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

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.Author summary: The eukaryotic genome is compactly packaged into the cell nucleus. Within the nucleus, DNA forms protein-DNA complexes called nucleosomes. The nucleosome is the fundamental structural unit of chromatin. It is composed of a histone octamer around which DNA wraps about twice. During cellular processes such as DNA transcription, replication and repair, the DNA must be unwrapped from the structure. This unwrapping has been investigated experimentally, but details of the process at the atomic level are not yet well understood. We carried out molecular dynamics simulations using an enhanced sampling method to obtain free energy profiles for unwrapping the outer superhelical turn of the nucleosomal DNA. Our analysis shows that some energy cost is required to unwrap the first 5 bps at one end of the DNA, after which a second 5 bps unwrap with no increase in free energy. The unwrapping then proceeds at the other end of the DNA for up to 10 bps. In this way, DNA unwrapping occurs asymmetrically from one end. These findings provide insight into how DNA dynamics are related to gene regulation.