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- W2006056178 abstract "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/fα noise or pink noise in DNA dynamics is ubiquitous. For histone-bound nucleotide dynamics α→ 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 α as a function of position, the measure of power law for dynamical behavior, which we observe in the nucleosome simulation. The unique correspondence (high α to DNA–histone interaction sites, low α to free DNA sites), suggests that α may be an important and new quantification of protein–DNA interactions for future experiments." @default.
- W2006056178 created "2016-06-24" @default.
- W2006056178 creator A5003492695 @default.
- W2006056178 creator A5010337376 @default.
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- W2006056178 date "2009-01-01" @default.
- W2006056178 modified "2023-09-27" @default.
- W2006056178 title "Relaxation dynamics of nucleosomal DNA" @default.
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- W2006056178 cites W1968472876 @default.
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- W2006056178 cites W1970071803 @default.
- W2006056178 cites W1973047728 @default.
- W2006056178 cites W1977475134 @default.
- W2006056178 cites W1980075189 @default.
- W2006056178 cites W1981186983 @default.
- W2006056178 cites W1981962803 @default.
- W2006056178 cites W1991098690 @default.
- W2006056178 cites W1992755218 @default.
- W2006056178 cites W1996682272 @default.
- W2006056178 cites W2002286553 @default.
- W2006056178 cites W2005509806 @default.
- W2006056178 cites W2006585002 @default.
- W2006056178 cites W2008485113 @default.
- W2006056178 cites W2008879046 @default.
- W2006056178 cites W2009460178 @default.
- W2006056178 cites W2010368710 @default.
- W2006056178 cites W2010398837 @default.
- W2006056178 cites W2010673698 @default.
- W2006056178 cites W2011480164 @default.
- W2006056178 cites W2012510869 @default.
- W2006056178 cites W2012636089 @default.
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- W2006056178 doi "https://doi.org/10.1039/b910937b" @default.
- W2006056178 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/20145808" @default.
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