Energetics Decomposition of Sac7d:DNA Decrypts Amino Acids Role Without DNA Sequence Selectivity

Sac7d is a 7 kDa protein belonging to the class of the small chromosomal proteins from archeon Sulfolobus acidocaldarius. Sac7d was discovered in 1974 in Yellowstone National Parks geysers, and studied extensively since then for its remarkable stability at large pH and temperature ranges. Sac7d binds to the DNA minor groove, thereby protecting the host genome from extreme conditions by increasing the DNA melting temperature. In this study, we analyzed the Sac7d-DNA complex using 1 μs molecular dynamics simulations. The interaction energy of the interface was decomposed using Molecular Mechanics with Generalized Born Surface Area (MM/GBSA) to determine the residues that contributed most significantly to DNA binding. Out of 12 amino acids considered essential for DNA binding, three were newly identified in this study and had not been previously reported. One of these new amino acids, R63, may be involved in a dynamic protein-DNA interaction. The simulations performed also revealed a sliding motion of Sac7d over double-stranded DNA, suggesting a minimal sequence dependence interaction. Our analysis thus provides novel insights into how the Sac7d chaperones allow to protect DNA from degradation in extreme conditions.