Supporting Material for “Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions”
نویسندگان
چکیده
The DNA is treated using the discretized wormlike bead-chain model, where each “bead” represents a 3 nm segment of relaxed DNA (1, 2). Each bead is assigned a salt-dependent charge qdna according to Stigter (3). The DNA bead-chain is also assigned an intramolecular force field comprising of stretching, bending, twisting terms that capture all aspects of DNA mechanics. The stretching energy Ustr of the DNA is given by
منابع مشابه
Dynamics of forced nucleosome unraveling and role of nonuniform histone-DNA interactions.
A coarse-grained model of the nucleosome is introduced to investigate the dynamics of force-induced unwrapping of DNA from histone octamers. In this model, the DNA is treated as a charged, discrete worm-like chain, and the octamer is treated as a rigid cylinder carrying a positively charged superhelical groove that accommodates 1.7 turns of DNA. The groove charges are parameterized to reproduce...
متن کاملMultiscale modeling of nucleosome dynamics.
Nucleosomes form the fundamental building blocks of chromatin. Subtle modifications of the constituent histone tails mediate chromatin stability and regulate gene expression. For this reason, it is important to understand structural dynamics of nucleosomes at atomic levels. We report a novel multiscale model of the fundamental chromatin unit, a nucleosome, using a simplified model for rapid dis...
متن کاملForced unraveling of chromatin fibers with nonuniform linker DNA lengths.
The chromatin fiber undergoes significant structural changes during the cell's life cycle to modulate DNA accessibility. Detailed mechanisms of such structural transformations of chromatin fibers as affected by various internal and external conditions such as the ionic conditions of the medium, the linker DNA length, and the presence of linker histones, constitute an open challenge. Here we uti...
متن کاملThe role of histone tails in the nucleosome: a computational study.
Histone tails play an important role in gene transcription and expression. We present here a systematic computational study of the role of histone tails in the nucleosome, using replica exchange molecular dynamics simulations with an implicit solvent model and different well-established force fields. We performed simulations for all four histone tails, H4, H3, H2A, and H2B, isolated and with in...
متن کاملEffect of force on mononucleosomal dynamics.
Using single-molecule optical-trapping techniques, we examined the force-induced dynamic behavior of a single nucleosome core particle. Our experiments using the DNA construct containing the 601 nucleosome-positioning sequence revealed that the nucleosome unravels in at least two major stages. The first stage, which we attributed to the unraveling of the first DNA wrap around the histone octame...
متن کامل