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

Abstract

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.

Free energy profile for unwrapping outer superhelical turn of CENP-A nucleosome

“…Furthermore, we showed a free energy profile for unwrapping DNA from the canonical nucleosome. The profile suggested that a free energy for unwrapping the outer superhelical turn is about 11.5 kcal/mol which agrees well with values obtained in single molecule experiments [20]. The detailed analysis showed that asymmetric unwrapping of DNA is dominant, i.e., either end of DNA firstly unwraps from the histone core by up to 10 bps, then the other end of DNA starts to unwrap.…”

“…This differs from the canonical NCP where asymmetric unwrapping conformations were dominantly observed (see Fig. 6 in a reference [20]).…”

“…Surprisingly, these contacts were somehow maintained up to 10 bp unwrapped states, indicating that these residues were dragged by unwrapped DNA. In contrast, the contacts of most of the residues were lost at 4 bp unwrapped state in the canonical NCP [20], probably because the αN helix in which these residues are involved is longer than that of CENP-A NCP and has a stronger packing to the histone H4.…”

“…The free energy comparison with the canonical NCP clearly indicates that canonical NCP is the most stable when DNA is fully wrapped around the histone core [20] whereas the most of CENP-A NCP populations adopt various conformations in which both ends of DNA are partially unwrapped. In the canonical NCP, once the first 5 bp of DNA were unwrapped from either end of DNA, the unwrapping proceeded spontaneously up to 10 bp in the same end.…”

“…The resolution of the reaction coordinate, Δd was set at 1.0 Å. The relaxation time in the ABMD, τ F was set at 100 ps for maintaining dsDNA conformation based on our previous calculation [20], and the ABMD biasing potential was updated every step.…”