Dynamics and mechanisms of interactions between ring-shaped heterohexameric TIP49a/b protein complexes and double-stranded DNA

Abstract

TIP49a and TIP49b, highly conserved proteins belonging to the AAA+ superfamily of DNA-dependent ATPases, participate in numerous cell processes, such as chromatin remodeling, regulation of gene transcription and mitotic cell division, maintenance of genome stability, and snoRNP biogenesis, as well as in the formation of active DNA–telomerase complexes. It has been shown that they are involved in complex networks of protein–protein interactions and, in spite of their structural similarity, sometimes perform opposite functions. Although these proteins exhibit a wide range of activities, the mechanisms of their actions are still poorly understood. In this work, ring-shaped heterohexameric TIP49a/b complexes containing in their central channel short fragments of double-stranded DNA (dsDNA, 20 base pairs of different GC composition) were obtained for the first time using the molecular docking technique, while methods of molecular dynamics in a periodic water box were applied to investigate the conformational dynamics of these proteins and the mechanisms of their helicase activity. It was found that (1) interaction of a DNA helix with positively charged protein loops inside the central channel of the ring-shaped hexameric complex caused unwinding of the helix; (2) the unwinding occurred only inside the hexameric ring, whereas the tails of the helix, which lie outside, retained the initial classical B-form conformation throughout the 50 ns of molecular dynamics; and (3) the presence of ATP in TIP49a/b complexes affected the dynamics and the final structure of dsDNA, causing partial breaking of complementary bonds in GC-poor DNA sequences.