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Rigid-body molecular dynamics of DNA inside a nucleosome
, Article European Physical Journal E ; Volume 36, Issue 3 , March , 2013 ; 12928941 (ISSN) ; Berdy Besya, A ; Ejtehadi, M. R ; Schiessel, H ; Sharif University of Technology
2013
Abstract
The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use...