Molecular Simulations Discern the Cooperative Binding of Human Brahma-Related Gene 1 Bromodomain and At-Hook Regions in DNA Binding

Abstract

Human brahma-related gene 1 (Brg1) is a central ATPase in the human SWI/SNF chromatin remodeling complex. It contains a bromodomain, which associates with acetylated nucleosomes and is critical in DNA damage response along with a small AT-hook motif that recognizes DNA and enhances the DNA-binding activity. NMR spectroscopy, CD spectroscopy and isothermal calorimetry studies have been conducted on both the Brg1 bromodomain and the AT-hook interacting with the DNA separately. The results show that the Brg1 bromodomain can bind the DNA through an interaction patch which includes the A helix and the AB and ZA loops while the AT-hook prefers to bind in the minor groove. Information about the mechanism of the simultaneous binding are still unknown and, since Brg1 mutations are involved in several human tumors, understanding the function of DNA-Brg1 complex is of key importance to develop specific inhibitors. Here, we’ve combined molecular docking, classic molecular dynamics, and metadynamics simulations to investigate how the Brg1 bromodomain identifies specific binding sites within the DNA helix, both in the presence and absence of the AT-hook motif. Free energy surface discriminate the different binding modes found for both complexes and show that the most likely configurations adopted primarily involve the AT-hook binding in the minor groove while the A helix is parallel to the DNA. Without the AT-hook, the DNA/Brg complex binds to the DNA through the A helix interactions in a perpendicular orientation with the major groove. Our results suggest that the DNA/Brg1 binding mechanism is different in presence and absence of the AT-hook segment in the Brg1 sequence.