The chromatin folding problem is an exciting and rich field for modern research. On the most basic level, chromatin fiber consists of a collection of protein-nucleic acid complexes, known as nucleosomes, joined together by segments of linker DNA. Understanding how the cell successfully compacts meters of highly charged DNA into a micrometer size nucleus while still enabling rapid access to the genetic code for transcriptional processes is a challenging goal.
In an article published in JACS, the Papoian Group, discusses the way mobile ions condense around the nucleosome core particle, as revealed by an extensive all-atom molecular dynamics simulation. Overall, this research facilitates a better understanding of the way ionic and hydration interactions within a nucleosome may affect internucleosomal interactions in higher order chromatin fibers.
In a review published as the cover story in The Journal of Physical Chemistry B, researchers from the Papoian Group provide a brief introduction to some of the core concepts required in the discussion of the protein native dynamics using energy landscapes ideas.
Proteins are highly complex molecules with features exquisitely selected by nature to carry out essential biological functions. Physical chemistry and polymer physics provide tools needed to elucidate this complexity. Upon translation, many proteins fold to a thermodynamically stable form known as the native state. The native state is not static, but consists of a hierarchy of conformations, that are continuously explored through dynamics.