Coupled MD simulations and NMR reveal that the intrinsically disordered domain of the breast-cancer susceptibility 1 protein (BRCA1) binds head-on to DNA double-strand ends

Abstract

Mutations of the breast cancer susceptibility 1 (BRCA1) gene are associated with high risks of breast and ovarian cancer, not least due to the vital role of the BRCA1 gene product in DNA double-strand repair. Strikingly, little is known about the structural dynamics of BRCA1-DNA complexes, despite their importance for maintaining a healthy cell cycle and the potential boost for rational targeting of BRCA1 by their detailed understanding. Aiming to address this shortcoming, we present a model resulting from the direct binding of the intrinsically disordered region (IDR) of BRCA1 to DNA oligomers. To this end, we developed a workflow combining in-silico structural predictions, computational docking, and molecular dynamics simulations with chemical shift perturbations in ¹H-³¹P crosspeaks obtained by nuclear magnetic resonance spectroscopy of a binding DNA oligomer. Our data show that the BRCA1-DNA complexes are stabilized, mainly through ‘head-on’ interaction between BRCA1 and the DNA double-strand ends. ‘Side-on’ binding to the DNA major grove was insufficient to form stable complexes. When bound to the nucleic acid, the IDR maintained high degrees of flexibility in our simulations reminiscent of ‘fuzzy’ complexes. Illustrating the structural dynamics underlying BRCA1-DNA complexes is essential for the bottom-up reconstruction of the role BRCA1 plays in DNA double-strand break repair. The presented work makes a step in this direction, aiming to complement existing assays with models that can assist in the functional screening of hereditary breast and ovarian cancer (HBOC)-relevant mutations.