbyqxmd.com/read/28227132/effect-specific-analysis-of-pathogenic-snvs-in-human-interactome-leveraging-edge-based-network-robustness
#1
Hongzhu Cui, Dmitry Korkin, Hongzhu Cui, Dmitry Korkin, Dmitry Korkin, Hongzhu Cui
Study of genetic variants in the context of molecular networks has recently gained much attention. However, many of these studies suffer from the lack of functional information about the network rewiring effect of genetic variants. After large-scale homology modeling, plus extracting native structure from PDB database, we performed structure-based prediction about the rewiring effect using our SNP-IN tool, and it covers significantly more variants than experimental characterization. The analysis result confirms the widespread perturbations in human interactome and reveals the network rewiring behavior based on edge-based network robustness concept...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225217/proteomic-analysis-of-the-cullin4b-interactome-using-proximity-dependent-biotinylation-in-living-cells
#2
Hailong Zhang, Shupeng Li, Pingting Liu, Frankie H F Lee, Albert H C Wong, Fang Liu
Cullin 4B (CUL4B) mutations have been implicated in mental retardation and dopamine-related behaviors due to disruptions in their interaction with Cullin-RING E3 ligases (CRLs). Thus, further identification of CUL4B substrates can increase the knowledge of protein homeostasis and illuminate the role of CUL4B in neuropsychiatric disease. However, the transient nature of the coupling between CUL4B and its substrates is difficult to detect in vivo using current approaches, thus hampers efforts to investigate functions of CRLs within unperturbed living systems...
February 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28224124/the-mammalian-septin-interactome
#3
REVIEW
Katharina Neubauer, Barbara Zieger
Septins are GTP-binding and membrane-interacting proteins with a highly conserved domain structure involved in various cellular processes, including cytoskeleton organization, cytokinesis, and membrane dynamics. To date, 13 different septin genes have been identified in mammals (SEPT1 to SEPT12 and SEPT14), which can be classified into four distinct subgroups based on the sequence homology of their domain structure (SEPT2, SEPT3, SEPT6, and SEPT7 subgroup). The family members of these subgroups have a strong affinity for other septins and form apolar tri-, hexa-, or octameric complexes consisting of multiple septin polypeptides...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28224022/introduction-of-inflammatory-bowel-disease-biomarkers-panel-using-protein-protein-interaction-ppi-network-analysis
#4
Hamid Asadzadeh-Aghdaee, Shabnam Shahrokh, Mohsen Norouzinia, Mostafa Hosseini, Aliasghar Keramatinia, Mostafa Jamalan, Bijan Naghibzadeh, Ali Sadeghi, Somayeh Jahani Sherafat, Mohammad Reza Zali
AIM: In the present study, a protein-protein interaction network construction is conducted for IBD. BACKGROUND: Inflammatory bowel diseases as serious chronic gastrointestinal disorders attracted many molecular investigations. Diverse molecular information is present for IBD. However, these molecular findings are not highlighted based on interactome analysis. On the other hand, PPI network analysis is a powerful method for study of molecular interactions in the protein level that provide useful information for highlighting the desired key proteins...
December 2016: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28222748/identification-of-host-cellular-proteins-that-interact-with-the-m-protein-of-a-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus-vaccine-strain
#5
Qian Wang, Yanwei Li, Hong Dong, Li Wang, Jinmei Peng, Tongqing An, Xufu Yang, Zhijun Tian, Xuehui Cai
BACKGROUND: The highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) continues to pose one of the greatest threats to the swine industry. M protein is the most conserved and important structural protein of PRRSV. However, information about the host cellular proteins that interact with M protein remains limited. METHODS: Host cellular proteins that interact with the M protein of HP-PRRSV were immunoprecipitated from MARC-145 cells infected with PRRSV HuN4-F112 using the M monoclonal antibody (mAb)...
February 22, 2017: Virology Journal
https://www.readbyqxmd.com/read/28217095/endogenous-protein-interactome-of-human-udp-glucuronosyltransferases-exposed-by-untargeted-proteomics
#6
Michèle Rouleau, Yannick Audet-Delage, Sylvie Desjardins, Mélanie Rouleau, Camille Girard-Bock, Chantal Guillemette
The conjugative metabolism mediated by UDP-glucuronosyltransferase enzymes (UGTs) significantly influences the bioavailability and biological responses of endogenous molecule substrates and xenobiotics including drugs. UGTs participate in the regulation of cellular homeostasis by limiting stress induced by toxic molecules, and by controlling hormonal signaling networks. Glucuronidation is highly regulated at genomic, transcriptional, post-transcriptional and post-translational levels. However, the UGT protein interaction network, which is likely to influence glucuronidation, has received little attention...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28215535/ambra1-a-novel-bh3-like-protein-new-insights-into-the-ambra1-bcl2-family-proteins-relationship
#7
A Di Rita, F Strappazzon
Cellular homeostasis swings like a pendulum backward and forward between life and death. Two of the main processes, which regulate this equilibrium, are autophagy and apoptosis. While autophagy is a highly conserved self-digestion mechanism that mediates degradation of damaged or surplus components, apoptosis is a programmed cell suicide in which typical death signals induce the elimination of undesired cells. Both these processes are highly regulated by complex molecular machineries, including some common proteins whose "dual role" favors one process or the other...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28210003/differential-signaling-through-p190-and-p210-bcr-abl-fusion-proteins-revealed-by-interactome-and-phosphoproteome-analysis
#8
J A Cutler, R Tahir, S K Sreenivasamurthy, C Mitchell, S Renuse, R S Nirujogi, A H Patil, M Heydarian, X Wong, X Wu, T-C Huang, M-S Kim, K Reddy, A Pandey
Two major types of leukemogenic BCR-ABL fusion proteins are p190(BCR-ABL) and p210(BCR-ABL). Although the two fusion proteins are closely related, they can lead to different clinical outcomes. A thorough understanding of the signaling programs employed by these two fusion proteins is necessary to explain these clinical differences. We took an integrated approach by coupling protein-protein interaction analysis using biotinylation identification (BioID) with global phosphorylation analysis to investigate the differences in signaling between these two fusion proteins...
