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. 2019 May 21;116(10):1845-1855.
doi: 10.1016/j.bpj.2019.03.021. Epub 2019 Apr 17.

The Oligomerization Landscape of Histones

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Free PMC article

The Oligomerization Landscape of Histones

Haiqing Zhao et al. Biophys J. .
Free PMC article

Abstract

In eukaryotes, DNA is packaged within nucleosomes. The DNA of each nucleosome is typically centered around an octameric histone protein core: one central tetramer plus two separate dimers. Studying the assembly mechanisms of histones is essential for understanding the dynamics of entire nucleosomes and higher-order DNA packaging. Here, we investigate canonical histone assembly and that of the centromere-specific histone variant, centromere protein A (CENP-A), using molecular dynamics simulations. We quantitatively characterize their thermodynamical and dynamical features, showing that two H3/H4 dimers form a structurally floppy, weakly bound complex, the latter exhibiting large instability around the central interface manifested via a swiveling motion of two halves. This finding is consistent with the recently observed DNA handedness flipping of the tetrasome. In contrast, the variant CENP-A encodes distinctive stability to its tetramer with a rigid but twisted interface compared to the crystal structure, implying diverse structural possibilities of the histone variant. Interestingly, the observed tetramer dynamics alter significantly and appear to reach a new balance when H2A/H2B dimers are present. Furthermore, we found that the preferred structure for the (CENP-A/H4)2 tetramer is incongruent with the octameric structure, explaining many of the unusual dynamical behaviors of the CENP-A nucleosome. In all, these data reveal key mechanistic insights and structural details for the assembly of canonical and variant histone tetramers and octamers, providing theoretical quantifications and physical interpretations for longstanding and recent experimental observations. Based on these findings, we propose different chaperone-assisted binding and nucleosome assembly mechanisms for the canonical and CENP-A histone oligomers.

Figures

Figure 1
Figure 1
The binding-free-energy landscapes of two H3 dimers and that of two CENP-A dimers. Two-dimensional FEPs are mapped as a function of the distance between two interacting dimers RCOM and of the quantification of the nativeness of their binding interface Qinterface for (H3/H4)2 (A) and (CENP-A/H4)2 (B). To see this figure in color, go online.
Figure 2
Figure 2
(CENP-A/H4)2 has a deeper FEP than (H3/H4)2. The potential of mean force along the distance R between histone dimers is deeper for (CENP-A/H4)2 (purple) than for (H3/H4)2 (green). R is measured from the center of mass of one dimer to the other. The shaded areas illustrate the standard deviations (SD) of the curves. To see this figure in color, go online.
Figure 3
Figure 3
(CENP-A/H4)2 is more compact than (H3/H4)2. (A) The initial conformations of the H3 tetramer (green) and CENP-A tetramer (purple) were taken from their nucleosome crystal structures (PDB: 1KX5 and 3AN2). Lateral view (i) and top view (ii) of aligned structures are displayed. (B) The CENP-A tetramer has a smaller radius of gyration, Rg, than the H3 tetramer, with a narrower distribution. The vertical dashed lines mark the measured Rg values of the initial structures. To see this figure in color, go online.
Figure 4
Figure 4
The H3 tetramer swivels around its binding interface, whereas the CENP-A tetramer remains relatively stable. (A) The distribution for the dihedral angle between α2 helices features one prominent peak for (CENP-A/H4)2 and three smaller peaks for (H3/H4)2, indicating (CENP-A/H4)2 maintains a more fixed orientation than (H3/H4)2. Vertical dashed lines are the corresponding dihedral angles of the initial structures. (B) Representative conformations from each population are displayed. (C) Positive (+) and negative (−) dihedral angles of the histone tetramer measured here correspond to the left-handed and right-handed DNA superhelical wrapping in the tetrasome, respectively. To see this figure in color, go online.
Figure 5
Figure 5
(CENP-A/H4)2 has a more stable four-helix bundle than (H3/H4)2. (A) (H3/H4)2 (green) forms fewer contacts than (CENP-A/H4)2 (purple) in the four-helix bundle region. The histogram of the number of contacts for (H3/H4)2 has two peaks at 13 and 25, whereas (CENP-A/H4)2 has a single peak at 27. The dash lines mark the four-helix contacts number in corresponding crystal structures. (B) Corresponding representative structures demonstrate that the (H3/H4)2 four-helix bundle becomes broken or disrupted by αN helices (pink), whereas the four-helix bundle (α2 and α3, blue and yellow) remains stable in (CENP-A/H4)2 throughout the simulation. α2 and α3 helices are marked in blue and yellow. CENP-A-specific residues L112, T113, L114, and V126 and H3-specific V46 and A47 are shown in coarse-grained spheres. To see this figure in color, go online.
Figure 6
Figure 6
H2A/H2B stabilizes (H3/H4)2 but not (CENP-A/H4)2. (A) The probability distribution of H3 tetramer Rg features a more focused peak in the context of an octamer compared to that of the solo H3 tetramer (Fig. 3 C), whereas one peak and one shoulder exist in the same distribution for the CENP-A tetramer in the context of an octamer. (B) Distributions of the dihedral angle between α2 helices demonstrate that in the presence of H2A/H2B, (H3/H4)2 becomes more similar to (CENP-A/H4)2; both curves feature a prominent peak around 80°. Vertical dashed lines in both panels are the corresponding tetrameric Rg values and dihedral angles measured from the initial octamer. To see this figure in color, go online.
Figure 7
Figure 7
Suggested different models for histones and their chaperones during deposition. (Left) H3/H4 may be deposited in the form of a tetramer with each external side bracketed by a CAF-1 chaperone, which may stabilize the tetramer. (Right) CENP-A may be deposited as dimers; each dimer is loaded by one HJURP chaperone. To see this figure in color, go online.

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