Sort   by:  
 Page size 
GenomicsLigand-dependent dynamics of retinoic acid receptor binding during early neurogenesis
Among its many roles in development, retinoic acid determines the anterior-posterior identity of differentiating motor neurons by activating Retinoic Acid Receptor (RAR)-mediated transcription. RAR is thought to bind the genome constitutively, and only induce transcription in the presence of the ret...
ORGANISM(S): Mus musculus 
2010-12-10 | E-GEOD-19409 | biostudies-arrayexpress
MetabolomicsIntegrating two chromatographies in a co-fractionation mass spectrometry approach improved protein-metabolite interactions (PMIs) mapping capabilities and revealed novel protein-ligand pairings in Escherichia coli.
The protein-metabolite interactome remains understudied. We previously developed a co-fractionation mass-spectrometry-based approach called PROMIS to address this gap. PROMIS relies on size separation chromatography of protein-metabolite complexes from lysates, followed by proteomics and metabolomic...
2025-04-25 | MTBLS9098 | MetaboLights
MetabolomicsAntioxidant Activity, Phytochemical Profiling by UPLC-QTOF-MS, and In Silico Targeting of the RNA-Binding Protein DRBD18 of Trypanosoma brucei by Bioactive Compounds from Tetradenia riparia and Tetracera poggei
Oxidative stress plays a key role in the pathogenesis of African trypanosomiasis, and plant-derived antioxidants represent a promising source of dual-action compounds capable of both scavenging reactive oxygen species and interfering with parasite survival. The present study investigates the antioxi...
2026-09-10 | MTBLS15597 | MetaboLights
MetabolomicsPomegranate Peel Extract as an Inhibitor of SARS-CoV-2 Spike Binding to Human ACE2 Receptor (in vitro): A Promising Source of Novel Antiviral Drugs
Plant extracts are rich in bioactive compounds, such as polyphenols, sesquiterpenes, and triterpenes, which potentially have antiviral activities. As a consequence of the coronavirus disease 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus, thousands of...
2021-10-06 | MTBLS2309 | MetaboLights
ProteomicsLigand binding and conformational dynamics of the E. coli nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry
Nicotinamide nucleotide transhydrogenases are integral membrane proteins that utilizes the proton motive force to reduce NADP+ to NADPH while converting NADH to NAD+. Atomic structures of various transhydrogenases in different ligand-bound states have become available, and it is clear that the molec...
ORGANISM(S): Escherichia coli 
2022-10-26 | PXD037413 | Pride
Channel opening Membrane protein Small ligand binding Hdx-ms Cyclic ims‑ms 
TranscriptomicsLigand-Dependent Enhancer Activation Regulated by Topoisomerase-I Activity
The discovery that enhancers are regulated transcription units, encoding eRNAs, has raised new questions about the mechanisms of their activation. Here, we report an unexpected molecular mechanism that underlies ligand-dependent enhancer activation, based on DNA nicking to relieve torsional stress f...
ORGANISM(S): Homo sapiens 
2015-01-22 | E-GEOD-63202 | biostudies-arrayexpress
TranscriptomicsMolecular mechanism of DNA minor groove binding ligand as a radiation modulator
Radiation-induced DNA damage initiates a complex series of overlapping responses responsible for the maintenance of genome integrity. This study reports the expression analysis in response to DNA minor groove binding ligand (DMA-5-(4-methylpiperazin-1-yl)-2-[2’-(3,4-dimethoxyphenyl)-5`-benzimidazoly...
ORGANISM(S): Homo sapiens 
2011-07-31 | E-GEOD-30044 | biostudies-arrayexpress
ProteomicsSILAC-Based Strategy for Proteome-Wide Analysis of Protein-Ligand Binding Interactions (Part 1/2)
A quantitative mass spectrometry-based proteomics method for the large-scale thermodynamic analysis of protein-ligand binding interactions is described here. The methodology utilizes a chemical modification strategy termed, Stability of Proteins from Rates of Oxidation (SPROX), in combination with ...
ORGANISM(S): Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 
2014-07-31 | PXD000858 | Pride
Shot-gun proteomics Yeast Cyclosporine a Atp 
ProteomicsSILAC-Based Strategy for Proteome-Wide Analysis of Protein-Ligand Binding Interactions (Part 2/2)
A quantitative mass spectrometry-based proteomics method for the large-scale thermodynamic analysis of protein-ligand binding interactions. The methodology utilizes a chemical modification strategy termed, Stability of Proteins from Rates of Oxidation (SPROX), in combination with a Stable Isotope L...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2014-07-31 | PXD000860 | Pride
Shot-gun proteomics Yeast Cyclosporine a Atp 
ProteomicsLigand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations
We have studied both the Spy and the FKBP protein-ligand systems by structural proteomics and molecular -dynamics simulations. We have used hydrogen/deuterium exchange, differential crosslinking, and surface modification to characterize the conformational changes that occur upon both peptide bindin...
ORGANISM(S): Escherichia coli 
2021-09-08 | PXD015275 | Pride
Structural proteomics  mass spectrometry  discrete molecular dynamics simulations  protein-ligand interaction  hydrogen/deuterium exchange  crosslinking/mass spectrometry  surface modification  conformational change  quantitative protein structure  intrinsically disordered protein  protein folding 
Sort   by:  
 Page size