Escherichia phage T7
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA174292 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:A Fundamental Protein Property, Thermodynamic Stability, Revealed Solely From Large-Scale Measurements of Protein Function
| PRJNA175232 | ENA
Project description:Described here is the application of thermodynamic stability measurements to study age-related differences in the protein folding and stability of proteins in a rodent model of ageing. Using the Stability of Proteins from Rates of Oxidation (SPROX) technique the thermodynamic stability profiles were generated for 807 proteins in brain cell lystaes from mice, aged 6- (n=7) and 18-months (n=9). The biological variability of the protein stability measurements was low and within the experimental error of SPROX. A total of 83 protein hits were detected with age-related stability differences in the brain samples. Remarkably, the large majority of the brain protein hits were destabilized in the old mice, and the hits were enriched in proteins that have slow turnover rates (p <0.07). Furthermore, 70% of the hits have been previously linked to ageing or age-related diseases. These results help validate the use of thermodynamic stability measurements to capture relevant age-related proteomic changes, and they establish a new biophysical link between these proteins and ageing.
2016-12-22 | PXD005184 | Pride
Project description:Protein biomarkers can be used to characterize and diagnose disease states such as cancer. They can also serve as therapeutic targets. Current methods for protein biomarker discovery, which generally rely on the large-scale analysis of gene and/or protein expression levels, fail to detect protein biomarkers with disease-related functions and unaltered expression levels. Here we describe the large-scale use of thermodynamic measurements of protein folding and stability for disease state characterization and the discovery of protein biomarkers. Using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique, we assayed ~800 proteins for protein folding and stability changes in three different cell culture models of breast cancer including the MCF-10A, MCF-7, and MDA-MB-231 cell lines. The thermodynamic stability profiles generated here created distinct molecular markers for the three cell lines, and a significant fraction (~45%) of the differentially stabilized proteins did not have altered expression levels. Thus, the protein biomarkers reported here created novel molecular signatures of breast cancer and provided additional insight into the molecular basis of the disease. Our results establish the utility of protein folding and stability measurements for the study of disease processes.
2017-03-29 | MSV000080760 | MassIVE
Project description:Protein biomarkers can be used to characterize and diagnose disease states such as cancer. They can also serve as therapeutic targets. Current methods for protein biomarker discovery, which generally rely on the large-scale analysis of gene and/or protein expression levels, fail to detect protein biomarkers with disease-related functions and unaltered expression levels. Here we describe the large-scale use of thermodynamic measurements of protein folding and stability for disease state characterization and the discovery of protein biomarkers. Using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique, we assayed ~800 proteins for protein folding and stability changes in three different cell culture models of breast cancer including the MCF-10A, MCF-7, and MDA-MB-231 cell lines. The thermodynamic stability profiles generated here created distinct molecular markers for the three cell lines, and a significant fraction (~45%) of the differentially stabilized proteins did not have altered expression levels. Thus, the protein biomarkers reported here created novel molecular signatures of breast cancer and provided additional insight into the molecular basis of the disease. Our results establish the utility of protein folding and stability measurements for the study of disease processes.
2017-03-29 | MSV000080761 | MassIVE
Project description:Protein biomarkers can be used to characterize and diagnose disease states such as cancer. They can also serve as therapeutic targets. Current methods for protein biomarker discovery, which generally rely on the large-scale analysis of gene and/or protein expression levels, fail to detect protein biomarkers with disease-related functions and unaltered expression levels. Here we describe the large-scale use of thermodynamic measurements of protein folding and stability for disease state characterization and the discovery of protein biomarkers. Using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique, we assayed ~800 proteins for protein folding and stability changes in three different cell culture models of breast cancer including the MCF-10A, MCF-7, and MDA-MB-231 cell lines. The thermodynamic stability profiles generated here created distinct molecular markers for the three cell lines, and a significant fraction (~45%) of the differentially stabilized proteins did not have altered expression levels. Thus, the protein biomarkers reported here created novel molecular signatures of breast cancer and provided additional insight into the molecular basis of the disease. Our results establish the utility of protein folding and stability measurements for the study of disease processes.
2015-04-10 | PXD001848 | Pride
Project description:Protein biomarkers can be used to characterize and diagnose disease states such as cancer. They can also serve as therapeutic targets. Current methods for protein biomarker discovery, which generally rely on the large-scale analysis of gene and/or protein expression levels, fail to detect protein biomarkers with disease-related functions and unaltered expression levels. Here we describe the large-scale use of thermodynamic measurements of protein folding and stability for disease state characterization and the discovery of protein biomarkers. Using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique, we assayed ~800 proteins for protein folding and stability changes in three different cell culture models of breast cancer including the MCF-10A, MCF-7, and MDA-MB-231 cell lines. The thermodynamic stability profiles generated here created distinct molecular markers for the three cell lines, and a significant fraction (~45%) of the differentially stabilized proteins did not have altered expression levels. Thus, the protein biomarkers reported here created novel molecular signatures of breast cancer and provided additional insight into the molecular basis of the disease. Our results establish the utility of protein folding and stability measurements for the study of disease processes.
2015-04-10 | PXD001847 | Pride
Project description:Most natural proteins fold into a native conformation stabilized by non-covalent interactions. The energy difference between native and denatured states (Gfolding) is highly variable between proteins and can range from less than -10 kcal per mole for highly stable proteins to positive values for intrinsically disordered proteins. Folding stability is a dynamic property of proteins and can be modulated by molecular chaperones and binding interactions. The stability of a protein influences its tendency to aggregate, degrade or become covalently modified in cells. Despite its significance to understanding protein folding and function, quantitative analyses of thermodynamic stability have been mostly limited to small soluble proteins in purified systems. Here, we have used a highly multiplexed bottom-up proteomics approach, based on analyses of rates of methionine oxidation, to quantify the thermodynamic stabilities of the human proteome in crude extracts obtained from dermal fibroblasts. Our data provide structural and stability information for more than 10,000 unique regions and domains within more than 3,200 proteins. The data identifies lysosomal and extracellular proteins as the most stable ontological subsets of the proteome. We show that the stability of proteins can impact their tendency to become oxidized and are globally altered by the osmolyte trimethylamine-N-oxide (TMAO). We also show that most proteins designated as IDPs retain their unfolded structure in the complex milieu of the cell and most cannot be refolded by TMAO. Together, the data provide a census of the stability of the human proteome and validate a methodology for global analysis of protein thermodynamic stabilities.
2018-11-21 | PXD011456 | Pride
Project description:Escherichia phage T7 strain:T7 Genome sequencing and assembly
| PRJNA733815 | ENA
Project description:Enterobacteria phage T7 expanded genetic code evolution
| PRJNA198202 | ENA
Project description:Bacteriophage T7 Genome Sequencing of Mutated Genomes
| PRJNA187454 | ENA