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https://www.readbyqxmd.com/read/28439867/mapping-protein-protein-interactions-using-affinity-purification-and-mass-spectrometry
#1
Chin-Mei Lee, Christopher Adamchek, Ann Feke, Dmitri A Nusinow, Joshua M Gendron
The mapping of protein-protein interaction (PPI) networks and their dynamics are crucial steps to deciphering the function of a protein and its role in cellular pathways, making it critical to have comprehensive knowledge of a protein's interactome. Advances in affinity purification and mass spectrometry technology (AP-MS) have provided a powerful and unbiased method to capture higher-order protein complexes and decipher dynamic PPIs. However, the unbiased calling of nonspecific interactions and the ability to detect transient interactions remains challenging when using AP-MS, thereby hampering the detection of biologically meaningful complexes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28438609/novel-replicons-and-trans-encapsidation-systems-for-hepatitis-c-virus-proteins-live-imaging-and-virus-host-interaction-proteomics
#2
Ovidiu Vlaicu, Tudor Selescu, Florin Pastrama, Cristian Munteanu, Laura Riva, Jean Dubuisson, Yves Rouille, Costin-Ioan Popescu
Proteomics and imaging techniques are used more and more in tandem to investigate the virus-host interaction. Herein we present novel replicons, methods and trans-encapsidation systems suitable for determination of Hepatitis C Virus (HCV) proteins interactomes and live imaging of viral proteins dynamics in HCV cell culture (HCVcc) system. To identify endogenous factors involved in the HCV life cycle, we constructed full-length functional replicons with affinity purification (AP) tags fused to NS2 and NS5A proteins...
April 21, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28433760/elucidation-of-the-dynamic-nature-of-interactome-networks-a-practical-tutorial
#3
Sandra I Anjo, Tania Martins-Marques, Paulo Pereira, Henrique Girão, Bruno Manadas
Considering that proteins are usually engaged in complex and dynamic networks of interactions to exert their activity, a way to understand proteins' functions and the molecular mechanisms in which those proteins are involved, is by studying their interactome. In this sense, this tutorial presents a simple pipeline for the analysis of the network of interactions of a protein in order to reach a biological interpretation of the mechanisms modulated by those interactions, and understand how these interactions are affected by the experimental conditions...
April 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28431525/membrane-enriched-proteome-changes-and-prion-protein-expression-during-neural-differentiation-and-in-neuroblastoma-cells
#4
J A Macedo, D Schrama, I Duarte, E Tavares, J Renaut, M E Futschik, P M Rodrigues, E P Melo
BACKGROUND: The function of the prion protein, involved in the so-called prion diseases, remains a subject of intense debate and the possibility that it works as a pleiotropic protein through the interaction with multiple membrane proteins is somehow supported by recent reports. Therefore, the use of proteomic and bioinformatics combined to uncover cellular processes occurring together with changes in the expression of the prion protein may provide further insight into the putative pleiotropic role of the prion protein...
April 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28431233/a-compendium-of-rna-binding-proteins-that-regulate-microrna-biogenesis
#5
Thomas Treiber, Nora Treiber, Uwe Plessmann, Simone Harlander, Julia-Lisa Daiß, Norbert Eichner, Gerhard Lehmann, Kevin Schall, Henning Urlaub, Gunter Meister
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28424586/app-protein-family-signaling-at-the-synapse-insights-from-intracellular-app-binding-proteins
#6
REVIEW
Suzanne Guénette, Paul Strecker, Stefan Kins
Understanding the molecular mechanisms underlying amyloid precursor protein family (APP/APP-like proteins, APLP) function in the nervous system can be achieved by studying the APP/APLP interactome. In this review article, we focused on intracellular APP interacting proteins that bind the YENPTY internalization motif located in the last 15 amino acids of the C-terminal region. These proteins, which include X11/Munc-18-interacting proteins (Mints) and FE65/FE65Ls, represent APP cytosolic binding partners exhibiting different neuronal functions...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28423660/progerin-impairs-vascular-smooth-muscle-cell-growth-via-the-dna-damage-response-pathway
#7
Daisuke Kinoshita, Ayako Nagasawa, Ippei Shimizu, Takashi K Ito, Yohko Yoshida, Masanori Tsuchida, Atsushi Iwama, Toshiya Hayano, Tohru Minamino
Mutations of the lamin A gene cause various premature aging syndromes, including Hutchinson-Gilford progeria syndrome (HGPS) and atypical Werner syndrome. In HGPS (but not atypical Werner syndrome), extensive loss of vascular smooth muscle cells leads to myocardial infarction with premature death. The underlying mechanisms how single gene mutations can cause various phenotypes are largely unknown. We performed an interactome analysis using mutant forms of lamin A involved in progeroid syndromes. We found that the mutant lamin A responsible for HGPS, known as progerin, could not bind to proteins related to the DNA damage response, including DNA-dependent protein kinase (DNA-PK)...
