A hydrophobic vector association model of nucleosomes in chromatin

The structure of chromatin and its association mechanisms are studied using the biological membrane (BM) model with a formalism of electric and hydrophobic dipole interactions. This model establishes that hydrophobic moments attract each other, associating in parallel in a manner analogous to how phospholipids associate to form a biological membrane. The structure of DNA is reviewed as the stacking of the hydrophobic dipole moments of its bases in relation to their separation distances. Archaeal chromatin is revisited, which is associated with a structure resembling a continuous coil of DNA, in which each turn contains three protohistone dimers hydrophobically attached to it. A description follows of the hydrophobic association of histones H2A, H2B, H3, and H4, forming the well-known octamer, and its binding to two DNA strands that constitute the nucleosome. This association is nuanced with electrostatic interactions, highlighting the fundamental role of hydrophobic interactions. Simulated alternative forms of histone association are compared, and it is confirmed that the structure present in the nucleosome is the most energetically stable. This type of interaction is also the basis of the hydrophobic association mechanisms of nucleosome stacking, by the parallel alignment of their hydrophobic dipole moments. These associations in parallel stacks have variable strengths, depending on their specific sequence compositions. Also the role of histone H1 and linker DNAs is addressed in its mechanisms of joining the extensions of nucleosomal DNA to join another nucleosome.