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Reading and erasing of the phosphonium analogue of trimethyllysine by epigenetic proteins

Lookup NU author(s): Dr Roman Belle, Dr Vinod Kumar, Professor Akane Kawamura

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

Nε-Methylation of lysine residues in histones plays an essential role in the regulation of eukaryotic transcription. The ‘highest’ methylation mark, Nε-trimethyllysine, is specifically recognised by Nε-trimethyllysine binding ‘reader’ domains, and undergoes demethylation, as catalysed by 2-oxoglutarate dependent JmjC oxygenases. We report studies on the recognition of the closest positively charged Nε-trimethyllysine analogue, i.e. its trimethylphosphonium derivative (KPme3), by Nε-trimethyllysine histone binding proteins and Nε-trimethyllysine demethylases. Calorimetric and computational studies with histone binding proteins reveal that H3KP4me3 binds more tightly than the natural H3K4me3 substrate, though the relative differences in binding affinity vary. Studies with JmjC demethylases show that some, but not all, of them can accept the phosphonium analogue of their natural substrates and that the methylation state selectivity can be changed by substitution of nitrogen for phosphorus. The combined results reveal that very subtle changes, e.g. substitution of nitrogen for phosphorus, can substantially affect interactions between ligand and reader domains / demethylases, knowledge that we hope will inspire the development of highly selective small molecules modulating their activity.


Publication metadata

Author(s): Belle R, Kamps JJAG, Poater J, Kumar K, Pieters BJGE, Salah E, Claridge TDW, Paton RS, Bickelhaupt FM, Kawamura A, Schofield CJ, Mecinovic J

Publication type: Article

Publication status: Published

Journal: Communications Chemistry

Year: 2022

Volume: 5

Online publication date: 07/03/2022

Acceptance date: 03/02/2022

Date deposited: 09/03/2022

ISSN (electronic): 2399-3669

Publisher: Springer Nature

URL: https://doi.org/10.1038/s42004-022-00640-4

DOI: 10.1038/s42004-022-00640-4


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Funding

Funder referenceFunder name
C8717/A28285
ChemEpigen-715691
C8717/A18245
EP/L015838/1
EP/M50659X/1
EP/L003376/1
MDM-2017-0767
PID2019-106830GB-I00

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