February 17, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28205554/the-oncoppi-network-of-cancer-focused-protein-protein-interactions-to-inform-biological-insights-and-therapeutic-strategies
#9
Zenggang Li, Andrei A Ivanov, Rina Su, Valentina Gonzalez-Pecchi, Qi Qi, Songlin Liu, Philip Webber, Elizabeth McMillan, Lauren Rusnak, Cau Pham, Xiaoqian Chen, Xiulei Mo, Brian Revennaugh, Wei Zhou, Adam Marcus, Sahar Harati, Xiang Chen, Margaret A Johns, Michael A White, Carlos Moreno, Lee A D Cooper, Yuhong Du, Fadlo R Khuri, Haian Fu
As genomics advances reveal the cancer gene landscape, a daunting task is to understand how these genes contribute to dysregulated oncogenic pathways. Integration of cancer genes into networks offers opportunities to reveal protein-protein interactions (PPIs) with functional and therapeutic significance. Here, we report the generation of a cancer-focused PPI network, termed OncoPPi, and identification of >260 cancer-associated PPIs not in other large-scale interactomes. PPI hubs reveal new regulatory mechanisms for cancer genes like MYC, STK11, RASSF1 and CDK4...
February 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28203709/defining-age-and-lactocrine-sensitive-elements-of-the-neonatal-porcine-uterine-microrna-mrna-interactome%C3%A2-%C3%A2
#10
Ashley F George, Kathleen M Rahman, Meredith E Camp, Nripesh Prasad, Frank F Bartol, Carol A Bagnell
No abstract text is available yet for this article.
February 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28203524/in-vivo-mapping-of-a-dynamic-ribonucleoprotein-granule-interactome-in-early-drosophila-embryos
#11
Jimiao Zheng, Ming Gao, Nhan Huynh, Samuel J Tindell, Hieu D L Vo, W Hayes McDonald, Alexey L Arkov
Macromolecular complexes and organelles play crucial roles within cells, but their native architectures are often unknown. Here, we use an evolutionarily conserved germline organelle, the germ granule, as a paradigm. In Drosophila embryos, we map one of its interactomes using a novel in vivo crosslinking approach that employs two interacting granule proteins and determines their common neighbor molecules. We identified an in vivo granule assembly of Tudor, Aubergine, motor and metabolic proteins, and RNA helicases, and provide evidence for direct interactions within this assembly using purified components...
December 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/28199843/the-sin3a-hdac-corepressor-complex-functionally-cooperates-with-nanog-to-promote-pluripotency
#12
Arven Saunders, Xin Huang, Miguel Fidalgo, Michael H Reimer, Francesco Faiola, Junjun Ding, Carlos Sánchez-Priego, Diana Guallar, Carmen Sáenz, Dan Li, Jianlong Wang
Although SIN3A is required for the survival of early embryos and embryonic stem cells (ESCs), the role of SIN3A in the maintenance and establishment of pluripotency remains unclear. Here, we find that the SIN3A/HDAC corepressor complex maintains ESC pluripotency and promotes the generation of induced pluripotent stem cells (iPSCs). Members of the SIN3A/HDAC corepressor complex are enriched in an extended NANOG interactome and function in transcriptional coactivation in ESCs. We also identified a critical role for SIN3A and HDAC2 in efficient reprogramming of somatic cells...
February 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28188528/lumier-a-discovery-tool-for-mammalian-protein-interaction-networks
#13
Miriam Barrios-Rodiles, Jonathan D Ellis, Benjamin J Blencowe, Jeffrey L Wrana
Protein-protein interactions (PPIs) play an essential role in all biological processes. In vivo, PPIs occur dynamically and depend on extracellular cues. To discover novel protein-protein interactions in mammalian cells, we developed a high-throughput automated technology called LUMIER (LUminescence-based Mammalian IntERactome). In this approach, we co-express a Luciferase (LUC)-tagged fusion protein along with a Flag-tagged protein in an efficiently transfectable cell line such as HEK-293T cells. The interaction between the two proteins is determined by co-immunoprecipitation using an anti-Flag antibody, and the presence of the LUC-tagged interactor in the complex is subsequently detected via its luciferase activity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28186491/combinatorial-bzip-dimers-define-complex-dna-binding-specificity-landscapes
#14
Jose A Rodriguez-Martinez, Aaron W Reinke, Devesh Bhimsaria, Amy E Keating, Aseem Z Ansari
How transcription factor dimerization impacts DNA binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or 'emergent' sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers...
