ArticleAnalytical chemistry2021
Utilization of Hydrophobic Microenvironment Sensitivity in Diethylpyrocarbonate Labeling for Protein Structure Prediction.
Article in Analytical chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 33 citations in OpenAlex.
- Mass spectrometry-based mapping of conformational epitopes on SARS-CoV-2 antigens targeted by monoclonal antibodies.International journal of biological macromolecules · 2026Article
- Comprehensive Tutorial for Computational Methods of Protein Structure Prediction Incorporating Mass Spectrometry Data.Mass spectrometry reviews · 2026Review
- Incorporating Surfaced-Induced Dissociation Mass Spectrometry Data into an AlphaFold-derived deep learning network improves protein structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.Journal of chemical theory and computation · 2026Article
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Ion Mobility Mass Spectrometry Guided Modeling with AlphaFold and Rosetta Improves Protein Complex Structure Prediction.bioRxiv : the preprint server for biology · 2026Article
- Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling.bioRxiv : the preprint server for biology · 2026Article
- Cross-Linking and Covalent Labeling Mass Spectrometry Reveal Proteoform-Driven Conformational Changes in Alpha Synuclein.Analytical chemistry · 2026Article
- Deep-learning structure elucidation from single-mutant deep mutational scanning.Nature communications · 2025Article
- Mass Spectrometry-Driven Epitope Mapping: Application of Diethylpyrocarbonate Covalent Labeling for the Immunotherapeutic Target Programmed Cell Death Protein 1.Journal of the American Society for Mass Spectrometry · 2025Article
- Experimental Evidence for Phosphorylation-Driven Allosteric Regulation of Alpha Synuclein Function.bioRxiv : the preprint server for biology · 2025Article
- Energy Resolved Mass Spectrometry Data from Surfaced Induced Dissociation Improves Prediction of Protein Complex Structure.Analytical chemistry · 2025Article
- Probing the functional hotspots inside protein hydrophobic pockets byChemical science · 2024Article
- Site-Specific Structural Changes in Long-Term-Stressed Monoclonal Antibody Revealed with DEPC Covalent-Labeling and Quantitative Mass Spectrometry.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver.Briefings in bioinformatics · 2023Article
- Workflow for Validating Specific Amino Acid Footprinting Reagents for Protein Higher Order Structure Elucidation.Analytical chemistry · 2023Article
- Membrane Protein Binding Interactions Studied in Live Cells via Diethylpyrocarbonate Covalent Labeling Mass Spectrometry.Analytical chemistry · 2023Article
- Diethylpyrocarbonate-Based Covalent Labeling Mass Spectrometry of Protein Interactions in a Membrane Complex System.Journal of the American Society for Mass Spectrometry · 2023Article
- Modeling of protein conformational changes with Rosetta guided by limited experimental data.Structure (London, England : 1993) · 2022Article
- Protein shape sampled by ion mobility mass spectrometry consistently improves protein structure prediction.Nature communications · 2022Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Diethylpyrocarbonate (DEPC) labeling analyzed with mass spectrometry can provide important insights into higher order protein structures. It has been previously shown that neighboring hydrophobic residues promote a local increase in DEPC concentration such that serine, threonine, and tyrosine residues are more likely to be labeled despite low solvent exposure. In this work, we developed a Rosetta algorithm that used the knowledge of labeled and unlabeled serine, threonine, and tyrosine residues and assessed their local hydrophobic environment to improve protein structure prediction. Additionally, DEPC-labeled histidine and lysine residues with higher relative solvent accessible surface area values (i.e., more exposed) were scored favorably. Application of our score term led to reductions of the root-mean-square deviations (RMSDs) of the lowest scoring models. Additionally, models that scored well tended to have lower RMSDs. A detailed tutorial describing our protocol and required command lines is included. Our work demonstrated the considerable potential of DEPC covalent labeling data to be used for accurate higher order structure determination.
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