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J Biol Chem. 2017 Dec 22;292(51):20947-20959. doi: 10.1074/jbc.M117.799700. Epub 2017 Oct 26.

Conformational dynamics of the TTD-PHD histone reader module of the UHRF1 epigenetic regulator reveals multiple histone-binding states, allosteric regulation, and druggability.

Author information

1
From the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
2
the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
3
the Small-Angle X-ray Scattering Core Facility, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc., Frederick, Maryland 21702, and.
4
the NCI, National Institutes of Health, Frederick, Maryland 21702.
5
From the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada, carrow@uhnresearch.ca.

Abstract

UHRF1 is a key mediator of inheritance of epigenetic DNA methylation patterns during cell division and is a putative target for cancer therapy. Recent studies indicate that interdomain interactions critically influence UHRF1's chromatin-binding properties, including allosteric regulation of its histone binding. Here, using an integrative approach that combines small angle X-ray scattering, NMR spectroscopy, and molecular dynamics simulations, we characterized the dynamics of the tandem tudor domain-plant homeodomain (TTD-PHD) histone reader module, including its 20-residue interdomain linker. We found that the apo TTD-PHD module in solution comprises a dynamic ensemble of conformers, approximately half of which are compact conformations, with the linker lying in the TTD peptide-binding groove. These compact conformations are amenable to cooperative, high-affinity histone binding. In the remaining conformations, the linker position was in flux, and the reader adopted both extended and compact states. Using a small-molecule fragment screening approach, we identified a compound, 4-benzylpiperidine-1-carboximidamide, that binds to the TTD groove, competes with linker binding, and promotes open TTD-PHD conformations that are less efficient at H3K9me3 binding. Our work reveals a mechanism by which the dynamic TTD-PHD module can be allosterically targeted with small molecules to modulate its histone reader function for therapeutic or experimental purposes.

KEYWORDS:

drug screening; epigenetics; molecular dynamics; molecular modeling; nuclear magnetic resonance (NMR); protein dynamic

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