Integrative Modeling of the ISWI Chromatin Remodeling Enzyme from Cross-Linking/Mass Spectrometry and Saxs Data

The eukaryotic genome is organized in the form of chromatin, a complex of DNA with compacting and regulatory proteins. The basic packing unit is the nucleosome where DNA is wrapped tightly around histone proteins. This packaging inevitably leads to the occlusion of DNA sequences that can no longer be accessed by regulatory proteins. To allow dynamic and regulated use of the genome, ATP-consuming nucleosome remodeling enzymes exchange histones and reposition, assemble, and disassemble nucleosomes. The ISWI remodeler protein, a member of the Snf2 family, slides nucleosomes along DNA. However, the basic mechanism of nucleosome translocation is not yet understood. Structural information for the Snf2 family is scarce and hence, atomistic insight into ISWI's repositioning mechanism and its (auto-)regulation are lacking to date. Here, we performed integrative modeling combining cross-linking/mass spectrometry and SAXS data in the ATTRACT docking engine [1]. We obtained structural models of the ATPase domain and the full length protein (including the C-terminal DNA-binding HAND-SANT-SLIDE domain). The resulting models revealed inactive and active conformations of the ISWI ATPase domain and suggested a binding site on lobe 2 for the inhibitory AutoN motif and a basic patch on the histone H4 tail. We also investigated possible binding modes of ISWI on its nucleosomal substrate. Our developed integrative modeling approach is broadly applicable to many transient multi-component assemblies.[1] de Vries et al. “A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT.” Biophys. J. (2015).