Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands

We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes sign...

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Bibliographic Details
Published in:Journal of molecular biology 2003-02, Vol.326 (2), p.371-380
Main Authors: Suto, Robert K., Edayathumangalam, Rajeswari S., White, Cindy L., Melander, Christian, Gottesfeld, Joel M., Dervan, Peter B., Luger, Karolin
Format: Article
Language:English
Subjects:
Animals
Binding Sites
chromatin remodeling
Crystallization
Crystallography, X-Ray
Deoxyribonuclease I - metabolism
DNA
DNA - chemistry
DNA - genetics
DNA - metabolism
DNA Footprinting
DNA, Satellite - chemistry
DNA, Satellite - genetics
DNA, Satellite - metabolism
histone
Histones - chemistry
Histones - metabolism
Humans
Imidazoles - chemistry
Imidazoles - metabolism
Ligands
Models, Molecular
Nucleic Acid Conformation
nucleosome core particle
Nucleosomes - chemistry
Nucleosomes - genetics
Nucleosomes - metabolism
Nylons - chemistry
Nylons - metabolism
Polymers - chemistry
pyrrole-imidazole polyamide
Pyrroles - chemistry
Pyrroles - metabolism
Thermodynamics
Xenopus laevis
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Summary:We determined the crystal structures of three nucleosome core particles in complex with site-specific DNA-binding ligands, the pyrrole-imidazole polyamides. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes significant structural changes at the ligand-binding sites and in adjacent regions to accommodate the ligands. Our findings suggest that twist diffusion occurs over long distances through tightly bound nucleosomal DNA. This may be relevant to the mechanism of ATP-dependent and spontaneous nucleosome translocation, and to the effect of bound factors on nucleosome dynamics.
ISSN:0022-2836
1089-8638
DOI:10.1016/S0022-2836(02)01407-9