Evidence map›Paper›PMID 40097432›Full record

ArticleNature communications2025

Genetically encoding ε-N-methacryllysine into proteins in live cells.

Tian-Yi Zhu, Shi-Yi Chen, Mengdi Zhang, Heyu Li, Ting Wu, Emmanuel Ajiboye, Jia Wen Wang, Bi-Kun Jin, Dan-Dan Liu, Xintong Zhou and 13 more

Abstract read
In one paragraph

Article in Nature communications, 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. Article
  2. Review
  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

23 authors.

Tian-Yi Zhu *Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Shi-Yi Chen *Department of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Mengdi ZhangDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Heyu LiDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Ting WuDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.ORCID http://orcid.org/0000-0002-0434-3700
Emmanuel AjiboyeDepartment of Chemistry and Biochemistry, Wichita State University, Wichita, KS, USA.
Jia Wen WangDepartment of Chemistry and Biochemistry, Wichita State University, Wichita, KS, USA.
Bi-Kun JinDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Dan-Dan LiuDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Xintong ZhouDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
He HuangComputational Medicine Beijing Co. Ltd., Beijing, China.
Xiaobo WanComputational Medicine Beijing Co. Ltd., Beijing, China.
Ke SunKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.ORCID http://orcid.org/0009-0004-4700-9077
Peilong LuKey Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.ORCID http://orcid.org/0000-0001-5894-9268
Yaxin FuSchool of Basic Medical Sciences, Capital Medical University, Beijing, China.
Ying YuanDepartment of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.ORCID http://orcid.org/0000-0002-3922-9553
Hai SongDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.ORCID http://orcid.org/0000-0003-3228-6616
Anna A SablinaVIB-KU Leuven Center for Cancer Biology, VIB, Leuven, Belgium.ORCID http://orcid.org/0000-0001-9526-4014
Chao TongDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China.
Long ZhangDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China. l_zhang@zju.edu.cn.ORCID http://orcid.org/0000-0001-8139-0474
Ming WuDepartment of Thoracic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China. iwuming22@zju.edu.cn.ORCID http://orcid.org/0000-0002-1009-5387
Haifan WuDepartment of Chemistry and Biochemistry, Wichita State University, Wichita, KS, USA. haifan.wu@wichita.edu.
Bing YangDepartment of Medical Oncology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Life Science Institute, Zhejiang University, Hangzhou, Zhejiang, China. bingyang@zju.edu.cn.ORCID http://orcid.org/0000-0001-6739-2932

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Lysine acylation is a ubiquitous post-translational modification (PTM) that plays pivotal roles in various cellular processes, such as transcription, metabolism, protein localization and folding. Thousands of lysine acylation sites have been identified based on advances in antibody enrichment strategies, highly sensitive analysis by mass spectrometry (MS), and bioinformatics. However, only 27 lysine methacrylation (Kmea) sites have been identified exclusively in histone proteins. It is hard to separate, purify and differentiate the Kmea modification from its structural isomer lysine crotonylation (Kcr) using general biochemical approaches. Here, we identify Kmea sites on a non-histone protein, Cyclophillin A (CypA). To investigate the functions of Kmea in CypA, we develop a general genetic code expansion approach to incorporate a non-canonical amino acid (ncAA) ε-N-Methacryllysine (MeaK) into target proteins and identify interacting proteins of methacrylated CypA using affinity-purification MS. We find that Kmea at CypA site 125 regulates cellular redox homeostasis, and HDAC1 is the regulator of Kmea on CypA. Moreover, we discover that genetically encode Kmea can be further methylated to ε-N-methyl-ε-N-methacrylation (Kmemea) in live cells.

Indexed as

Cyclophilin ALysineAcylationHEK293 CellsHistone Deacetylase 1HumansOxidation-ReductionProtein Processing, Post-TranslationalCyclophilin AHDAC1 protein, humanHistone Deacetylase 1Lysine

Identifiers

PMID40097432
PMCPMC11914497

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.