Evidence map›Paper›PMID 39812643›Full record

ArticleThe Journal of cell biology2025

TanGIBLE: A selective probe for evaluating hydrophobicity-exposed defective proteins in live cells.

Yasuyuki Iwasa, Sohtaroh Miyata, Takuya Tomita, Naoto Yokota, Maho Miyauchi, Ruka Mori, Shin Matsushita, Rigel Suzuki, Yasushi Saeki, Hiroyuki Kawahara

Abstract read
In one paragraph

Article in The Journal of cell biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

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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

10 authors.

Yasuyuki Iwasa *Department of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0009-0006-1520-6206
Sohtaroh Miyata *Department of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0009-0009-3190-8576
Takuya TomitaDepartment of Protein Metabolism, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID 0000-0003-4568-9940
Naoto YokotaDepartment of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0000-0001-7260-889X
Maho MiyauchiDepartment of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0009-0006-5783-2774
Ruka MoriDepartment of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0009-0000-4066-2680
Shin MatsushitaDepartment of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0009-0003-5847-2035
Rigel SuzukiDepartment of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0000-0002-2700-4867
Yasushi SaekiDepartment of Protein Metabolism, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.ORCID 0000-0002-9202-5453
Hiroyuki KawaharaDepartment of Biological Sciences, Laboratory of Cell Biology and Biochemistry, Tokyo Metropolitan University, Tokyo, Japan.ORCID 0000-0001-8506-9012

Funding

Japan Society for the Promotion of Science 24H01905Naito FoundationTakeda Science FoundationTokyo Metropolitan Government R4-1University of Tokyo
6 · The paper itself

Abstract

The accumulation of defective polypeptides in cells is a major cause of various diseases. However, probing defective proteins is difficult because no currently available method can retrieve unstable defective translational products in a soluble state. To overcome this issue, there is a need for a molecular device specific to structurally defective polypeptides. In this study, we developed an artificial protein architecture comprising tandemly aligned BAG6 Domain I, a minimum substrate recognition platform responsible for protein quality control. This tandem-aligned entity shows enhanced affinity not only for model defective polypeptides but also for endogenous polyubiquitinated proteins, which are sensitive to translational inhibition. Mass-spectrometry analysis with this probe enabled the identification of endogenous defective proteins, including orphaned subunits derived from multiprotein complexes and misassembled transmembrane proteins. This probe is also useful for the real-time visualization of protein foci derived from defective polypeptides in stressed cells. Therefore, this "new molecular trap" is a versatile tool for evaluating currently "invisible" pools of defective polypeptides as tangible entities.

Indexed as

Molecular ProbesHEK293 CellsHeLa CellsHumansHydrophobic and Hydrophilic InteractionsPeptidesMolecular ProbesPeptides

Identifiers

PMID39812643
PMCPMC11734626

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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.