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Dynamic Proteomics: a database for dynamics and localizations of endogenous fluorescently-tagged proteins in living human cells

Milana Frenkel-Morgenstern, Ariel A. Cohen, Naama Geva-Zatorsky, Eran Eden, Jaime Prilusky, Irina Issaeva, Alex Sigal, Cellina Cohen-Saidon, Yuvalal Liron, Lydia Cohen, Tamar Danon, Natalie Perzov (+1 others)
2009 Nucleic Acids Research  
Recent advances allow tracking the levels and locations of a thousand proteins in individual living human cells over time using a library of annotated reporter cell clones (LARC).  ...  Each cell-line clone in LARC has a protein tagged with yellow fluorescent protein, expressed from its endogenous chromosomal location, under its natural regulation.  ...  The authors also thank Pierre Choukroun and Michael Green for the UNIX system administration; Malka Cymbalista and Shlomit Afgin for a technical help in the website and database construction.  ... 
doi:10.1093/nar/gkp808 pmid:19820112 pmcid:PMC2808965 fatcat:wq2cfejow5dplnhejf2qfsuljy

Nucleolar proteome dynamics

Jens S. Andersen, Yun W. Lam, Anthony K. L. Leung, Shao-En Ong, Carol E. Lyon, Angus I. Lamond, Matthias Mann
2005 Nature  
The lumbar enlargement was collected, paraffin embedded, and serially sectioned at 14 mm, for a total of 140 sections.  ...  Levels of GLT1 protein were quantified by immunoblots 3 .  ...  Lee and C. Cocci for technical assistance; K. Tanaka for GLT1-null mice; C. Leahy for ALS mouse studies; and J. Heemskerk for initiating the project, discussions and encouragement.  ... 
doi:10.1038/nature03207 pmid:15635413 fatcat:5dx7j4ru7bhdtbve7kj7g2yx3i

Profiling protease activities by dynamic proteomics workflows

Diana Klingler, Markus Hardt
2012 Proteomics  
Recently, activity-based workflows have come to the forefront to tackle the dynamic aspects of proteolytic processing networks in vitro, ex vivo and in vivo.  ...  To fully understand the functional role of proteases in these processes, it is necessary to characterize the target specificity of the enzymes, identify endogenous substrates and cleavage products as well  ...  Acknowledgments This work was partially supported by a grant from the National Institute of Dental and Craniofacial Research (R01 DE 019796) to Markus Hardt.  ... 
doi:10.1002/pmic.201100399 pmid:22246865 pmcid:PMC3431026 fatcat:p5bsupjguvgmthjmkp3rkjcbjm

Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins

Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Inbal Alaluf, Naamah Swerdlin, Natalie Perzov, Tamar Danon, Yuvalal Liron, Tal Raveh, Anne E Carpenter (+2 others)
2006 Nature Methods  
We examined cell cycle-dependent changes in the proteome of human cells by systematically measuring protein dynamics in individual living cells.  ...  This approach to dynamic proteomics can aid in discovery and accurate quantification of the extensive regulation of protein concentration and localization in individual living cells.  ...  Sharp from the Weizmann flow cytometry unit for assistance, and M. Springer, P. Bordalo, O. Zuk and members of the Alon lab for discussions of the manuscript.  ... 
doi:10.1038/nmeth892 pmid:16791210 fatcat:xbzntzl7cbgobn6uasltb3gjsy

Dynamic Proteomics of Herpes Simplex Virus Infection

Nir Drayman, Omer Karin, Avi Mayo, Tamar Danon, Lev Shapira, Dor Rafael, Anat Zimmer, Anat Bren, Oren Kobiler, Uri Alon, Angus C. Wilson, Stephen P. Goff
2017 mBio  
Here we address this by dynamic proteomics—imaging and tracking 400 yellow fluorescent protein (YFP)-tagged host proteins in individual cells infected by herpes simplex virus 1.  ...  These proteins are cell cycle markers, and we find that the position in the cell cycle at the time of infection (along with the cell motility and local cell density) can reasonably predict in which individual  ...  ACKNOWLEDGMENTS We thank Roger Everett for the pEGFP-110-wt plasmid and the dl1403 HSV-1 mutant. We thank Matthew Weitzman for the kind gift of the KOS and 7134 strains.  ... 
doi:10.1128/mbio.01612-17 pmid:29114028 pmcid:PMC5676043 fatcat:l3mqi3t3cnhcjpgz2ae45guham

