The relationship between geometric patterns of hydrogen bonds and periodic dinucleotides in nucleosome structures
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Author(s)
Related Research Unit(s)
Detail(s)
Original language | English |
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Pages (from-to) | 136-141 |
Journal / Publication | Journal of Theoretical Biology |
Volume | 313 |
Publication status | Published - 21 Nov 2012 |
Link(s)
Abstract
Statistical analysis of hydrogen bonds between the DNA chain and histones in nucleosomes shows that there is a periodicity about 10 base pairs along the DNA sequence. This periodicity also exists in dinucleotides which are found to be highly correlated with these hydrogen bonds. By analyzing the components of these protein-DNA hydrogen bonds, we find that more than 86% of them are formed in periodic dinucleotides and one or more hydrogen bonds exist in the majority of periodic dinucleotides. We use the alpha shape model to study the geometric properties of hydrogen bonds in nucleosomes, and find that periodic dinucleotides have convex surface curvatures, which indicates that they have close contact with the histones. The results in this work show that hydrogen bonds in the periodic dinucleotides play a crucial role in the formation of a nucleosome. © 2012 Elsevier Ltd.
Research Area(s)
- Alpha shape model, Dinucleotide periodicity, Nucleosome structure, Solid angle
Citation Format(s)
The relationship between geometric patterns of hydrogen bonds and periodic dinucleotides in nucleosome structures. / Guan, Pearl P.; Zhou, Weiqiang; Yan, Hong.
In: Journal of Theoretical Biology, Vol. 313, 21.11.2012, p. 136-141.
In: Journal of Theoretical Biology, Vol. 313, 21.11.2012, p. 136-141.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review