Significant compaction of H4 histone tail upon charge neutralization by acetylation and its mimics, possible effects on chromatin structure

Abstract

The intrinsically disordered, positively charged H4 histone tail is important for chromatin structure and function. We have explored conformational ensembles of human H4 tail in solution, with varying levels of charge neutralization via acetylation or amino-acid substitutions such as K→Q. We have employed an explicit water model shown recently to be well suited for simulations of intrinsically disordered proteins. Upon progressive neutralization of the H4, its radius of gyration decreases linearly with the tail charge q, the trend is explained using a simple polymer model. While the wild type state (q=+8) is essentially a random coil, hyper-acetylated H4 (q=+3) is virtually as compact and stable as a globular protein of the same number of amino-acids. Conformational ensembles of acetylated H4 match the corresponding K→X substitutions only approximately: based on the ensemble similarity, we propose K→M as a possible alternative to the commonly used K→Q. Possible effects of the H4 tail compaction on chromatin structure are discussed within a qualitative model in which the chromatin is highly heterogeneous, easily inter-converting between various structural forms. We predict that upon progressive charge neutralization of the H4 tail, the least compact sub-states of chromatin de-condense first, followed by de-condensation of more compact structures, e.g. those that harbor a high fraction of stacked di-nucleosomes. The predicted hierarchy of DNA accessibility increase upon progressive acetylation of H4 might be utilized by the cell for selective DNA accessibility control.

Keywords: Acetylation; Chromatin compaction; DNA accessibility; Intrinsically disordered.

Figure 1:

A (fully extended) structure of the H4 histone tail. Lysine residues – targets of post-translation modifications such as acetylation – are shown as blue spheres and indicated by arrows.

Figure 2:

1D free energy landscapes of three charge (q) states of H4 histone tail. Left: wild type, q = +8; Middle: hyper-acetylated, q = +3; Right: the hyper-acetylated state q = +3 is mimicked by K → Q substitutions at all of the five lysine positions, Fig. 1. The low energy extensibility, D_EE(k_BT), of the polymer chain is defined as the landscape width (end-to-end distance) at k_BT level above the global free energy minimum, while D_MAX (k_BT) is the origin-to-end distance at k_BT level.

Figure 3:

Linear dependence of the (relative) radius of gyration, R_g, of the H4 histone tail upon its total charge. The tail charge corresponds to the different states of acetylation and K → Q shown in Table 1. Right y-axis R_g normalized by $R_g^{GP}$ of a globular protein of the same number of residues. Left y-axis R_g normalized by $R_g^{RC}$ of the corresponding random coil. The separate figures can be found in the SI.

Figure 4:

Two distinct mechanisms for decrease of the over-all size of H4 tail upon charge neutralization of its amino-acids. (1): The decrease is driven by formation of local regions of highly compact secondary structure, e.g. formation of local helical fragments. Red zig-zag lines indicate portions of the polymer chain that have been locally compacted. (2): The entire chain undergoes a more-or-less uniform, global compaction of its tertiary structure.

Figure 5:

Equilibrium size R_eq (black solid line) of a N = 26 segment long polymer coil as a function of its total charge q, as predicted by Eq. 2. A linear fit to the model in the range 3 ≤ q ≤ 8 is shown as dashed orange line.

Figure 6:

2D free energy landscapes of the wild type (left) and hyper-acetylated (right) H4 histone tail. The black arrows indicate representative snapshots from the lowest free energy state, within 1k_BT of the global minimum. The position of the global free energy minimum of the WT ensemble is indicated by a small white dot, which is replicated in every panel. The white arrow in the “All K Acetylated” panel shows a putative “folding path” – transition from an extended state (purple zone), which is the global minimum in this case, to the highly compact structures corresponding to the WT minimum (the white dot).

Figure 7:

Examples of di-nucleosome conformations observed in available X-ray structures (PDB ID indicated in each panel). Shown are two of the four examples from Ref. [66], intended here to illustrate the wide range of nucleosome-nucleosome distances and mutual orientations. The radius of each dark blue sphere equals the low energy extensibility, D_MAX, of the H4 tail located closest to the neighboring nucleosome. Progressive charge neutralization of H4 via lysine acetylation reduces D_MAX, thus reducing the likelihood of forming stabilizing H4-mediated inter-nucleosome interactions. The reduction is more pronounced in less compact di-nucleosomes, which may lead to selective de-condensation of the corresponding chromatin structures.

Figure 8:

Probability distributions of the radius of gyration, R_g, of the wild type H4 histone tail and its several states of charge neutralization by acetylation (left) and K → Q substitution (right), Table 1. The WT distribution (purple line) is the most broad, becoming significantly narrower upon progressive charge neutralization of the lysine residues. Black vertical lines indicate the range of R_g seen in globular proteins of the same number of amino acids.