Protein localization in proteomics

Trisha N Davis
2004 Current Opinion in Chemical Biology  
These studies typically use green fluorescent protein as a tag for proteins in living cells. Improvements in the yellow and sapphire color variants will increase their utility.  ...  A global analysis of the localization of 4156 yeast proteins has just been accomplished. Smaller scale analyses have been performed in a variety of organisms.  ...  of proteins in living cells.  ... 
doi:10.1016/j.cbpa.2003.11.003 pmid:15036156 fatcat:7eseoazervgtfbyb2zxurvgv3u

In VivoInteraction Proteomics inCaenorhabditis elegansEmbryos Provides New Insights into P Granule Dynamics

Jia-Xuan Chen, Patricia G. Cipriani, Desirea Mecenas, Jolanta Polanowska, Fabio Piano, Kristin C. Gunsalus, Matthias Selbach
2016 Molecular & Cellular Proteomics  
In addition, we find that GEI-12 also induces granule formation in mammalian cells, suggesting a common regulatory mechanism in worms and humans.  ...  Here, we combine in vivo expressed GFP-tagged proteins with quantitative proteomics to identify protein-protein interactions of selected key proteins involved in early C. elegans embryogenesis.  ...  Fluorescence Microscopy-Live and fixed embryo fluorescence imaging and time-lapse microscopy were carried out using a Leica DM RA2 microscope equipped with a Hamamatsu C9100 -12 EM-CCD camera.  ... 
doi:10.1074/mcp.m115.053975 pmid:26912668 pmcid:PMC4858945 fatcat:pbjhavqeibcg3gkd4pmeuu7b4a

A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

François-Michel Boisvert, Yasmeen Ahmad, Marek Gierliński, Fabien Charrière, Douglas Lamont, Michelle Scott, Geoff Barton, Angus I. Lamond
2011 Molecular & Cellular Proteomics  
Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization, and turnover rates, on a whole proteome level remains a major challenge in the postgenome era.  ...  Here we describe a combined pulse-labeling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation, and turnover rates of endogenously expressed  ...  Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization, and turnover rates, on a whole proteome level remains a major challenge in the postgenome era.  ... 
doi:10.1074/mcp.m111.011429 pmid:21937730 pmcid:PMC3316722 fatcat:2g67usel4fcrpkbgcppwfx3p3a

Organellar proteomics: turning inventories into insights

Jens S Andersen, Matthias Mann
2006 EMBO Reports  
Here, we review the emerging trends in this rapidly expanding area and discuss the role of organellar proteomics in the context of functional genomics and systems biology.  ...  Researchers are now applying robust mass-spectrometry-based proteomics methods to obtain an inventory of biochemically isolated organelles that contain hundreds of proteins.  ...  The mass and fragmentation information is matched against a sequence database by a search algorithm, resulting in a list of reported protein identifications for the organelle.  ... 
doi:10.1038/sj.embor.7400780 pmid:16953200 pmcid:PMC1559674 fatcat:5daq62knu5bstb45scn42pb2sy

Interactive proteomics: what lies ahead?

