Synergistic Folding and Binding of Two Intrinsically Disordered Proteins

Abstract

The nuclear coactivator-binding domain (NCBD) of CREB binding protein is an intrinsically disordered protein (IDP), which exists as molten globule like structures in the unbound state. As one of the most folded IDPs, NCBD folds synergistically with another IDP, activator for thyroid hormone and retinoid receptor (ACTR) of the p160 steroid receptor. A topology-based Go-like coarse-grained protein model has been used to investigate the mechanism of the NCBD:ACTR interaction. The simulation results support a largely cooperative mechanism for the folding of the two IDPs. Specifically, while the binding induced folding follows multiple pathways, the α2 helix of ACTR most frequently initiates the binding by interacting with a preformed structural motif of NCBD, where the α2 and α3 helices of NCBD are mostly folded and correctly packed. This initial binding is followed by the binding and folding of rest of the helices of both IDPs in a highly cooperative fashion. This is consistent with the importance of the disordered leucine-rich motifs in specificity of NCBD:ACTR established by previous biochemical and biophysical data, and further supported by unpublished mass spectroscopy data from David Weis's lab. Compared to ACTR, folding of NCBD appear to mostly involve assembly of pre-folded of α1 and α2 helices, and only α3 folding appears to be initiated by ACTR binding.