Evidence map›Paper›PMID 40583194›Full record

ArticleACS chemical biology2025

CIAA: Integrated Proteomics and Structural Modeling for Understanding Cysteine Reactivity with Iodoacetamide Alkyne.

Lisa M Boatner, Jerome Eberhardt, Flowreen Shikwana, Matthew Holcomb, Peiyuan Lee, Kendall N Houk, Stefano Forli, Keriann M Backus

Abstract read
In one paragraph

Article in ACS chemical biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
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.

Lisa M BoatnerBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States.ORCID 0000-0003-0757-4982
Jerome EberhardtDepartment of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, United States.
Flowreen ShikwanaBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States.
Matthew HolcombDepartment of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, United States.ORCID 0000-0002-8409-4344
Peiyuan LeeDepartment of Statistics and Data Science, UCLA, Los Angeles, California 90095, United States.
Kendall N HoukDepartment of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095, United States.ORCID 0000-0002-8387-5261
Stefano ForliDepartment of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California 92037, United States.ORCID 0000-0002-5964-7111
Keriann M BackusBiological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, United States.ORCID 0000-0001-8541-1404

Funding

UCLA SPORE in Brain CancerP50CA211015 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Yvonne Yu-Hsuan Chen · 2017 to 2026
$25.2M
AutoDock Suite: Next Generation Environment for Drug DesignR01GM069832 · NIGMS · SCRIPPS RESEARCH INSTITUTE, THE · PI FORLI, STEFANO · 2004 to 2025
$10.9M
Systems in Integrative BiologyT32GM008185 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI CHOU, TOM · 1987 to 2022
$4.6M
NCI NIH HHS P50 CA211015NIGMS NIH HHS R01 GM069832NIGMS NIH HHS T32 GM008185
6 · The paper itself

Abstract

Cysteine residues play key roles in protein structure and function and can serve as targets for chemical probes and even drugs. Chemoproteomic studies have revealed that heightened cysteine reactivity toward electrophilic probes, such as iodoacetamide alkyne (IAA), is indicative of likely residue functionality. However, while the cysteine coverage of chemoproteomic studies has increased substantially, these methods still provide only a partial assessment of proteome-wide cysteine reactivity, with cysteines from low-abundance proteins and tough-to-detect peptides still largely refractory to chemoproteomic analysis. Here, we integrate cysteine chemoproteomic reactivity data sets with structure-guided computational analysis to delineate key structural features of proteins that favor elevated cysteine reactivity toward IAA. We first generated and aggregated multiple descriptors of cysteine microenvironment, including amino acid content, solvent accessibility, residue proximity, secondary structure, and predicted p

Indexed as

AlkynesCysteineIodoacetamideProteomicsModels, MolecularAlkynesCysteineIodoacetamide

Identifiers

PMID40583194
PMCPMC12503369

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Registered trials

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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.