# Origins of Ligand Binding and Selectivity in Methyllysine Reader and Writer Proteins

> **NIH NIH R01** · UNIV OF NORTH CAROLINA CHAPEL HILL · 2020 · $286,878

## Abstract

Abstract.
Histone protein lysine (Lys) methylation is an epigenetic regulator of gene expression. Histone Lys
methyltransferases (HKMTs or “writers”) install methylated Lys (KMen, n = 1-3) at specific positions, and Lys
methylation recruits a diverse family of “reader proteins” that bind these dynamic post translational
modifications and induce downstream events leading to either initiation or silencing of transcription.
Dysregulation in these events is associated with a wide range of diseases including cancer. While these reader
and writer proteins are potential medicinal targets, few studies have probed the mechanism by which they
recognize native KMen substrates or by which small molecules or histone mutations lead to their inhibition.
This proposal aims to determine the balance of forces that provide binding affinity, selectivity, and catalysis for
KMen as well as recently discovered inhibitors of these protein-protein interactions with the aim of gaining
insights that will further the effort to develop inhibitors for these proteins. To this end, the mechanism of KMen
recognition will be investigated through a combination of protein- and ligand-directed structure-activity
relationships. Complementary methodology will be developed for the site-selective incorporation of
electronically tuned unnatural amino acids, including substituted-phenylalanine and tyrosine residues and
fluorinated aromatic residues. Using this methodology in conjunction with established techniques, the
electronics of aromatic and charged residues will be systematically altered to determine the contribution of
cation-pi interactions, van der Waals interactions, the hydrophobic effect, and salt bridges on affinity and
selectivity across a range of di- and tri-methyl lysine reader proteins marked by subtly different binding
pockets. Additionally, the role of aromatic residues in the active site of HKMTs will be investigated with respect
to both catalysis and inhibition. In all cases, X-ray crystallography will be used to provide structural insights into
the mechanism of recognition. Additionally, the mechanism of binding to methyl lysine mimetics and known
inhibitors of reader and writer proteins will be characterized to determine whether novel mechanisms for
binding and inhibition are feasible. In total, these comprehensive studies will provide a quantitative framework
for the development of high quality molecular probes and next-generation inhibitors with the degree of affinity
and selectivity necessary for application to disease. Furthermore, this work should readily extend to other
important protein families, including methyl lysine erasers and writers as well as methyl arginine readers,
writers, and erasers.

## Key facts

- **NIH application ID:** 9989864
- **Project number:** 5R01GM118499-04
- **Recipient organization:** UNIV OF NORTH CAROLINA CHAPEL HILL
- **Principal Investigator:** MARCEY L WATERS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $286,878
- **Award type:** 5
- **Project period:** 2017-09-01 → 2021-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9989864

## Citation

> US National Institutes of Health, RePORTER application 9989864, Origins of Ligand Binding and Selectivity in Methyllysine Reader and Writer Proteins (5R01GM118499-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9989864. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*