Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.

酵母Chd1蛋白的功能是在全基因组范围内定位核小体（nucleosome）。本研究对溶液状态下以及结合核小体时的Chd1蛋白结构进行建模分析。在未结合配体的空态（apo state）下，DNA结合结构域（DNA-binding domain）会接触核小体的边缘；而当体系中加入非水解ATP类似物（non-hydrolyzable ATP analog）ADP-铍氟化物（ADP-beryllium fluoride）时，我们观测到ATP酶结构域（ATPase domain）与距对称二聚轴1.5个螺旋圈的相邻DNA环产生额外相互作用。该构象下的结合过程涉及解开核小体DNA的外侧螺旋圈，且需要DNA结合结构域相对于ATP酶结构域发生显著的取向重排。DNA结合结构域的取向由N端序列介导，对该区域进行的突变会对Chd1的活性产生正向与负向调控效应。上述观测结果表明，溶液中C端DNA结合区域的不利取向是导致蛋白处于自抑制状态的重要诱因。