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  • 1
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    Biochemical basis of oxidative protein folding in the endoplasmic reticulum (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-11-25
    Description: The endoplasmic reticulum (ER) supports disulfide bond formation by a poorly understood mechanism requiring protein disulfide isomerase (PDI) and ERO1. In yeast, Ero1p-mediated oxidative folding was shown to depend on cellular flavin adenine dinucleotide (FAD) levels but not on ubiquinone or heme, and Ero1p was shown to be a FAD-binding protein. We reconstituted efficient oxidative folding in vitro using FAD, PDI, and Ero1p. Disulfide formation proceeded by direct delivery of oxidizing equivalents from Ero1p to folding substrates via PDI. This kinetic shuttling of oxidizing equivalents could allow the ER to support rapid disulfide formation while maintaining the ability to reduce and rearrange incorrect disulfide bonds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tu, B P -- Ho-Schleyer, S C -- Travers, K J -- Weissman, J S -- New York, N.Y. -- Science. 2000 Nov 24;290(5496):1571-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11090354" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carboxypeptidases/chemistry/metabolism ; Cathepsin A ; Chemistry, Physical ; Disulfides/chemistry ; Endoplasmic Reticulum/*metabolism ; Flavin-Adenine Dinucleotide/*metabolism ; Glutathione/metabolism ; Glycoproteins/*metabolism ; Microsomes/metabolism ; Mutation ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors ; Physicochemical Phenomena ; Protein Disulfide-Isomerases/genetics/*metabolism ; *Protein Folding ; Ribonuclease, Pancreatic/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; *Saccharomyces cerevisiae Proteins
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Evidence for the prion hypothesis: induction of the yeast [PSI+] factor by in vitro- converted Sup35 protein (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-08-01
    Description: Starting with purified, bacterially produced protein, we have created a [PSI(+)]-inducing agent based on an altered (prion) conformation of the yeast Sup35 protein. After converting Sup35p to its prion conformation in vitro, we introduced it into the cytoplasm of living yeast using a liposome transformation protocol. Introduction of substoichiometric quantities of converted Sup35p greatly increased the rate of appearance of the well-characterized epigenetic factor [PSI+], which results from self-propagating aggregates of cellular Sup35p. Thus, as predicted by the prion hypothesis, proteins can act as infectious agents by causing self-propagating conformational changes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sparrer, H E -- Santoso, A -- Szoka, F C Jr -- Weissman, J S -- New York, N.Y. -- Science. 2000 Jul 28;289(5479):595-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143-0450, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10915616" target="_blank"〉PubMed〈/a〉
    Keywords: Biopolymers ; Culture Media ; Cytoplasm/chemistry ; Fungal Proteins/*chemistry/genetics/physiology ; Liposomes ; Microscopy, Fluorescence ; Mutation ; Peptide Termination Factors ; Phenotype ; Plasmids ; Prions/*chemistry/genetics/physiology ; Protein Biosynthesis ; Protein Conformation ; Saccharomyces cerevisiae/*chemistry/genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Orm family proteins mediate sphingolipid homeostasis (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-02-26
    Description: Despite the essential roles of sphingolipids both as structural components of membranes and critical signalling molecules, we have a limited understanding of how cells sense and regulate their levels. Here we reveal the function in sphingolipid metabolism of the ORM genes (known as ORMDL genes in humans)-a conserved gene family that includes ORMDL3, which has recently been identified as a potential risk factor for childhood asthma. Starting from an unbiased functional genomic approach in Saccharomyces cerevisiae, we identify Orm proteins as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. We also define a regulatory pathway in which phosphorylation of Orm proteins relieves their inhibitory activity when sphingolipid production is disrupted. Changes in ORM gene expression or mutations to their phosphorylation sites cause dysregulation of sphingolipid metabolism. Our work identifies the Orm proteins as critical mediators of sphingolipid homeostasis and raises the possibility that sphingolipid misregulation contributes to the development of childhood asthma.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877384/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877384/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breslow, David K -- Collins, Sean R -- Bodenmiller, Bernd -- Aebersold, Ruedi -- Simons, Kai -- Shevchenko, Andrej -- Ejsing, Christer S -- Weissman, Jonathan S -- N01-HV-28179/HV/NHLBI NIH HHS/ -- P50 GM073210/GM/NIGMS NIH HHS/ -- P50 GM073210-06/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Feb 25;463(7284):1048-53. doi: 10.1038/nature08787.