H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

<div><p>Acetylation of lysine residues in histone tails is associated with gene transcription. Because histone tails are structurally flexible and intrinsically disordered, it is difficult to experimentally determine the tail conformations and the impact of acetylation. In this work, we performed simulations to sample H3 tail conformations with and without acetylation. The results show that irrespective of the presence or absence of the acetylation, the H3 tail remains in contact with the DNA and assumes an α-helix structure in some regions. Acetylation slightly weakened the interaction between the tail and DNA and enhanced α-helix formation, resulting in a more compact tail conformation. We inferred that this compaction induces unwrapping and exposure of the linker DNA, enabling DNA-binding proteins (e.g., transcription factors) to bind to their target sequences. In addition, our simulation also showed that acetylated lysine was more often exposed to the solvent, which is consistent with the fact that acetylation functions as a post-translational modification recognition site marker.</p></div

The initial and final conformations in the outer DNA unwrapping simulations.

<p>Shown are DNA numbering and unwrapped DNA regions in stages 1 (a) and 2 (b). H3: blue, H4: green, H2A: yellow and H2B: red.</p

Histone-DNA contacts changing as a function of the number of unwrapped bps at one DNA end during stage 2.

<p>(a) H2Aa-DNA end2 contacts. (b) H2Ba-DNA end2 contacts. Plotted are the contact probabilities of each residue in the conformational ensemble. Contact is counted if at least one pair of atoms in the histone and DNA is within 4 Å of each other. (c) Close-up view of the H2Aa-DNA end2 interface. Residues 16 to 32 and 75 to 77 are shown as stick models. H2A and H2B are shown as cartoon models and are colored yellow and red, respectively. (d) Close-up view of the H2Ba-DNA end2 interface. The DNA and residues 36 to 43 are shown as space filling and stick models, respectively. H2A and H2B are shown as cartoon models and are colored yellow and red, respectively.</p

Differences in the spatial distributions between the unacetylated and K14ac systems.

<p>Differences in the H3 tails and DNA are shown in the upper and lower panels, respectively. Blue and red contour maps show spatial regions preferred in the unacetylated and K14ac system, respectively. The coloring of the molecules and the nucleosome model are the same as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004788#pcbi.1004788.g001" target="_blank">Fig 1</a>.</p

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA

<div><p>The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core. To function in cellular processes, however, nucleosomal DNA must be unwrapped. Although this unwrapping has been experimentally investigated, details of the process at an atomic level are not yet well understood. Here, we used molecular dynamics simulation with an enhanced sampling method to calculate the free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. A free energy change of about 11.5 kcal/mol for the unwrapping agrees well with values obtained in single molecule experiments. This simulation revealed a variety of conformational states, indicating there are many potential paths to outer superhelicdal turn unwrapping, but the dominant path is likely asymmetric. At one end of the DNA, the first five bps unwrap, after which a second five bps unwrap at the same end with no increase in free energy. The unwrapping then starts at the other end of the DNA, where 10 bps are unwrapped. During further unwrapping of 15 bps, the unwrapping advances at one of the ends, after which the other end of the DNA unwraps to complete the unwrapping of the outer superhelical turn. These results provide insight into the construction, disruption, and repositioning of nucleosomes, which are continuously ongoing during cellular processes.</p></div

Schematic view of the dominant pathway to the unwrapping of outer DNA with estimated changes in free energy.

<p>Schematic view of the dominant pathway to the unwrapping of outer DNA with estimated changes in free energy.</p

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation

We investigate the problem of artifacts caused by the periodic boundary conditions (PBC) used in molecular simulation studies. Despite the long history of simulations with PBCs, the existence of measurable artifacts originating from PBCs applied to inherently <i>non</i>periodic physical systems remains controversial. Specifically, these artifacts appear as differences between simulations of the same system but with different simulation-cell sizes. Earlier studies have implied that, even in the simple case of a small model peptide in water, sampling inefficiency is a major obstacle to understanding these artifacts. In this study, we have resolved the sampling issue using the replica exchange molecular dynamics (REMD) enhanced-sampling method to explore PBC artifacts. Explicitly solvated zwitterionic polyalanine octapeptides with three different cubic-cells, having dimensions of <i>L</i> = 30, 40, and 50 Å, were investigated to elucidate the differences with 64 replica × 500 ns REMD simulations using the AMBER parm99SB force field. The differences among them were not large overall, and the results for the <i>L</i> = 30 and 40 Å simulations in the conformational free energy landscape were found to be very similar at room temperature. However, a small but statistically significant difference was seen for <i>L</i> = 50 Å. We observed that extended conformations were slightly overstabilized in the smaller systems. The origin of these artifacts is discussed by comparison to an electrostatic calculation method without PBCs

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA - Fig 3

<p><b>Free energy profiles plotted as a function of the total number of unwrapped bps (a) and (b), or as a function of the total number of unwrapped bps and end-to-end distance (c) and (d).</b> (a) and (c) stage 1. (b) and (d) stage 2. Colors in (c) and (d) denote the relative free energy in each stage.</p

Impact of K14ac on H3 tail conformation.

<p>(A) Average α-helical content ratio with the standard error for each residue of unacetylated and K14ac H3 tails. The error bars represent the standard errors calculated from 256 independent trajectories. (B) Rg distributions for unacetylated and K14ac H3 tails.</p

Differences in unwrapped bps between the two DNA ends.

<p><b>The differences are plotted as a function of the total number of unwrapped bps.</b> The bp differences are normalized to the number of conformations with the same total number of unwrapped bps. (a) stage 1. (b) stage 2.</p