Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

Lens epithelium-derived growth factor (LEDGF) is a chromatin-binding protein. It regulates gene transcription and is associated with acquired immunodeficiency syndrome and cancer. Its PWWP domain binds to histone H3 at K36 (H3K36). The binding affinity depends on H3K36 methylation. To investigate this dependency, we performed molecular dynamics simulations of the PWWP domain and histone fragments. We found that not only hydrophobic interaction but also electrostatic interaction is important. The binding is not maintained with nonmethylated and monomethylated H3K36 because the tips of these H3K36s form hydrogen bonds with water molecules, while dimethylated and trimethylated H3K36 form no such hydrogen bond, making this binding stable.

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Publication Details

Journal
The Journal of Chemical Physics
Published
2025-05-08
DOI
https://doi.org/10.1063/5.0259337
Primary Topic
Cancer-related gene regulation
Type
article
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article

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

Hisashi Okumura, Satoru Itoh, H SUZUKI
The Journal of Chemical Physics
Cancer-related gene regulation
article

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

Hisashi Okumura, Satoru Itoh, H SUZUKI
article en

Abstract

Lens epithelium-derived growth factor (LEDGF) is a chromatin-binding protein. It regulates gene transcription and is associated with acquired immunodeficiency syndrome and cancer. Its PWWP domain binds to histone H3 at K36 (H3K36). The binding affinity depends on H3K36 methylation. To investigate this dependency, we performed molecular dynamics simulations of the PWWP domain and histone fragments. We found that not only hydrophobic interaction but also electrostatic interaction is important. The binding is not maintained with nonmethylated and monomethylated H3K36 because the tips of these H3K36s form hydrogen bonds with water molecules, while dimethylated and trimethylated H3K36 form no such hydrogen bond, making this binding stable.

The Journal of Chemical PhysicsVol. 162(18)
Shinshu University (JP), The Graduate University for Advanced Studies, SOKENDAI (JP), Institute for Molecular Science (JP), Living Systems (United States) (US), The Exploratory Research Center on Life and Living Systems (JP)
Openalex Percentile: Top 91%
Cancer-related gene regulation
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