H4 histone tail mediated DNA-DNA interaction and effects on DNA structure, flexibility, and counterion binding: a molecular dynamics study

All-atom molecular dynamics (MD) simulations were performed during 30-45 ns for a system of three identical DNA 22-mers, 14 short fragments of the charged H4 histone tail peptide fragment (amino acids 5-12, KGGKGLGK) with K(+) counterions, and explicit water. The simulation setup mimics the crowded conditions of DNA in eukaryotic chromatin. To assess the influence of tail fragments on DNA structure and dynamics, a "control" 20 ns MD simulation was carried for a system with the same DNA and water content but in the absence of oligopeptides. Results of DNA interaction with the histone tail fragments, K(+), and water is presented. DNA structure and dynamics and its interplay with the histone tail fragments binding are described. The charged side chains of the lysines play a major role in mediating DNA-DNA attraction by forming bridges and coordinating to phosphate groups and electronegative sites in the minor groove. Binding of all species to DNA is dynamic. Some of the tail fragments while being flexible and mobile in each of its functional groups remain associated near certain locations of the DNA oligomer. The present work allows capturing typical features of the histone tail-counterion-DNA structure, interaction, and dynamics.