Integrating Theory, Simulations and Experiments to Reveal the Recognition-Specific Pathways in the Nuclear Co-Activator Binding Domain Ensemble

Abstract

The nuclear receptor co-activator binding domain (NCBD) selectively recruits transcription co-activators (TCAs) during the formation of the transcription pre-initiation complex. However, the biophysical mechanisms of NCBD:TCA recognition remain unclear as both NCBD and several of its corresponding TCAs are intrinsically disordered. We therefore probed the conformational diversity of the apo- and holo-forms of NCBD using all-atom, explicit solvent molecular dynamics simulations (∼100 μ1/4s) and small-angle neutron scattering experiments. We integrated theory, simulations and experiments into a unified framework called anharmonic conformational analysis (ACA). ACA identifies a hierarchy of conformational sub-states, intermediates and pathways that play a key role in NCBD:TCA recognition. The transitions between sub-states can be modeled by a bent paperclip, whose arms correspond to helices, α1-α2-α3. The pathways reveal that α1 and α2 adopt conformations close to the holo-form and α3 undergoes extensive conformational changes in response to different TCAs (Fig. 1). The specificity binding loop in NCBD adopts intermediates that enables the bending and twisting of α1 and α2 into its final orientation with the target TCA. We hope this quantitative view of NCBD:TCA landscape can aid the design of novel cancer therapeutics.View Large Image | View Hi-Res Image | Download PowerPoint Slide