ArticleJournal of molecular biology2011
Energetics-based discovery of protein-ligand interactions on a proteomic scale.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 62 citations in OpenAlex.
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- Unifying perspectives on the activity and genotypic targeting of pharmacological chaperones.The Journal of biological chemistry · 2025Review
- Target Engagement Assays in Early Drug Discovery.Journal of medicinal chemistry · 2025Review
- Top-Down Stability of Proteins from Rates of Oxidation (TD-SPROX) Approach for Measuring Proteoform-Specific Folding Stability.Analytical chemistry · 2024Article
- Analysis of Brain Protein Stability Changes in a Mouse Model of Alzheimer's Disease.Journal of proteome research · 2024Article
- Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.Analytical chemistry · 2024Article
- Comparative Analysis of Protein Folding Stability-Based Profiling Methods for Characterization of Biological Phenotypes.Journal of the American Society for Mass Spectrometry · 2023Article
- Databases and Tools to Investigate Protein-Metabolite Interactions.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Bet v 1 and other birch allergens are more resistant to proteolysis and more abundant than other birch pollen proteins.Allergy · 2022Article
- Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability.Journal of the American Chemical Society · 2022Article
- Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of anRSC chemical biology · 2022Article
- Metabolization and sequestration of plant specialized metabolites in insect herbivores: Current and emerging approaches.Frontiers in physiology · 2022Review
- Analysis of Brain Protein Stability Changes in Mouse Models of Normal Aging and α-Synucleinopathy Reveals Age- and Disease-Related Differences.Journal of proteome research · 2021Article
- Chemoproteomic methods for covalent drug discovery.Chemical Society reviews · 2021Review
- Protein Folding Stability Changes Across the Proteome Reveal Targets of Cu Toxicity inACS chemical biology · 2021Article
- Chaperone action of a cofactor in protein folding.Protein science : a publication of the Protein Society · 2020Article
- Comparative Analysis of Mass-Spectrometry-Based Proteomic Methods for Protein Target Discovery Using a One-Pot Approach.Journal of the American Society for Mass Spectrometry · 2020Article
- Tryptophan scanning mutagenesis as a way to mimic the compound-bound state and probe the selectivity of allosteric inhibitors in cells.Chemical science · 2020Article
- Chemo-Selection Strategy for Limited Proteolysis Experiments on the Proteomic Scale.Analytical chemistry · 2018Article
- Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale.Journal of proteome research · 2018Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Biochemical functions of proteins in cells frequently involve interactions with various ligands. Proteomic methods for the identification of proteins that interact with specific ligands such as metabolites, signaling molecules, and drugs are valuable in investigating the regulatory mechanisms of cellular metabolism, annotating proteins with unknown functions, and elucidating pharmacological mechanisms. Here we report an energetics-based target identification method in which target proteins in a cell lysate are identified by exploiting the effect of ligand binding on their stabilities. Urea-induced unfolding of proteins in cell lysates is probed by a short pulse of proteolysis, and the effect of a ligand on the amount of folded protein remaining is monitored on a proteomic scale. As proof of principle, we identified proteins that interact with ATP in the Escherichia coli proteome. Literature and database mining confirmed that a majority of the identified proteins are indeed ATP-binding proteins. Four identified proteins that were previously not known to interact with ATP were cloned and expressed to validate the result. Except for one protein, the effects of ATP on urea-induced unfolding were confirmed. Analyses of the protein sequences and structure models were also employed to predict potential ATP binding sites in the identified proteins. Our results demonstrate that this energetics-based target identification approach is a facile method to identify proteins that interact with specific ligands on a proteomic scale.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.