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Bennett K.L.,Austrian Academy of Sciences | Wang X.,University of Cincinnati | Bystrom C.E.,Cleveland HeartLab | Chambers M.C.,Vanderbilt University | And 11 more authors.
Molecular and Cellular Proteomics | Year: 2015

Questions concerning longitudinal data quality and reproducibility of proteomic laboratories spurred the Protein Research Group of the Association of Biomolecular Resource Facilities (ABRF-PRG) to design a study to systematically assess the reproducibility of proteomic laboratories over an extended period of time. Developed as an open study, initially 64 participants were recruited from the broader mass spectrometry community to analyze provided aliquots of a six bovine protein tryptic digest mixture every month for a period of nine months. Data were uploaded to a central repository, and the operators answered an accompanying survey. Ultimately, 45 laboratories submitted a minimum of eight LC-MSMS raw data files collected in data-dependent acquisition (DDA) mode. No standard operating procedures were enforced; rather the participants were encouraged to analyze the samples according to usual practices in the laboratory. Unlike previous studies, this investigation was not designed to compare laboratories or instrument configuration, but rather to assess the temporal intralaboratory reproducibility. The outcome of the study was reassuring with 80% of the participating laboratories performing analyses at a medium to high level of reproducibility and quality over the 9-month period. For the groups that had one or more outlying experiments, the major contributing factor that correlated to the survey data was the performance of preventative maintenance prior to the LC-MSMS analyses. Thus, the Protein Research Group of the Association of Biomolecular Resource Facilities recommends that laboratories closely scrutinize the quality control data following such events. Additionally, improved quality control recording is imperative. This longitudinal study provides evidence that mass spectrometry-based proteomics is reproducible. When quality control measures are strictly adhered to such reproducibility is comparable among many disparate groups. Data from the study are available via ProteomeXchange under the accession code PXD002114. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc. Source


Kenoth R.,University of Minnesota | Simanshu D.K.,Sloan Kettering Cancer Center | Kamlekar R.K.,University of Minnesota | Pike H.M.,University of Minnesota | And 8 more authors.
Journal of Biological Chemistry | Year: 2010

HET-C2 is a fungal protein that transfers glycosphingolipids between membranes and has limited sequence homology with human glycolipid transfer protein (GLTP). The human GLTP fold is unique among lipid binding/transfer proteins, defining the GLTP superfamily. Herein, GLTP fold formation by HET-C2, its glycolipid transfer specificity, and the functional role(s) of its two Trp residues have been investigated. X-ray diffraction (1.9 Å) revealed a GLTP fold with all key sugar headgroup recognition residues (Asp66, Asn70, Lys73, Trp109, and His147) conserved and properly oriented for glycolipid binding. Far-UV CD showed secondary structure dominated by α-helices and a cooperative thermal unfolding transition of 49°C, features consistent with a GLTP fold. Environmentally induced optical activity of Trp/Tyr/Phe (2:4:12) detected by near-UVCDwas unaffected by membranes containing glycolipid but was slightly altered by membranes lacking glycolipid. Trp fluorescence was maximal at ∼355 nm and accessible to aqueous quenchers, indicating free exposure to the aqueous milieu and consistent with surface localization of the two Trps. Interaction with membranes lacking glycolipid triggered significant decreases in Trp emission intensity but lesser than decreases induced by membranes containing glycolipid. Binding of glycolipid (confirmed by electrospray injection mass spectrometry) resulted in a blue-shifted emission wavelength maximum (∼6 nm) permitting determination of binding affinities. The unique positioning of Trp208 at the HET-C2 C terminus revealed membrane-induced conformational changes that precede glycolipid uptake, whereas key differences in residues of the sugar headgroup recognition center accounted for altered glycolipid specificity and suggested evolutionary adaptation for the simpler glycosphingolipid compositions of filamentous fungi. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc. Source


Aguilera J.R.,Pablo De Olavide University | Venegas V.,Pablo De Olavide University | Venegas V.,Research Center Cooperativa en Biociencias | Oliva J.M.,Pablo De Olavide University | And 6 more authors.
RSC Advances | Year: 2016

Tannic acid (TA) has multiple effects against cancer, being especially promising in those types that overexpress the epidermal growth factor receptor (EGFR), as TA modulates its activation and downstream signaling pathways, triggering apoptosis. Nonetheless, despite the important role of this receptor in the pathogenesis and progression of a wide variety of tumors, no TA systems targeted to this receptor have been described yet. In this work, we synthesize, characterize by physico-chemical techniques and study the cytotoxic effect and cell uptake of TA nanoparticles targeted to EGFR in both tumoral and normal human skin cells. Our nanoparticles exhibited an extremely high entrapment efficiency, and were only toxic for the tumoral cells. The uptake assay demonstrated that nanoparticles are able to enter the cells through a receptor-mediated mechanism. Furthermore, we have included fluorescent markers in these nanoparticles to combine imaging and therapeutic applications, thus building effectively a multifunctional tool for biomedicine. © The Royal Society of Chemistry 2016. Source


Fortian A.,Research Center Cooperativa en Biociencias | Gonzalez E.,Research Center Cooperativa en Biociencias | Castano D.,Research Center Cooperativa en Biociencias | Falcon-Perez J.M.,Research Center Cooperativa en Biociencias | Millet O.,Research Center Cooperativa en Biociencias
Journal of Biological Chemistry | Year: 2011

A single mutation (C73R) in the enzyme uroporphyrinogen III synthase (UROIIIS) is responsible for more than one-third of all of the reported cases of the rare autosomal disease congenital erythropoietic porphyria (CEP). CEP patients carrying this hotspot mutation develop a severe phenotype of the disease, including reduced life expectancy. Here, we have investigated the molecular basis for the functional deficit in the mutant enzyme both in vitro and in cellular systems. We show that a Cys in position 73 is not essential for the catalytic activity of the enzyme but its mutation to Arg speeds up the process of irreversible unfolding and aggregation. In the mammalian cell milieu, the mutant protein levels decrease to below the detection limit, whereas wild type UROIIIS can be detected easily. The disparate response is not produced by differences at the level of transcription, and the results with cultured cells and in vitro are consistent with a model where the protein becomes very unstable upon mutation and triggers a degradation mechanism via the proteasome. Mutant protein levels can be restored upon cell treatment with the proteasome inhibitor MG132. The intracellularly recovered C73R-UROIIIS protein shows enzymatic activity, paving the way for a new line of therapeutic intervention in CEP patients. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc. Source

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