Fig. 4: The C-terminal third of CHD4 contains an auto-inhibitory domain that binds the DNA translocase. | Nature Communications

Fig. 4: The C-terminal third of CHD4 contains an auto-inhibitory domain that binds the DNA translocase.

From: The role of auxiliary domains in modulating CHD4 activity suggests mechanistic commonality between enzyme families

Fig. 4

A RTFA data for C-terminal truncations of CHD4. Data for CHD4(1–1230) are reproduced from Fig. 2C for the purpose of comparison. B MST data for C-terminal truncations of CHD4. Data for WT CHD4 are reproduced from Fig. 3E for the purpose of comparison. C Covalent crosslinks (XLs) observed for CHD4 in which at least one of the crosslinked residues lies in the C1a region. XLs were visualized using XiNET (https://crosslinkviewer.org/). D Data-driven molecular dynamics modelling of the CHD4 XLs involving the C1a region. Top. An initial homology model of the CHD4 ATPase domain was created using CHD1 as a template (PDB 3MWY). A combination of the same structure and the AlphaFold prediction for CHD4 was used to create a starting model the C1a region. Approximately 50% of the XLs were satisfied in this model (blue XLs; red XLs were violated). Bottom. In the interactive molecular dynamics program ISOLDE, manual restraints were used to fix most of the translocase structure and the model was further constrained by the XLs. ISOLDE was then used to search for conformations that better satisfied the XLs than the starting conformation. Multiple models were obtained (only one is shown) that satisfied ~85% of the XLs. The distributions of XL distances (Cα-Cα) in the initial and final models are shown on the right. Raw data for A and B are provided as a Source Data file, XLMS data can be found in ProteomeXchange using identifier PXD033633.

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