Structural Transitions Of a Helicase-Partial Duplex DNA Complex during ATP Hydrolysis Cycle

Abstract

The chromatin remodeling complex Isw2 from S. cerevisiae (yIsw2) mobilizes nucleosomes through an ATP-dependent reaction that is coupled to the translocation of the enzyme along intranucleosomal DNA. In this study we demonstrate that yIsw2 is capable of translocating along single-stranded DNA in a reaction that is coupled to ATP hydrolysis. We find that single-stranded DNA translocation by yIsw2 occurs through a series of repeating uniform steps with an overall macroscopic processivity of P ¼ (0.92 5 0.01); this processivity corresponds to an average translocation distance of (24 5 4) nucleotides before dissociation. This processivity corresponds well to the processivity of nucleosome sliding by yIsw2 thus arguing that single-stranded DNA translocation may be fundamental to the double-stranded DNA translocation required for effective nucleosome mobilization by the enzyme. Furthermore, we find that a slow initiation process, following DNA binding, is required to make yIsw2 competent for DNA translocation. We also provide both evidence that this slow initiation process likely corresponds to the second step of a two-step DNA binding mechanism by yIsw2 and a quantitative description of the kinetics of this DNA binding mechanism.