ArticleAnalytical chemistry2014
Dissecting the binding mode of low affinity phage display peptide ligands to protein targets by hydrogen/deuterium exchange coupled to mass spectrometry.
Article in Analytical chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed.
- Pushing the limits of hydrogen/deuterium exchange mass spectrometry to study protein:fragment low affinity interactions.Communications chemistry · 2025Article
- Structural and functional characterization of Aedes aegypti pupal cuticle protein that controls dengue virus infection.Protein science : a publication of the Protein Society · 2023Article
- Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems.Chemical reviews · 2022Review
- Computational Evolution Protocol for Peptide Design.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Structure-Activity Relationships of Baicalein and its Analogs as Novel TSLP Inhibitors.Scientific reports · 2019Article
- Analysis of phosphoinositide 3-kinase inhibitors by bottom-up electron-transfer dissociation hydrogen/deuterium exchange mass spectrometry.The Biochemical journal · 2017Article
- Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Conformational Analysis of Proteins in Highly Concentrated Solutions by Dialysis-Coupled Hydrogen/Deuterium Exchange Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Phage display (PD) is frequently used to discover peptides capable of binding to biological protein targets. The structural characterization of peptide-protein complexes is often challenging due to their low binding affinities and high structural flexibility. Here, we investigate the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to characterize interactions of low affinity peptides with their cognate protein targets. The HDX-MS workflow was optimized to accurately detect low-affinity peptide-protein interactions by use of ion mobility, electron transfer dissociation, nonbinding control peptides, and statistical analysis of replicate data. We show that HDX-MS can identify regions in the two epigenetic regulator proteins KDM4C and KDM1A that are perturbed through weak interactions with PD-identified peptides. Two peptides cause reduced HDX on opposite sides of the active site of KDM4C, indicating distinct binding modes. In contrast, the perturbation site of another PD-selected peptide inhibiting the function of KDM1A maps to a GST-tag. Our results demonstrate that HDX-MS can validate and map weak peptide-protein interactions and pave the way for understanding and optimizing the binding of peptide scaffolds identified through PD and similar ligand discovery approaches.
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Registered trials
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