http://precedings.nature.com/tags/Signal%20transduction Recently posted documents tagged with 'Signal transduction' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://precedings.nature.com/documents/3271/version/1 In this essay we attempt to reconsider the concept of the “Leucine Zipper” (LZ) protein oligomerization motif. Reasoning on the wealth of existing data, we suggest that despite of the structural similarity with highly stable extended “Coiled Coil” motifs, on the functional level short and moderately stable “Leucine Zippers” might stand out as a distinct group. Namely, this family of oligomerization motifs facilitates combinatorial protein-protein recognition in the course of signal transduction events, thus going beyond the structural role of the extended “Coiled Coils”. Summarizing the existing knowledge on stability, specificity and folding of Leucine Zippers we demonstrate how a simple set of rules, applied in the context of the universal coiled coil scaffold, creates a robust LZ interaction vocabulary. Owing to the high abundance of Leucine Zippers, this motif might account for coupling of distinct protein signalling pathways into a unified intracellular signalling network. In the last part of this essay we provide examples demonstrating prevalence of the LZ-mediated signal transduction and illustrate applicability of the “LZ code” formalism to interpret evidences of couplings between cytoplasmic and nuclear signalling networks. http://precedings.nature.com/documents/3271/version/1 Fri, 22 May 2009 15:19:37 UTC Rethinking Leucine Zipper – a ubiquitous signal transduction motif hdl:10101/npre.2009.3271.1 2009-05-22 Yaroslav Nikolaev Nature Precedings 2009-05-22T15:19:37Z Manuscript Cancer Immunology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/2243/version/1 The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the U.S. National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools. http://precedings.nature.com/documents/2243/version/1 Fri, 29 Aug 2008 10:33:26 UTC PID: The Pathway Interaction Database hdl:10101/npre.2008.2243.1 2008-11-18 Kira Anthony Nature Precedings 2008-08-29T10:33:26Z Manuscript Cancer Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.1311.1 The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely availablecollection of curated and peer-reviewed signaling pathways composed of humanbiomolecular interactions and cellular processes. Created in a collaboration between theU.S. National Cancer Institute and Nature Publishing Group, the database is a researchtool for cell biologists, biochemists, computational biologists and bioinformaticians.The PID offers a range of tools to facilitate pathway exploration. Users can browse thepre-defi ned set of pathways and also create interaction network maps centered ona single molecule of interest or an extensive list of molecules. In addition, users candownload complete data sets in extensible markup language (XML) and BiologicalPathway Exchange (BioPAX) Level 2 formats. The database is updated every month andsupplemented by a concise editorial section that provides synopses of recent noteworthypapers in cell signaling and specially commissioned articles on the practical uses ofother relevant online tools. Users can sign up for free email alerts or RSS feeds to receivedatabase updates. http://dx.doi.org/10.1038/npre.2007.1311.1 Mon, 12 Nov 2007 16:51:55 UTC The NCI-Nature Pathway Interaction Database: A cell signaling resource. doi:10.1038/npre.2007.1311.1 2007-11-12 Kira Anthony Nature Precedings 2007-11-12T16:51:55Z Poster Cancer Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1196/version/1 Members of the G protein receptor kinase (GRK) family that regulates receptor desensitization and members of the nuclear transcription factors family NFκB have been recently and convincingly demonstrated to interact, although the effects on transcription and gene expression have not yet been described. Using overexpression, knockdown (small interfering RNA) and mutagenesis experiments, we demonstrate that GRK5 couples to and stabilizes the NFκB inhibitor IκBα, and inhibits NFκB activity. Studies with minigenes suggest that the N-terminal Regulation of G protein Signaling (RGS) homology (RH) domain confers GRK5 such ability. GRK5-RH domain overexpression affects NFκB dependent phenotypes, such as apoptosis protection, cytokine production and inflammation and tissue regeneration. Our results reveal a novel, unexpected role of GRK5 in NFκB transcription activity regulation that represents a possible target for diagnostic and therapeutics. http://precedings.nature.com/documents/1196/version/1 Mon, 01 Oct 2007 20:53:14 UTC Kinase independent inhibition of NFκB transcriptional activity by GRK5 through IκBα stabilization. hdl:10101/npre.2007.1196.1 2007-10-01 Guido Iaccarino Nature Precedings 2007-10-01T20:53:14Z Manuscript Immunology Molecular Cell Biology http://creativecommons.org/licenses/by/2.5/