Molecular modeling of the chromatosome particle

Abstract

In an effort to understand the role of the linker histone in chromatin folding, its structure and location in the nucleosome has been studied by molecular modeling methods. The structure of the globular domain of the rat histone H1d, a highly conserved part of the linker histone, built by homology modeling methods, revealed a three-helical bundle fold that could be described as a helix-turn-helix variant with its characteristic properties of binding to DNA at the major groove. Using the information of its preferential binding to four-way Holliday junction (HJ) DNA, a model of the domain complexed to HJ was built, which was subsequently used to position the globular domain onto the nucleosome. The model revealed that the primary binding site of the domain interacts with the extra 20 bp of DNA of the entering duplex at the major groove while the secondary binding site interacts with the minor groove of the central gyre of the DNA superhelix of the nucleosomal core. The positioning of the globular domain served as an anchor to locate the C-terminal domain onto the nucleosome to obtain the structure of the chromatosome particle. The resulting structure had a stem-like appearance, resembling that observed by electron microscopic studies. The C-terminal domain which adopts a high mobility group (HMG)-box-like fold, has the ability to bend DNA, causing DNA condensation or compaction. It was observed that the three S/TPKK motifs in the C-terminal domain interact with the exiting duplex, thus defining the path of linker DNA in the chromatin fiber. This study has provided an insight into the probable individual roles of globular and the C-terminal domains of histone H1 in chromatin organization.

Figure 1

(A) Domain architecture in rat histone H1d. The binding site residues in the globular domain as well as the three S/TPKK motifs in the C-terminal domain are highlighted. Residue numbers for the binding site residues of gH1d (40, 42, 67, 69, 73, 85) correspond to the numbering scheme used in the literature and in PDB: 1HST and will correspond to residues 50, 52, 78, 80 and 95 in the sequence P15865, respectively. (B) Model of the gH1d (cartoon representation) complexed with DNA (ribbon). Residues Lys69, Arg73 and Lys85 in the primary site and Lys40 and Arg42 in the secondary binding site are shown as space-filled objects.

Figure 2

(A) A stereo view of the globular domain (red)–HJ (blue) complex. Interactions of the globular domain at both the primary and secondary sites with two arms of the HJ are clearly seen. Residues in the binding site are labeled. (B) Stereo view of the globular domain docked onto the nucleosome by superposing two arms of the gH1d–HJ (red–blue) complex onto the nucleosomal core (pink). The fourth arm of the HJ is not shown for clarity.

Figure 2

(A) A stereo view of the globular domain (red)–HJ (blue) complex. Interactions of the globular domain at both the primary and secondary sites with two arms of the HJ are clearly seen. Residues in the binding site are labeled. (B) Stereo view of the globular domain docked onto the nucleosome by superposing two arms of the gH1d–HJ (red–blue) complex onto the nucleosomal core (pink). The fourth arm of the HJ is not shown for clarity.

Figure 3

(A) The HMG-box fold in the structure of the C-terminal domain of rat H1d (yellow) and its interactions with DNA (pink). Lysine residues in the three S/TPKK motifs (green) are also shown. The inset shows a superposition of different HMG-box proteins that were used as templates to model the H1d_C. (B and C) Two alternate models proposed for the whole H1d_C. The two models differ from each other only in their first 26 residues (shown in red). The first figure shows the model where this segment was modeled based on the sub-structure in malate dehydrogenase while the second picture indicates a model where the segment is based on cytochrome C4. The latter model was found to fit better in the context of the whole chromatin particle (see text).

Figure 4

(A) Stereo view of a model of the chromatosome particle containing the nucleosomal core shown as a green ribbon [core histones not shown for clarity in this and in (B)], globular domain (red) and the C-terminal domain (cyan) placed side-by-side with the globular domain. The DNA segments interacting with the globular and the C-terminal domains are shown as pink ribbons. (B) Stereo view of an alternate model of the chromatosome particle which differs from the first in the position of the C-terminal domain. Here, H1d_C (protein in red and DNA in cyan) is positioned on top of the globular domain (green).

Figure 4

(A) Stereo view of a model of the chromatosome particle containing the nucleosomal core shown as a green ribbon [core histones not shown for clarity in this and in (B)], globular domain (red) and the C-terminal domain (cyan) placed side-by-side with the globular domain. The DNA segments interacting with the globular and the C-terminal domains are shown as pink ribbons. (B) Stereo view of an alternate model of the chromatosome particle which differs from the first in the position of the C-terminal domain. Here, H1d_C (protein in red and DNA in cyan) is positioned on top of the globular domain (green).

Figure 5

Final model of the chromatosome particle based on the position of H1d_C as shown in Figure 4B. In this model, H1d_C is seen to bridge both the entering (left) and the exiting (right) duplexes while significantly bending the exiting duplex. The nucleosome core (yellow), the globular domain (red) and the C-terminal domain (cyan) of H1d, along with the segments of DNA directly associated with them, comprise the final model. The blue stretch indicates the additional segment that would be required to accommodate the H1d_C domain in this orientation (see text). When extended using standard B-DNA, the additional segments will be placed on both the entry and exit duplexes, as represented by the pink segments.