Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics as a Tool to Gain Next Level Insights into Biopolymer Modifications

ABSTRACT: The distribution of introduced photo-crosslinkable moieties onto a protein can affect a biomaterial’s crosslinking behavior, and therefore also the mechanical and biological properties. However, this information is also vital when developing biomaterials for tissue engineering and regenerative medicine applications. In the present work, photo-crosslinkable moieties have been introduced on the primary amine groups of: (i) a recombinant collagen peptide (RCPhC1) with a known amino acid (AA) sequence, and (ii) bovine skin collagen (COL BS) with an unknown AA sequence. The degree of substitution (DS) was quantified with two standard techniques: an ortho-phthalic dialdehyde (OPA) assay and 1H-NMR spectroscopy. However, neither of both provides information on the type and exact location of the modified AAs. Therefore, for the first time, proteomic analysis was evaluated herein as a tool to identify functionalized AAs as well as the exact position of the photo-crosslinkable moieties along the AA sequence, thereby enabling an in-depth, unprecedented characterization of functionalized biopolymers. Moreover, our strategy also enabled to visualize the spatial distribution of the modifications within the overall structure of the protein. Proteomics has proven to provide unprecedented insight in the distribution of photo-crosslinkable moieties along the protein backbone, undoubtedly contributing to superior biomaterial design in the future.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Bos Taurus (bovine)

SUBMITTER: BRAY FABRICE

LAB HEAD: Ahmed Mazzah

PROVIDER: PXD024622 | Pride | 2022-04-26

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	COL-BS_1_SDS.msf	Msf
	COL-BS_2_SDS.msf	Msf
	COL-BS_3_SDS.msf	Msf
	COL-BS_4_SDS.msf	Msf
	COL-MA-05EQ-1_SDS.msf	Msf

Items per page:

1 - 5 of 71

Similar Datasets

PALEOPROTEOMICS APPLIED TO THE WAZIERS SITE

Project description:The ancient preserved molecules in bones offer the opportunity to gain a better knowledge on the biological past. In recent years, bones proteomics has become an attractive method to study extinct species and phylogenetic evolution as an alternative to DNA analysis which is limited by DNA amplification present in ancient samples and its contamination. The analysis of fossils must consume a low quantity of material to avoid damaging the samples. Another difficulty is the absence of genomic data for most of the extinct species. This study applied a proteomic methodology to mammalian bones of 130,000 / 120,000 years old from the last Chibanian and the earlier Upper Pleistocene site of Waziers (France). The presence of lithic artefacts and the traces of butchery observed on the bones indicate the presence of Neanderthal Man on this site. Starting from 5 milligram samples, our results show that most detected peptides match collagen I alpha 1 and alpha 2 proteins with a sequence coverage up to 60 %. Using sequence homology with modern sequences, a biological classification was successfully achieved. Each bone taxonomic rank by proteomics was consistent with the existing osteomorphological studies and palaeoenvironmental and palaeodietary data.

2023-04-20 | PXD039657 | Pride

Differential Gene Expression between African American and European American Colorectal Cancer Patients

Project description:The incidence and mortality of colorectal cancer (CRC) is higher in African Americans (AAs) than in other ethnic groups in the U. S., but reasons for the disparities are unknown. We performed gene expression profiling and microsatellite instability (MSI) analysis of sporadic CRCs from AAs vs. European Americans (EAs) to assess the contribution to CRC disparities. We evaluated gene expression of 43 AA and 43 EA CRC tumors matched by stage and 40 normal colon tissues using the Agilent human whole genome 4x44K cDNA arrays. Gene and pathway analysis were performed using Significance Analysis of Microarrays (SAM), 10-fold Cross Validation (10-fCV) and Ingenuity Pathway Analysis (IPA). MSI analysis was assessed with five NIH Bethesda markers. SAM revealed that 95 genes were differentially expressed between AA and EA patients at a false discovery rate of <5%. A 10f-CV demonstrated that 9 genes were differentially expressed between AA and EA with an accuracy of 97%. Nine genes (CRYBB2, PSPH, ADAL, VSIG10L, C17orf81, ARSE, ANKRD36B, ZNF835, ARHGAP6) were validated and differential expression confirmed by qRT-PCR in independent test set of 21 patients (10 AA, 11 EA). We also analyzed MSI in 57 of the CRC subjects. Overall, 15.8% of CRC patients had MSI, with a higher rate observed in EA (20%) than in AA (12%). MSI distribution by tumor site was 77% right and 23% left colon. Previously, genetic, epigenetic and environmental factors have been implicated in the etiology of CRC. Our results are the first to implicate differential gene expression in CRC disparities and support the existence of distinct tumor microenvironments in these two patients' populations. 126 total samples: 1) 43 white cancer samples; 2) 43 black cancer samples; 3) 27 white control samples; 4) 13 black control samples.

2012-05-22 | E-GEOD-28000 | biostudies-arrayexpress

Differential Gene Expression between African American and European American Colorectal Cancer Patients

2012-05-23 | GSE28000 | GEO

Valine-restricted diet regulates DNA methylation [TET2 ChIP-Seq]

Project description:The abundancy of intracellular amino acid (AA) levels is precisely sensed by complex machineries to regulate various signaling pathways and control cell functions. Insufficient intracellular AAs may block the release of tRNA molecules from the general control non-derepressible 2 (GCN2), and consequently activate GCN2-ATF4 pathways, which is an indirect mechanism for sensing general AAs levels. Additionally, the intracellular levels of some AAs can be sensed by direct binding to specific sensors. Nowadays, the sensors of arginine and leucine levels are most well-characterized, including CASTor1/2, SLC38A9, Sestrin2 and SAR1B, which regulate the mechanistic target of rapamycin complex 1 (mTORC1) pathway, and couple AA availability to cell growth and metabolism. However, it is still unclear whether and how other types of amino acids are directly sensed to regulate cellular functions except tRNA synthetases. Moreover, epigenetics is known to be regulated by the metabolism of amino acids, but it is incompletely understood how AA abundancy regulates the epigenetics, especially DNA methylation. The long-sought sensor of amino acids for epigenetic regulation has thus far been unknown. Here, we present evidence that valine sensor regulated DNA demethylation.

2024-09-23 | GSE274881 | GEO