February 10, 2017: ELife
https://www.readbyqxmd.com/read/28185045/identification-and-in-silico-analysis-of-major-redox-modulated-proteins-from-brassica-juncea-seedlings-using-2d-redox-sds-page-2-dimensional-diagonal-redox-sodium-dodecyl-sulfate-polyacrylamide-gel-electrophoresis
#15
Satya Prakash Chaurasia, Renu Deswal
The thiol-disulphide exchange regulates the activity of proteins by redox modulation. Many studies to analyze reactive oxygen species (ROS), particularly, hydrogen peroxide (H2O2) induced changes in the gene expression have been reported, but efforts to detect H2O2 modified proteins are comparatively few. Two-dimensional diagonal redox sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) was used to detect polypeptides which undergo thiol-disulphide exchange in Brassica juncea seedlings following H2O2 (10 mM) treatment for 30 min...
February 9, 2017: Protein Journal
https://www.readbyqxmd.com/read/28179399/differential-proteomics-profiling-identifies-lipid-droplet-proteins-and-biological-functions-in-high-fat-diet-induced-fatty-livers
#16
Mingwei Liu, Rui Ge, Wanlin Liu, Qiongming Liu, Xia Xia, Mi Lai, Lizhu Liang, Chen Li, Lei Song, Bei Zhen, Jun Qin, Chen Ding
Eukaryotic cells store neutral lipids in cytoplasmic lipid droplets (LD) enclosed in a monolayer of phospholipids and associated proteins (LDP). Growing evidence has demonstrated that LDPs play important roles in the pathogenesis of liver diseases. However, the composition of liver LDPs and role of their alterations in hepatosteatosis is not well understood. In this study, we performed liver proteome and lipid droplet sub-proteome profiling to identify enriched proteins in LD as LDPs, and quantified their changes in a high fat diet induced (HFD) fatty liver model...
February 8, 2017: Journal of Lipid Research
https://www.readbyqxmd.com/read/28174237/single-cell-transcriptomics-of-the-human-placenta-inferring-the-cell-communication-network-of-the-maternal-fetal-interface
#17
Mihaela Pavličev, Günter P Wagner, Arun Rajendra Chavan, Kathryn Owens, Jamie Maziarz, Caitlin Dunn-Fletcher, Suhas G Kallapur, Louis Muglia, Helen Jones
Organismal function is, to a great extent, determined by interactions among their fundamental building blocks, the cells. In this work, we studied the cell-cell interactome of fetal placental trophoblast cells and maternal endometrial stromal cells, using single-cell transcriptomics. The placental interface mediates the interaction between two semiallogenic individuals, the mother and the fetus, and is thus the epitome of cell interactions. To study these, we inferred the cell-cell interactome by assessing the gene expression of receptor-ligand pairs across cell types...
February 7, 2017: Genome Research
https://www.readbyqxmd.com/read/28174230/crispr-cas9-coupled-affinity-purification-mass-spectrometry-analysis-revealed-a-novel-role-of-neurofibromin-in-mtor-signaling
#18
Xu Li, Min Gao, Jong Min Choi, Beom-Jun Kim, Mao-Tian Zhou, Zhen Chen, Antrix N Jain, Sung Yun Jung, Jingsong Yuan, Wenqi Wang, Yi Wang, Junjie Chen
Neurofibromin (NF1) is a well-known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high-quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knockout technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings...
February 7, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28173629/enhanced-dependency-of-kras-mutant-colorectal-cancer-cells-on-rad51-dependent-homologous-recombination-repair-identified-from-genetic-interactions-in-saccharomyces-cerevisiae
#19
Murugan Kalimutho, Amanda L Bain, Bipasha Mukherjee, Purba Nag, Devathri M Nanayakkara, Sarah K Harten, Janelle L Harris, Goutham Narayanan Subramanian, Debottam Sinha, Senji Shirasawa, Sriganesh Srihari, Sandeep Burma, Kum Kum Khanna
Activating KRAS mutations drive colorectal cancer tumorigenesis and influence response to anti-EGFR targeted therapy. Despite recent advances in understanding Ras signaling biology and the revolution in therapies for melanoma using BRAF inhibitors, no targeted agents have been effective in KRAS mutant cancers, mainly due to activation of compensatory pathways. Here, by leveraging the largest synthetic lethal genetic interactome in yeast, we identify that KRAS-mutated colorectal cancer cells have augmented homologous recombination repair (HRR) signaling...
February 7, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28172852/differential-regulation-of-cryptic-genetic-variation-shapes-the-genetic-interactome-underlying-complex-traits
#20
Anupama Yadav, Kaustubh Dhole, Himanshu Sinha
No abstract text is available yet for this article.
December 1, 2016: Genome Biology and Evolution
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