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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Function
The N-terminal tails of core histones in a nucleosome core particle (NCP) aid in a multitude of functions such as structural stability, thermal stability, and the stimulation of transcription binding factors.[3]
Importance
The N-terminal tail interactions of the H4 histone are crucial in order to correctly fold the nucleosomes into compact units that can be used to form chromatin fibers. This interaction occurs on the G14 to R19 or K16 to N25 residues that reside on the N-terminal tail of H4 and the acidic patch of the neighboring nucleosome. The tetra-acetylation of the H4 histone significantly increased the B-factor or electron density spacing on the outward regions of the DNAs in 7 -8 superhelical locations (SHL) in comparison to the inward regions, terminal regions, and regions near the dyad which were barely affected. The H4 – K16-acetylated nucleosome inhibited the formation of 30nm fibers and cross-fiber interactions thus displaying the its critical role in chromatin decompaction. Through biochemical analysis of acetylated nucleosome core particles (NCPs) that were prepared via native chemical ligation, it was revealed that cation-induced self-association was reduced by the tetra-acetylation of residues H4-K5, K8, K12, and K16.
Relevance
Through various observations, the scientists have presumed that the acetylation of the nucleosome itself is what regulates the decompaction of the higher-order chromatin structure, even in the absence of chromatin- associated factors. The B-factors of the acetylated NCP when compared to the unmodified NCP was significantly higher in comparison around the superhelical locations (SHL): -1.5 and +5.5 respectively. These differences suggest that H4 tetra-acetylation causes greater fluctuation of the atomic positions around these SHLs. This lead scientists to conclude that intra- and inter-nucleosomal interactions exist between DNA and the residues 1-16 or 1-20 of the H4 tail.
Structural highlights
Below are the various structural highlight of the H4-tetra-acetylated NCP:
displays in green the molecule B which is composed of residues 1-20 while the color yellow represents the molecule F which highlights residues 1-15.
show the H4 nucleosome in its unaltered state.
References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ Wakamori M, Fujii Y, Suka N, Shirouzu M, Sakamoto K, Umehara T, Yokoyama S. Intra- and inter-nucleosomal interactions of the histone H4 tail revealed with a human nucleosome core particle with genetically-incorporated H4 tetra-acetylation. Sci Rep. 2015 Nov 26;5:17204. doi: 10.1038/srep17204. PMID:26607036 doi:http://dx.doi.org/10.1038/srep17204
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