March 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28421082/insights-into-the-structure-function-and-ion-mediated-signaling-pathways-transduced-by-plant-integrin-linked-kinases
#8
Sorina C Popescu, Elizabeth K Brauer, Gizem Dimlioglu, George V Popescu
Kinases facilitate detection of extracellular signals and set in motion cellular responses for plant adaptation and survival. Some of the energy utilized for kinase signal processing is produced through the activity of ion transporters. Additionally, the synergy between cellular ions and signal transduction influences plant response to pathogens, and their growth and development. In plants, the signaling elements that connect cell wall and membrane sensors with ion homeostasis and transport-mediated processes are largely unknown...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28412036/rna-binding-proteins-revisited-the-emerging-arabidopsis-mrna-interactome
#9
REVIEW
Tino Köster, Claudius Marondedze, Katja Meyer, Dorothee Staiger
RNA-protein interaction is an important checkpoint to tune gene expression at the RNA level. Global identification of proteins binding in vivo to mRNA has been possible through interactome capture - where proteins are fixed to target RNAs by UV crosslinking and purified through affinity capture of polyadenylated RNA. In Arabidopsis over 500 RNA-binding proteins (RBPs) enriched in UV-crosslinked samples have been identified. As in mammals and yeast, the mRNA interactomes came with a few surprises. For example, a plethora of the proteins caught on RNA had not previously been linked to RNA-mediated processes, for example proteins of intermediary metabolism...
April 12, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28409693/tpt1-tumor-protein-translationally-controlled-1-negatively-regulates-autophagy-through-the-becn1-interactome-and-an-mtorc1-mediated-pathway
#10
Seong-Yeon Bae, Sanguine Byun, Soo Han Bae, Do Sik Min, Hyun Ae Woo, Kyunglim Lee
TPT1/TCTP (tumor protein, translationally-controlled 1) is highly expressed in tumor cells, known to participate in various cellular activities including protein synthesis, growth and cell survival. In addition, TPT1 was identified as a direct target of the tumor suppressor TP53/p53 although little is known about the mechanism underlying the anti-survival function of TPT1. Here, we describe a role of TPT1 in the regulation of the MTORC1 pathway through modulating the molecular machinery of macroautophagy/autophagy...
February 15, 2017: Autophagy
https://www.readbyqxmd.com/read/28404750/human-adenine-nucleotide-translocases-physically-and-functionally-interact-with-respirasomes
#11
Ya-Wen Lu, Michelle Grace Acoba, Kandasamy Selvaraju, Tai-Chung Huang, Raja S Nirujogi, Gajanan Sathe, Akhilesh Pandey, Steven M Claypool
Members of the adenine nucleotide translocase (ANT) family exchange ADP for ATP across the mitochondrial inner membrane, an activity that is essential for oxidative phosphorylation (OXPHOS). Mutations in or dysregulation of ANTs is associated with progressive external ophthalmoplegia, cardiomyopathy, non-syndromic intellectual disability, apoptosis and the Warburg effect. Binding partners of human ANTs have not been systematically identified. The absence of such information has prevented a detailed molecular understanding of the assorted ANT-associated diseases including insight into their disparate phenotypic manifestations...