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California, San Francisco, 1700 4th Street, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20182505" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Asthma/metabolism ; Cell Line ; Conserved Sequence ; Fatty Acids, Monounsaturated/pharmacology ; HeLa Cells ; *Homeostasis ; Humans ; Molecular Sequence Data ; *Multigene Family ; Multiprotein Complexes/chemistry/metabolism ; Phosphoric Monoester Hydrolases/genetics/metabolism ; Phosphorylation ; Protein Binding ; Saccharomyces cerevisiae/drug effects/enzymology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/classification/genetics/*metabolism ; Serine C-Palmitoyltransferase/genetics/metabolism ; Sphingolipids/biosynthesis/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Systems biology: Reverse engineering the cell (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-08-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ingolia, Nicholas T -- Weissman, Jonathan S -- England -- Nature. 2008 Aug 28;454(7208):1059-62. doi: 10.1038/4541059a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18756243" target="_blank"〉PubMed〈/a〉
    Keywords: *Environment ; Galactose/metabolism ; *Gene Expression Regulation, Fungal/drug effects ; Glucose/metabolism/pharmacology ; Metabolic Networks and Pathways/drug effects/*genetics ; Microfluidics ; Models, Biological ; Osmotic Pressure ; RNA Stability/drug effects ; Saccharomyces cerevisiae/classification/drug effects/*genetics/*metabolism ; Systems Biology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Reexamination of the folding of BPTI: predominance of native intermediates (1991)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1991-09-20
    Description: Bovine pancreatic trypsin inhibitor (BPTI) continues to be the only protein for which a detailed pathway of folding has been described. Previous studies led to the conclusion that nonnative states are well populated in the oxidative folding of BPTI. This conclusion has broadly influenced efforts to understand protein folding. The population of intermediates present during the folding of BPTI has been reexamined by modern separation techniques. It was found that all well-populated folding intermediates contain only native disulfide bonds. These data emphasize the importance of native protein structure for understanding protein folding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weissman, J S -- Kim, P S -- GM 41307/GM/NIGMS NIH HHS/ -- RR 05927/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1991 Sep 20;253(5026):1386-93.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, MA 02142.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1716783" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aprotinin/*chemistry ; Chromatography, High Pressure Liquid ; Disulfides/analysis ; Indicators and Reagents ; Models, Structural ; Molecular Sequence Data ; Peptide Fragments/isolation & purification ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Response (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weissman, J S -- Kim, P S -- New York, N.Y. -- Science. 1992 Apr 3;256(5053):112-4.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17802598" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-02-14
    Description: Techniques for systematically monitoring protein translation have lagged far behind methods for measuring messenger RNA (mRNA) levels. Here, we present a ribosome-profiling strategy that is based on the deep sequencing of ribosome-protected mRNA fragments and enables genome-wide investigation of translation with subcodon resolution. We used this technique to monitor translation in budding yeast under both rich and starvation conditions. These studies defined the protein sequences being translated and found extensive translational control in both determining absolute protein abundance and responding to environmental stress. We also observed distinct phases during translation that involve a large decrease in ribosome density going from early to late peptide elongation as well as widespread regulated initiation at non-adenine-uracil-guanine (AUG) codons. Ribosome profiling is readily adaptable to other organisms, making high-precision investigation of protein translation experimentally accessible.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746483/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746483/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ingolia, Nicholas T -- Ghaemmaghami, Sina -- Newman, John R S -- Weissman, Jonathan S -- AG10770/AG/NIA NIH HHS/ -- GM080853/GM/NIGMS NIH HHS/ -- P01 AG010770/AG/NIA NIH HHS/ -- P01 AG010770-16/AG/NIA NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Apr 10;324(5924):218-23. doi: 10.1126/science.1168978. Epub 2009 Feb 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, and California Institute for Quantitative Biosciences, San Francisco, CA 94158, USA. ingolia@cmp.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19213877" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; *Codon ; Gene Library ; *Genome, Fungal ; Introns ; Peptide Chain Elongation, Translational ; Peptide Chain Initiation, Translational ; *Protein Biosynthesis ; RNA, Fungal/*genetics/metabolism ; RNA, Messenger/*genetics/metabolism ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/*genetics/metabolism/physiology ; Saccharomyces cerevisiae Proteins/*biosynthesis ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Road to ruin: targeting proteins for degradation in the endoplasmic reticulum (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-11-26
