To understand the interplay of residual structures and conformational fluctuations in the interaction of intrinsically
disordered proteins (IDPs), we first combined implicit solvent and replica exchange sampling to calculate atomistic
disordered ensembles of the nuclear co-activator binding domain (NCBD) of transcription coactivator CBP and the activation domain of the p160 steroid receptor coactivator ACTR. The calculated ensembles are in quantitative agreement with NMRderived residue helicity and recapitulate the experimental observation that, while free ACTR largely lacks residual secondary
structures, free NCBD is a molten globule with a helical content similar to that in the folded complex. Detailed conformational analysis reveals that free NCBD has an inherent ability to substantially sample all the helix configurations that have been previously observed either unbound or in complexes. Intriguingly, further high-temperature unbinding and
unfolding simulations in implicit and explicit solvents emphasize the importance of conformational fluctuations in
synergistic folding of NCBD with ACTR. A balance between preformed elements and conformational fluctuations appears
necessary to allow NCBD to interact with different targets and fold into alternative conformations. Together with previous
topology-based modeling and existing experimental data, the current simulations strongly support an ‘‘extended
conformational selection’’ synergistic folding mechanism that involves a key intermediate state stabilized by interaction
between the C-terminal helices of NCBD and ACTR. In addition, the atomistic simulations reveal the role of long-range as well as short-range electrostatic interactions in cooperating with readily fluctuating residual structures, which might enhance the encounter rate and promote efficient folding upon encounter for facile binding and folding interactions of IDPs. Thus, the current study not only provides a consistent mechanistic understanding of the NCBD/ACTR interaction, but also helps establish a multi-scale molecular modeling framework for understanding the structure, interaction, and
regulation of IDPs in general.
