pubmed.ncbi.nlm.nih.gov

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution - PubMed

️Tue Jan 01 2002

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

Curt A Davey et al. J Mol Biol. 2002.

Abstract

Solvent binding in the nucleosome core particle containing a 147 base pair, defined-sequence DNA is characterized from the X-ray crystal structure at 1.9 A resolution. A single-base-pair increase in DNA length over that used previously results in substantially improved clarity of the electron density and accuracy for the histone protein and DNA atomic coordinates. The reduced disorder has allowed for the first time extensive modeling of water molecules and ions. Over 3000 water molecules and 18 ions have been identified. Water molecules acting as hydrogen-bond bridges between protein and DNA are approximately equal in number to the direct hydrogen bonds between these components. Bridging water molecules have a dual role in promoting histone-DNA association not only by providing further stability to direct protein-DNA interactions, but also by enabling formation of many additional interactions between more distantly related elements. Water molecules residing in the minor groove play an important role in facilitating insertion of arginine side-chains. Water structure at the interface of the histones and DNA provides a means of accommodating intrinsic DNA conformational variation, thus limiting the sequence dependency of nucleosome positioning while enhancing mobility. Monovalent anions are bound near the N termini of histone alpha-helices that are not occluded by DNA phosphate groups. Their location in proximity to the DNA phosphodiester backbone suggests that they damp the electrostatic interaction between the histone proteins and the DNA. Divalent cations are bound at specific sites in the nucleosome core particle and contribute to histone-histone and histone-DNA interparticle interactions. These interactions may be relevant to nucleosome association in arrays.

PubMed Disclaimer

Cited by

Cockayne syndrome B protein acts as an ATP-dependent processivity factor that helps RNA polymerase II overcome nucleosome barriers.
Xu J, Wang W, Xu L, Chen JY, Chong J, Oh J, Leschziner AE, Fu XD, Wang D. Xu J, et al. Proc Natl Acad Sci U S A. 2020 Oct 13;117(41):25486-25493. doi: 10.1073/pnas.2013379117. Epub 2020 Sep 28. Proc Natl Acad Sci U S A. 2020. PMID: 32989164 Free PMC article.
Manipulating chromatin architecture in C. elegans.
Carter JL, Kempton CE, Hales EDS, Johnson SM. Carter JL, et al. Epigenetics Chromatin. 2022 Nov 29;15(1):38. doi: 10.1186/s13072-022-00472-5. Epigenetics Chromatin. 2022. PMID: 36443798 Free PMC article.
The carboxyl terminus of Rtt109 functions in chaperone control of histone acetylation.
Radovani E, Cadorin M, Shams T, El-Rass S, Karsou AR, Kim HS, Kurat CF, Keogh MC, Greenblatt JF, Fillingham JS. Radovani E, et al. Eukaryot Cell. 2013 May;12(5):654-64. doi: 10.1128/EC.00291-12. Epub 2013 Mar 1. Eukaryot Cell. 2013. PMID: 23457193 Free PMC article.
DNA damage response induces structural alterations in histone H3-H4.
Izumi Y, Fujii K, Yamamoto S, Matsuo K, Namatame H, Taniguchi M, Yokoya A. Izumi Y, et al. J Radiat Res. 2017 Jan;58(1):59-65. doi: 10.1093/jrr/rrw086. Epub 2016 Sep 26. J Radiat Res. 2017. PMID: 27672100 Free PMC article.
Correlation among DNA Linker Length, Linker Histone Concentration, and Histone Tails in Chromatin.
Luque A, Ozer G, Schlick T. Luque A, et al. Biophys J. 2016 Jun 7;110(11):2309-2319. doi: 10.1016/j.bpj.2016.04.024. Biophys J. 2016. PMID: 27276249 Free PMC article.

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution - PubMed