    Description: Some nascent proteins that fold within the endoplasmic reticulum (ER) never reach their native state. Misfolded proteins are removed from the folding machinery, dislocated from the ER into the cytosol, and degraded in a series of pathways collectively referred to as ER-associated degradation (ERAD). Distinct ERAD pathways centered on different E3 ubiquitin ligases survey the range of potential substrates. We now know many of the components of the ERAD machinery and pathways used to detect substrates and target them for degradation. Much less is known about the features used to identify terminally misfolded conformations and the broader role of these pathways in regulating protein half-lives.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864754/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864754/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Melanie H -- Ploegh, Hidde L -- Weissman, Jonathan S -- T32 GM007618/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Nov 25;334(6059):1086-90. doi: 10.1126/science.1209235.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Graduate Group in Biophysics and Howard Hughes Medical Institute, University of California-San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22116878" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Endoplasmic Reticulum/*metabolism ; *Endoplasmic Reticulum-Associated Degradation ; Humans ; Protein Transport ; Proteins/*metabolism ; Ubiquitin-Protein Ligases/*metabolism ; Yeasts/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Decoding human cytomegalovirus (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-11-28
    Description: The human cytomegalovirus (HCMV) genome was sequenced 20 years ago. However, like those of other complex viruses, our understanding of its protein coding potential is far from complete. We used ribosome profiling and transcript analysis to experimentally define the HCMV translation products and follow their temporal expression. We identified hundreds of previously unidentified open reading frames and confirmed a fraction by means of mass spectrometry. We found that regulated use of alternative transcript start sites plays a broad role in enabling tight temporal control of HCMV protein expression and allowing multiple distinct polypeptides to be generated from a single genomic locus. Our results reveal an unanticipated complexity to the HCMV coding capacity and illustrate the role of regulated changes in transcript start sites in generating this complexity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817102/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817102/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stern-Ginossar, Noam -- Weisburd, Ben -- Michalski, Annette -- Le, Vu Thuy Khanh -- Hein, Marco Y -- Huang, Sheng-Xiong -- Ma, Ming -- Shen, Ben -- Qian, Shu-Bing -- Hengel, Hartmut -- Mann, Matthias -- Ingolia, Nicholas T -- Weissman, Jonathan S -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2012 Nov 23;338(6110):1088-93. doi: 10.1126/science.1227919.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisico, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23180859" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Cytomegalovirus/*genetics ; Cytomegalovirus Infections/*virology ; Genetic Variation ; *Genome, Viral ; Humans ; *Open Reading Frames ; Protein Biosynthesis/genetics ; Proteome/genetics ; Sequence Analysis, DNA ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-11-08
    Description: Nearly all mitochondrial proteins are nuclear-encoded and are targeted to their mitochondrial destination from the cytosol. Here, we used proximity-specific ribosome profiling to comprehensively measure translation at the mitochondrial surface in yeast. Most inner-membrane proteins were cotranslationally targeted to mitochondria, reminiscent of proteins entering the endoplasmic reticulum (ER). Comparison between mitochondrial and ER localization demonstrated that the vast majority of proteins were targeted to a specific organelle. A prominent exception was the fumarate reductase Osm1, known to reside in mitochondria. We identified a conserved ER isoform of Osm1, which contributes to the oxidative protein-folding capacity of the organelle. This dual localization was enabled by alternative translation initiation sites encoding distinct targeting signals. These findings highlight the exquisite in vivo specificity of organellar targeting mechanisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263316/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263316/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Williams, Christopher C -- Jan, Calvin H -- Weissman, Jonathan S -- P50 GM102706/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2014 Nov 7;346(6210):748-51. doi: 10.1126/science.1257522.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉These authors contributed equally to this work. ; Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, California Institute for Quantitative Biosciences, Center for RNA Systems Biology, University of California, San Francisco, San Francisco, CA 94158, USA. These authors contributed equally to this work. jonathan.weissman@ucsf.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25378625" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Endoplasmic Reticulum/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/biosynthesis/chemistry/*metabolism ; *Peptide Chain Initiation, Translational ; Protein Folding ; Ribosomes/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Succinate Dehydrogenase/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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