Evidence map›Paper›PMID 40199130›Full record

ArticleBiochemical and biophysical research communications2025

Quantitative readout of methionine residue solvent accessibility in E. coli cells using radiolytic hydroxyl radical labeling and mass spectrometry.

Ezaz Ahmed, Rohit Jain, Daniela Schlatzer, Filipa Blasco Tavares Pereira Lopes, Janna Kiselar, David T Lodowski, Mark R Chance, Erik R Farquhar

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Biochemical and biophysical research communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Ezaz AhmedCenter for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
Rohit JainCenter for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
Daniela SchlatzerCenter for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
Filipa Blasco Tavares Pereira LopesDepartment of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
Janna KiselarDepartment of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
David T LodowskiDepartment of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
Mark R ChanceCenter for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA. Electronic address: mrc16@case.edu.
Erik R FarquharCenter for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA. Electronic address: efarquhar@bnl.gov.

Funding

Orbitrap Fusion Lumos Tribrid Mass SpectrometerS10OD026882 · OD · CASE WESTERN RESERVE UNIVERSITY · PI CHANCE, MARK R · 2019 to 2019
$1.0M
5-laser 30-parameter FACSymphony-S6 SORP Cell Sorter from BD BiosciencesS10OD026814 · OD · NORTHWESTERN UNIVERSITY AT CHICAGO · PI PERLMAN, HARRIS R · 2019 to 2019
$904k
Q Exactive HF-X hybrid quadrupole-Orbitrap mass spectrometer (QE HF-X)S10OD028614 · OD · CASE WESTERN RESERVE UNIVERSITY · PI CHANCE, MARK R · 2020 to 2020
$600k
NIH HHS S10 OD026814NIH HHS S10 OD026882NIH HHS S10 OD028614
6 · The paper itself

Abstract

Reactive oxygen species play a crucial role in cellular processes, but their effects on protein structure and function in vivo remain challenging to study. Here, we present an approach using synchrotron-based X-ray footprinting methods to probe protein structure, via quantitative LC-coupled mass spectrometry of methionine oxidation (MSOx) in live E. coli. A label-free proteomic analysis identified 2104 proteins from E. coli, with 465 proteins exhibiting MSOx modifications distributed across multiple cellular compartments. Changes in MSOx modification with increasing X-ray dose revealed a correlation between rates of modification and solvent-accessible surface area in vivo for selected proteins responsive to exposure, providing a direct probe of protein structure and its conformational plasticity in the cell. The approach developed here offers a unique in-cell quantitative readout of methionine oxidation and solvent accessibility through radiolytic hydroxyl radical labeling. With this method, the landscape of methionine oxidation in E. coli can be mapped, providing insights into protein behavior under oxidative stress. It represents a first step in developing radiolysis and E. coli as platforms for in vivo protein structure assessment. The potential applications in drug discovery, protein engineering, and systems biology of protein conformations are considerable.

Indexed as

Escherichia coliEscherichia coli ProteinsHydroxyl RadicalMethionineMass SpectrometryOxidation-ReductionOxidative StressProteomicsSolventsEscherichia coli ProteinsHydroxyl RadicalMethionineSolventsCell biologyCovalent labelingMass spectrometryMethionine sulfoxideReactive oxygen speciesSynchrotron radiationX-ray footprinting

Identifiers

PMID40199130
PMCPMC12516815

What OpenQuestion holds

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Registered trials

None linked

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.