April 12, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28400425/the-logic-of-transcriptional-regulator-recruitment-architecture-at-cis-regulatory-modules-controlling-liver-functions
#12
Julie Dubois-Chevalier, Vanessa Dubois, Hélène Dehondt, Parisa Mazrooei, Claire Mazuy, Aurélien A Sérandour, Céline Gheeraert, Guillaume Penderia, Eric Baugé, Bruno Derudas, Nathalie Hennuyer, Réjane Paumelle, Guillemette Marot, Jason S Carroll, Mathieu Lupien, Bart Staels, Philippe Lefebvre, Jérôme Eeckhoute
Control of gene transcription relies on concomitant regulation by multiple transcriptional regulators (TR). However, how recruitment of a myriad of TR is orchestrated at cis-regulatory modules (CRM) to account for co-regulation of specific biological pathways is only partially understood. Here, we have used mouse liver CRM involved in regulatory activities of the hepatic TR, NR1H4 (FXR; farnesoid X receptor), as our model system to tackle this question. Using integrative cistromic, epigenomic, transcriptomic and interactomic analyses, we reveal a logical organization where trans-regulatory modules (TRM), which consist of subsets of preferentially and co-ordinately co-recruited TR, assemble into hierarchical combinations at hepatic CRM...
April 11, 2017: Genome Research
https://www.readbyqxmd.com/read/28398072/the-reactive-species-interactome-evolutionary-emergence-biological-significance-and-opportunities-for-redox-metabolomics-and-personalized-medicine
#13
Miriam Margherita Cortese-Krott, Anne Koning, Gunter Georg Kuhnle, Peter Nagy, Christopher Bianco, Andreas Pasch, David A Wink, Jon Fukuto, Alan A Jackson, Harry van Goor, Kenneth R Olson, Martin Feelisch
SIGNIFICANCE: Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not administration of antioxidants is ineffective, suggesting our current understanding of the underlying regulatory processes is incomplete. Recent Advances. Similar to reactive oxygen and nitrogen species (ROS, RNS), reactive sulfur species (RSS) are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism and mitochondrial function...
April 11, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28397356/links-between-critical-proteins-drive-the-controllability-of-protein-interaction-networks
#14
Stefan Wuchty, Toni Boltz, Hande Küçük-McGinty
Focusing on the interactomes of H. sapiens, S. cerevisiae, and E. coli, we investigated interactions between controlling proteins. In particular, we determined critical, intermittent, and redundant proteins based on their tendency to participate in minimum dominating sets (MDSets). Independently of the organisms considered, we found that interactions that involved critical nodes had the most prominent effects on the topology of their corresponding networks. Furthermore, we observed that phosphorylation and regulatory events were considerably enriched when the corresponding transcription factors and kinases were critical proteins, while such interactions were depleted when they were redundant proteins...
April 10, 2017: Proteomics
https://www.readbyqxmd.com/read/28395323/defining-the-human-sperm-microtubulome-an-integrated-genomics-approach%C3%A2
#15
Fanny Jumeau, Frédéric Chalmel, Francisco-Jose Fernandez-Gomez, Céline Carpentier, Hélène Obriot, Meryem Tardivel, Marie-Laure Caillet-Boudin, Jean-Marc Rigot, Nathalie Rives, Luc Buée, Nicolas Sergeant, Valérie Mitchell
Sperm motility notably depends on the structural integrity of the flagellum and the regulation of microtubule dynamics. Although researchers have started to use "omics" techniques to characterize the human sperm's molecular landscape, the constituents responsible for the assembly, organization, and dynamics of the flagellum microtubule have yet to be fully defined. In this study, we defined a core set of 116 gene products associated with the human sperm microtubulome (including products potentially involved in abnormal ciliary phenotypes and male infertility disorders)...
