arXiv subjects

Thomas C. Bishop

Publications and source records attributed to Thomas C. Bishop.

3 recordsLinked to original sources

arXiv2004

Molecular Dynamics Simulations of a Nucleosome and Free DNA

Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution have been conducted. DNA helical parameters are extracted from each trajectory to compare the conformation, effective force constants, persistence length measures, and fluctuations of nucleosomal DNA to free DNA. A method for disassembling and reconstructing the conformation and dynamics of the nucleosome using Fourier analysis is presented. Results indicate that the superhelical path of DNA in the nucleosome is irregular. Long length variations in the conformation of nucleosomal DNA are identified other than those associated with helix repeat. These variations are required to create a proposed tetrasome conformation or to qualitatively reconstruct the 1.75 turns of the nuclesomal superhelix. Free DNA achieves enough bend and shear in solution to create an ideal nucleosome superhelix, but these deformations are not organized so the conformation is essentially linear. Reconstruction of free DNA using selected long wavelength variations in conformation can produce either a left-handed or a right-handed superhelix. DNA is less flexible in the nucleosome than when free in solution, however such measures are length scale dependent.

q-bio.BM↗

arXiv2001

Folding DNA into nucleosome and chromatin: dynamics

A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA and a simple fold geometry are assumed to derive constants for the higher order folding. The model predicts the correct order of magnitude for the experimentally determined Young's and shear modulus of condensed chromatin. Thus we have demonstrated that the elastic properties of DNA are the primary determinant of the elastic properties of each folded state. The derived elastic constants are then used to predict the speed of propagation of small amplitude waves. It is shown that extension/compression, twist, bend or shear waves can be excite in each folded state.

physics.bio-ph↗

arXiv2001

Elastic wave propagation along DNA

It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA can alter signal transmission. The overall effect is a method of signal processing by DNA binding proteins that creates a "cellular communications network". The propagation of small amplitude disturbances through DNA is treated according to the mechanical theory of elastic rods. According to the theory four types of mechanical waves affecting extension(compression), twist, bend or shear can propagate through DNA. Each type of wave has unique characteristic properties. Disturbances affecting all wave types can propagate independently of each other. Using a linear approximation to the theory of motion of elastic rods, the dispersion of these waves is investigated. The phase velocities of the waves lies in the range 5-8 angstroms/ps using constants suitable for a description of DNA. The dispersion of all wave types of arbitrary wave length is investigated for a straight, twisted rod. Based on these findings, we propose all-atom numerical simulations of DNA to investigate the propagation of these waves as an alternative measure of the wave velocity and dispersion analysis.

physics.bio-ph↗