Flexible histone tails in a new mesoscopic oligonucleosome model.
We describe a new mesoscopic model of oligonucleosomes that incorporates flexible histone tails. The nucleosome cores are modeled using the discrete surface-charge optimization model, which treats the nucleosome as an electrostatic surface represented by hundreds of point charges; the linker DNAs are treated using a discrete elastic chain model; and the histone tails are modeled using a bead/chain hydrodynamic approach as chains of connected beads where each bead represents five protein residues. Appropriate charges and force fields are assigned to each histone chain so as to reproduce the electrostatic potential, structure, and dynamics of the corresponding atomistic histone tails at different salt conditions. The dynamics of resulting oligonucleosomes at different sizes and varying salt concentrations are simulated by Brownian dynamics with complete hydrodynamic interactions. The analyses demonstrate that the new mesoscopic model reproduces experimental results better than its predecessors, which modeled histone tails as rigid entities. In particular, our model with flexible histone tails: correctly accounts for salt-dependent conformational changes in the histone tails; yields the experimentally obtained values of histone-tail mediated core/core attraction energies; and considers the partial shielding of electrostatic repulsion between DNA linkers as a result of the spatial distribution of histone tails. These effects are crucial for regulating chromatin structure but are absent or improperly treated in models with rigid histone tails. The development of this model of oligonucleosomes thus opens new avenues for studying the role of histone tails and their variants in mediating gene expression through modulation of chromatin structure.
Arya
Gaurav
G
Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA.
Zhang
Qing
Q
Schlick
Tamar
T
D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry* / Q000648:ultrastructure; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure; D004548:Elasticity; D006657:Histones / Q000737:chemistry* / Q000648:ultrastructure; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000648:ultrastructure; D011485:Protein Binding; D055672:Static Electricity; D013314:Stress, Mechanical
D002843:Chromatin; D006657:Histones; D009707:Nucleosomes; D004247:DNA