January 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28389583/development-of-large-scale-cross-linking-mass-spectrometry
#16
Helena Maria Barysz, Johan Malmstroem
Cross-linking mass spectrometry (CLMS) provides distance constraints to study the structure of proteins, multiprotein complexes and protein-protein interactions which are critical for the understanding of protein function. CLMS is an attractive technology to bridge the gap between high-resolution structural biology techniques and proteomic-based interactome studies. However, as outlined in this review there are still several bottlenecks associated with CLMS which limit its application on a proteome-wide level...
April 7, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28387482/proximity-dependent-labeling-methods-for-proteomic-profiling-in-living-cells
#17
REVIEW
Chiao-Lin Chen, Norbert Perrimon
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins with biotin. The biotinylated endogenous proteins can then be isolated for further analysis by MS...
April 7, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28381614/dynamic-rna-protein-interactions-underlie-the-zebrafish-maternal-to-zygotic-transition
#18
Vladimir Despic, Mario Dejung, Mengting Gu, Jayanth Krishnan, Jing Zhang, Lydia Herzel, Korinna Straube, Mark B Gerstein, Falk Butter, Karla M Neugebauer
During the maternal-to-zygotic transition (MZT), transcriptionally silent embryos rely on post-transcriptional regulation of maternal mRNAs until zygotic genome activation (ZGA). RNA-binding proteins (RBPs) are important regulators of post-transcriptional RNA processing events, yet their identities and functions during developmental transitions in vertebrates remain largely unexplored. Using mRNA interactome capture, we identified 227 RBPs in zebrafish embryos before and during ZGA, hereby named the zebrafish MZT mRNA-bound proteome...
April 5, 2017: Genome Research
https://www.readbyqxmd.com/read/28381538/chemokine-interactome-mapping-enables-tailored-intervention-in-acute-and-chronic-inflammation
#19
Philipp von Hundelshausen, Stijn M Agten, Veit Eckardt, Xavier Blanchet, Martin M Schmitt, Hans Ippel, Carlos Neideck, Kiril Bidzhekov, Julian Leberzammer, Kanin Wichapong, Alexander Faussner, Maik Drechsler, Jochen Grommes, Johanna P van Geffen, He Li, Almudena Ortega-Gomez, Remco T A Megens, Ronald Naumann, Ingrid Dijkgraaf, Gerry A F Nicolaes, Yvonne Döring, Oliver Soehnlein, Esther Lutgens, Johan W M Heemskerk, Rory R Koenen, Kevin H Mayo, Tilman M Hackeng, Christian Weber
Chemokines orchestrate leukocyte trafficking and function in health and disease. Heterophilic interactions between chemokines in a given microenvironment may amplify, inhibit, or modulate their activity; however, a systematic evaluation of the chemokine interactome has not been performed. We used immunoligand blotting and surface plasmon resonance to obtain a comprehensive map of chemokine-chemokine interactions and to confirm their specificity. Structure-function analyses revealed that chemokine activity can be enhanced by CC-type heterodimers but inhibited by CXC-type heterodimers...
April 5, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28379492/identification-and-dynamic-changes-of-rnas-isolated-from-raly-containing-ribonucleoprotein-complexes
#20
Annalisa Rossi, Albertomaria Moro, Toma Tebaldi, Nicola Cornella, Lisa Gasperini, Lorenzo Lunelli, Alessandro Quattrone, Gabriella Viero, Paolo Macchi
RALY is a member of the heterogeneous nuclear ribonucleoprotein family (hnRNP), a large family of RNA-binding proteins involved in many aspects of RNA metabolism. Although RALY interactome has been recently characterized, a comprehensive global analysis of RALY-associated RNAs is lacking and the biological function of RALY remains elusive. Here, we performed RIP-seq analysis to identify RALY interacting RNAs and assessed the role of RALY in gene expression. We demonstrate that RALY binds specific coding and non-coding RNAs and associates with translating mRNAs of mammalian cells...
April 4, 2017: Nucleic Acids Research
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