Bernhard Suter, Saranya Kittanakom, Igor Stagljar
2008 BioTechniques  
The inherent chemical and structural diversity of proteins, their different expression levels, and their distinct subcellular localizations pose unique challenges for the exploration of these networks,  ...  In the near future, attention will shift to the establishment of interaction networks in humans and their application in drug discovery and understanding of diseases.  ...  ACKNOWLEDGEMENTS We thank Jamie Snider for critically reading the manuscript. We also thank Andrew Emili, Jack Greenblatt, Janet Rossant,  ... 
doi:10.2144/000112799 pmid:18474045 fatcat:hyqonaieqzf7loux4q4mxy7eyu

Functional proteomics

Maria Monti, Stefania Orrù, Daniela Pagnozzi, Piero Pucci
2005 Clinica Chimica Acta  
Results and conclusions: The association of an unknown protein with partners belonging to a specific protein complex involved in a particular mechanism is strongly suggestive of the biological function  ...  The next goal will be to generate animal models bearing a tagged form of the bait protein.  ...  Acknowledgement This work was supported, in part, by MIUR (PRIN 2003).  ... 
doi:10.1016/j.cccn.2005.03.019 pmid:15946657 fatcat:fnopi6kqlff55pz7etu4xfeonm

TheTetrahymena thermophilaPhagosome Proteome

Mary Ellen Jacobs, Leroi V. DeSouza, Haresha Samaranayake, Ronald E. Pearlman, K. W. Michael Siu, Lawrence A. Klobutcher
2006 Eukaryotic Cell  
Live-cell confocal fluorescence imaging ofTetrahymenastrains expressing green fluorescent protein-tagged versions of four of the identified phagosome proteins provided evidence that at least three of the  ...  In vertebrates, phagocytosis occurs mainly in specialized cells of the immune system and serves as a primary defense against invading pathogens, but it also plays a role in clearing apoptotic cells and  ...  David Allis for providing cell lines and antibodies, Susan Krueger and Ann Cowan for assistance with microscopy, and Jacek Gaertig for providing GFP vectors.  ... 
doi:10.1128/ec.00195-06 pmid:17012537 pmcid:PMC1694822 fatcat:qsm5kv27vbckpcx5no7orfywgy

Proteomics reveals the importance of the dynamic redistribution of the subcellular location of proteins in breast cancer cells

Gabriella Pinto, Abdulrab Ahmed M Alhaiek, Jasminka Godovac-Zimmermann
2015 Espert Review of Proteomics  
Particularly notable have been several studies of expression levels and subcellular localization of endogenous proteins in HeLa cells [52,53] and viral infections [54].  ...  Similarly, subcellular translocation of 4-5% of cellular proteins was observed in a genomewide, fluorescence based study of the response of yeast cells to hypoxia [39] .For MCF7 breast cancer cells, a  ... 
doi:10.1586/14789450.2015.1002474 pmid:25591448 fatcat:4uons5ut45b6jc6frnz76fx6eu

A Proximity Labeling Strategy Provides Insights into the Composition and Dynamics of Lipid Droplet Proteomes

Kirill Bersuker, Clark W.H. Peterson, Milton To, Steffen J. Sahl, Victoria Savikhin, Elizabeth A. Grossman, Daniel K. Nomura, James A. Olzmann
2018 Developmental Cell  
Moreover, quantitative analysis of LD proteome dynamics uncovered a role for endoplasmic reticulumassociated degradation in controlling the composition of the LD proteome.  ...  To overcome this limitation, we developed a proximity labeling strategy that exploits LD-targeted APEX2 to biotinylate LD proteins in living cells.  ...  Acknowledgments We thank members of the Olzmann lab for useful discussions and Dr. Camille Pataki for critical reading of the manuscript.  ... 
doi:10.1016/j.devcel.2017.11.020 pmid:29275994 pmcid:PMC5764092 fatcat:gkk4mga6gnc6pezrf4gmam5q7u

The subcellular localization of the mammalian proteome comes a fraction closer

Jeremy C Simpson, Rainer Pepperkok
2006 Genome Biology  
Here we discuss this new work in the context of other strategies for large-scale subcellular localization.  ...  has been taken with a study using cellular fractionation and protein correlation profiling to identify and localize organellar proteins.  ...  Acknowledgements We would like to acknowledge funding by the Federal Ministry of Education and Research (BMBF) in the framework of the National Genome Research Network (NGFN-2 SMP-Cell FKZ01GR0423).  ... 
doi:10.1186/gb-2006-7-6-222 pmid:16938898 pmcid:PMC1779544 fatcat:t4i2hcer6nacnliuwqgtwm7ytu
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