Dynamic Conformations of Chromatin Remodeler ISWI during Nucleosome Sliding Revealed by Hydrogen-Deuterium Exchange Coupled to Mass Spectrometry

Abstract

Chromatin remodelers maintain the chromatin structure and hence gene expression. Imitation SWItch, ISWI, is a chromatin remodeler, which regulates nucleosome spacing across the genome by its adenosine 5′-triphosphate (ATP)-dependent nucleosome sliding activity. To understand how this happens requires identification of the conformational changes that occur in all domains of ISWI during the entire nucleosome sliding cycle. Using the hydrogen–deuterium exchange coupled to mass spectrometry (HDX-MS) methodology, we have monitored the conformational dynamics of Drosophila FL-ISWI at all the stages of nucleosome sliding. Our data show that, in the resting state, FL-ISWI is intrinsically dynamic in many regions, including the N- and C-terminal regulatory regions. During nucleosome sliding, different regions of the ATPase domain, which bind to the nucleosomal DNA, undergo a major conformational change, and the C-terminal HSS domain switches from a stable state to a more dynamic state. ISWI adopts distinct conformations in its nucleosome bound and sliding states as the interactions established by it upon binding to the nucleosome are broken during DNA translocation. HDX-MS has made it possible to characterize multiscale dynamics from small fluctuations to large structural changes occurring in all the domains of FL-ISWI during the different steps of nucleosome sliding. The structural mechanism revealed for ISWI has implications for several other protein families containing a Rec-A domain ATPase core.