ArticleJournal of the American Society for Mass Spectrometry2014
SILAC-pulse proteolysis: A mass spectrometry-based method for discovery and cross-validation in proteome-wide studies of ligand binding.
Article in Journal of the American Society for Mass Spectrometry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
- Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies.Biology · 2023Review
- 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
- An update of label-free protein target identification methods for natural active products.Theranostics · 2022Review
- Natural products in drug discovery: advances and opportunities.Nature reviews. Drug discovery · 2021Review
- Development of a target identification approach using native mass spectrometry.Scientific reports · 2021Article
- Protein Folding Stability Changes Across the Proteome Reveal Targets of Cu Toxicity inACS chemical biology · 2021Article
- Currently Available Strategies for Target Identification of Bioactive Natural Products.Frontiers in chemistry · 2021Review
- A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes.Nature communications · 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
- 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
- Time, space, and disorder in the expanding proteome universe.Proteomics · 2017Article
- Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach.Journal of proteome research · 2017Article
- Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins Using Limited Proteolysis.Journal of proteome research · 2016Article
- Discovery of Manassantin A Protein Targets Using Large-Scale Protein Folding and Stability Measurements.Journal of proteome research · 2016Article
- Energetic Coupling between Ligand Binding and Dimerization in Escherichia coli Phosphoglycerate Mutase.Biochemistry · 2016Article
- Global analysis of protein folding thermodynamics for disease state characterization.Journal of proteome research · 2015Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reported here is the use of stable isotope labeling with amino acids in cell culture (SILAC) and pulse proteolysis (PP) for detection and quantitation of protein-ligand binding interactions on the proteomic scale. The incorporation of SILAC into PP enables the PP technique to be used for the unbiased detection and quantitation of protein-ligand binding interactions in complex biological mixtures (e.g., cell lysates) without the need for prefractionation. The SILAC-PP technique is demonstrated in two proof-of-principle experiments using proteins in a yeast cell lysate and two test ligands including a well-characterized drug, cyclosporine A (CsA), and a non-hydrolyzable adenosine triphosphate (ATP) analogue, adenylyl imidodiphosphate (AMP-PNP). The well-known tight-binding interaction between CsA and cyclophilin A was successfully detected and quantified in replicate analyses, and a total of 33 proteins from a yeast cell lysate were found to have AMP-PNP-induced stability changes. In control experiments, the method's false positive rate of protein target discovery was found to be in the range of 2.1% to 3.6%. SILAC-PP and the previously reported stability of protein from rates of oxidation (SPROX) technique both report on the same thermodynamic properties of proteins and protein-ligand complexes. However, they employ different probes and mass spectrometry-based readouts. This creates the opportunity to cross-validate SPROX results with SILAC-PP results, and vice-versa. As part of this work, the SILAC-PP results obtained here were cross-validated with previously reported SPROX results on the same model systems to help differentiate true positives from false positives in the two experiments.
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