Paper Citing NAMD - Abstract
Ponomarev, Sergei Y.; Putkaradze, Vakhtang; Bishop, Thomas C.
Relaxation dynamics of nucleosomal DNA
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:10633-10643, 2009
Recent experimental and theoretical evidence demonstrates that proteins and water in the hydration layer can follow complex stretched exponential or power law relaxation dynamics. Here, we report on a 50 ns all atom molecular dynamics (MD) simulation of the yeast nucleosome, where the interactions between DNA, histones, surrounding water and ions are explicitly included. DNA interacts with the histone core in 14 locations, approximately every 10.4 base pairs. We demonstrate that all sites of interaction exhibit anomalously slow power law relaxation, extending up to 10 ns, while fast exponential relaxation dynamics of hundreds of picoseconds applies to DNA regions outside these locations. The appearance of 1/f(alpha) noise or pink noise in DNA dynamics is ubiquitous. For histone-bound nucleotide dynamics alpha -> 1 and is a signature of complexity of the protein-DNA interactions. For control purposes two additional DNA simulations free of protein are conducted. Both utilize the same sequence of DNA, as found the in the nucleosome. In one simulation the initial conformation of the double helix is a straight B-form. In the other, the initial conformation is super helical. Neither of these simulations exhibits the variation of alpha as a function of position, the measure of power law for dynamical behavior, which we observe in the nucleosome simulation. The unique correspondence (high alpha to DNA-histone interaction sites, low alpha to free DNA sites), suggests that alpha may be an important and new quantification of protein-DNA interactions for future experiments.
