Abstract
Several reader domain proteins that specifically recognize methyllysine-containing histones contain the negatively-charged aspartate or glutamate residues as part of the aromatic cage. Herein, we report thermodynamic analyses for the recognition of histone H3K4me3 and H3K4me2 by the tandem tudor domain of Sgf29 and its recognition site variants. Small uncharged and large aromatic substitutions on the Asp266 site resulted in a significant decrease in binding affinities for both H3K4me3 and H3K4me2, demonstrating the role of the negative charge of Asp266 in the readout process by Sgf29. This study emphasizes the essential contribution of electrostatic interactions to the overall binding affinity, and reveals that the underlying mechanisms for the recognition of Kme2/3 depend on the composition and arrangement of the aromatic cage.
Highlights
In order to structure the vast amount of genetic material stored within the cell, several mechanisms of DNA condensation have evolved in eukaryotic organisms
The process of lysine methylation is controlled by three types of proteins, namely histone lysine methyltransferases, histone lysine demethylases, and histone lysine reader domain proteins, that are capable of recognizing posttranslationally-modified histones[5,6]
Wild-type Sgf29 and its recognition site variants were expressed in E. coli and subsequently purified (S3 Fig)
Summary
In order to structure the vast amount of genetic material stored within the cell, several mechanisms of DNA condensation have evolved in eukaryotic organisms. The first level of condensation is achieved by wrapping DNA around a protein assembly of eight histone proteins to form the nucleosome[1]. The histone tails protruding from this assembly are especially accessible for various posttranslational modifications (PTM) such as acetylation, phosphorylation and methylation[2]. These PTMs have been found to be involved in processes such as gene activation, gene transcription and chromatin condensation. The process of lysine methylation is controlled by three types of proteins, namely histone lysine methyltransferases (writers), histone lysine demethylases (erasers), and histone lysine reader domain proteins ( known as chromatin effectors), that are capable of recognizing posttranslationally-modified histones[5,6]. A common feature of readers that recognize Kme and Kme is that they possess a methyllysine recognition
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