ArticleMolecular & cellular proteomics : MCP2015
Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry (MS).
Article in Molecular & cellular proteomics : MCP, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 60 citations in OpenAlex.
- Recommendations and considerations for hydroxyl radical protein footprinting-mass spectrometry.Nature methods · 2026Review
- Multidose Inline Size-Exclusion Chromatography-Flash Oxidation for Structural Analysis of Dynamic Protein-Ligand Interactions of Antithrombin III and Unfractionated Heparin.Analytical chemistry · 2026Article
- Radical footprinting in mammalian whole blood.Nature communications · 2026Article
- Structural exposure of different microtubule binding domains determines the propagation and toxicity of pathogenic tau conformers in Alzheimer's disease.PLoS pathogens · 2025Article
- Quantitative readout of methionine residue solvent accessibility in E. coli cells using radiolytic hydroxyl radical labeling and mass spectrometry.Biochemical and biophysical research communications · 2025Article
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Multiplex Chemical Labeling of Amino Acids for Protein Footprinting Structure Assessment.Analytical chemistry · 2022Article
- Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling.Communications biology · 2022Article
- Flash Oxidation (FOX) System: A Novel Laser-Free Fast Photochemical Oxidation Protein Footprinting Platform.Journal of the American Society for Mass Spectrometry · 2021Article
- Structurally distinct external solvent-exposed domains drive replication of major human prions.PLoS pathogens · 2021Article
- Self-Organized Amphiphiles Are Poor Hydroxyl Radical Scavengers in Fast Photochemical Oxidation of Proteins Experiments.Journal of the American Society for Mass Spectrometry · 2021Article
- Accurate protein structure prediction with hydroxyl radical protein footprinting data.Nature communications · 2021Article
- Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes.Journal of visualized experiments : JoVE · 2020Article
- Fast Protein Footprinting by X-ray Mediated Radical Trifluoromethylation.Journal of the American Society for Mass Spectrometry · 2020Article
- Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution.Journal of molecular biology · 2020Review
- Rapid Quantification of Peptide Oxidation Isomers From Complex Mixtures.Analytical chemistry · 2020Article
- Intrinsic Buffer Hydroxyl Radical Dosimetry Using Tris(hydroxymethyl)aminomethane.Journal of the American Society for Mass Spectrometry · 2020Article
- Development of Container Free Sample Exposure for Synchrotron X-ray Footprinting.Analytical chemistry · 2020Article
- Compensated Hydroxyl Radical Protein Footprinting Measures Buffer and Excipient Effects on Conformation and Aggregation in an Adalimumab Biosimilar.The AAPS journal · 2019Article
- Utility of Covalent Labeling Mass Spectrometry Data in Protein Structure Prediction with Rosetta.Journal of chemical theory and computation · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Hydroxyl radical footprinting based MS for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, for example, protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eightfold increase in structural resolution compared with peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca(+2)-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes.
Indexed as
Identifiers
What OpenQuestion holds
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.