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      The Protein Architecture of Human Secretory Vesicles Reveals Differential Regulation of Signaling Molecule Secretion by Protein Kinases

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          Abstract

          Secretory vesicles are required for release of chemical messengers to mediate intercellular signaling among human biological systems. It is necessary to define the organization of the protein architecture of the ‘human’ dense core secretory vesicles (DCSV) to understand mechanisms for secretion of signaling molecules essential for cellular regulatory processes. This study, therefore, conducted extensive quantitative proteomics and systems biology analyses of human DCSV purified from human pheochromocytoma. Over 600 human DCSV proteins were identified with quantitative evaluation of over 300 proteins, revealing that most proteins participate in producing peptide hormones and neurotransmitters, enzymes, and the secretory machinery. Systems biology analyses provided a model of interacting DCSV proteins, generating hypotheses for differential intracellular protein kinases A and C signaling pathways. Activation of cellular PKA and PKC pathways resulted in differential secretion of neuropeptides, catecholamines, and β-amyloid of Alzheimer's disease for mediating cell-cell communication. This is the first study to define a model of the protein architecture of human DCSV for human disease and health.

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          Most cited references54

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          Integration of biological networks and gene expression data using Cytoscape.

          Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.
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            TANDEM: matching proteins with tandem mass spectra.

            Tandem mass spectra obtained from fragmenting peptide ions contain some peptide sequence specific information, but often there is not enough information to sequence the original peptide completely. Several proprietary software applications have been developed to attempt to match the spectra with a list of protein sequences that may contain the sequence of the peptide. The application TANDEM was written to provide the proteomics research community with a set of components that can be used to test new methods and algorithms for performing this type of sequence-to-data matching. The source code and binaries for this software are available at http://www.proteome.ca/opensource.html, for Windows, Linux and Macintosh OSX. The source code is made available under the Artistic License, from the authors.
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              The mechanisms of vesicle budding and fusion.

              Genetic and biochemical analyses of the secretory pathway have produced a detailed picture of the molecular mechanisms involved in selective cargo transport between organelles. This transport occurs by means of vesicular intermediates that bud from a donor compartment and fuse with an acceptor compartment. Vesicle budding and cargo selection are mediated by protein coats, while vesicle targeting and fusion depend on a machinery that includes the SNARE proteins. Precise regulation of these two aspects of vesicular transport ensures efficient cargo transfer while preserving organelle identity.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2012
                16 August 2012
                20 August 2012
                : 7
                : 8
                : e41134
                Affiliations
                [1 ]Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
                [2 ]Department of Medicine, University of California San Diego, La Jolla, California, United States of America
                [3 ]Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, California, United States of America
                [4 ]Departments of Neurosciences and Pharmacology, University of California San Diego, La Jolla, California, United States of America
                Yale School of Medicine, United States of America
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: SJB JW LT MZ DO QM MS TI VH. Performed the experiments: SJB JW LT MZ MS TI VH. Analyzed the data: SJB JW LT MZ DO QM MS TI VH. Contributed reagents/materials/analysis tools: SJB JW LT MZ DO QM MS TI VH. Wrote the paper: SJB JW DO MS TI VH.

                Article
                PONE-D-12-10204
                10.1371/journal.pone.0041134
                3420874
                22916103
                3cdbf7f5-3f07-41a2-a2b8-8d649898a6ba
                Copyright @ 2012

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 April 2012
                : 17 June 2012
                Page count
                Pages: 13
                Funding
                The authors appreciate support of this research by grants from the National Institutes of Health (NIH) (R01DA04271, PO1HL58120, R01MH077305) and the Alzheimer's Association to V. Hook, NIH grant K01DA023065 to S. Bark, NIH grants P41RR031228 and R01GM070743 to T. Ideker, and NIH grant P01HL58120 to D. T. O'Connor. The grant agencies' websites are: http://www.nih.gov/ and http://www.alz.org/. The funders had no role in study design, data collection and analyses, decision to publish, or preparation of this manuscript.
                Categories
                Research Article
                Biology
                Molecular Cell Biology
                Cellular Structures
                Subcellular Organelles
                Membranes and Sorting
                Signal Transduction
                Neuroscience
                Cellular Neuroscience
                Proteomics
                Protein Abundance
                Spectrometric Identification of Proteins
                Systems Biology
                Medicine
                Endocrinology
                Neuroendocrinology

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                Uncategorized

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