Synergistic folding of two intrinsically disordered proteins: searching for conformational selection

Abstract

Intrinsically disordered proteins (IDPs) lack stable structures under physiological conditions but often fold into stable structures upon specific binding. These coupled binding and folding processes underlie the organization of cellular regulatory networks, and a mechanistic understanding is thus of fundamental importance. Here, we investigated the synergistic folding of two IDPs, namely, the NCBD domain of transcription coactivator CBP and the p160 steroid receptor coactivator ACTR, using a topology-based model that was carefully calibrated to balance intrinsic folding propensities and intermolecular interactions. As one of the most structured IDPs, NCBD is a plausible candidate that interacts through conformational selectionlike mechanisms, where binding is mainly initiated by pre-existing folded-like conformations.Indeed, the simulations demonstrate that, even though binding and folding of both NCBD and ACTR is highly cooperative on the baseline level, the tertiary folding of NCBD is best described by the "extended conformational selection" model that involves multiple stages of selection and induced folding. The simulations further predict that the NCBD/ACTR recognition is mainly initiated by forming a mini folded core that includes the second and third helices of NCBD and ACTR. These predictions are fully consistent with independent physics-based atomistic simulations as well as a recent experimental mapping of the H/D exchange protection factors.The current work thus adds to the limited number of existing mechanistic studies of coupled binding and folding of IDPs, and provides a first direct demonstration of how conformational selection might contribute to efficient recognition of IDPs. Interestingly, even for highly structured IDPs like NCBD, the recognition is initiated by the more disordered C-terminal segment and with substantial contribution from induced folding. Together with existing studies of IDP interaction mechanisms, this argues that induced folding is likely prevalent in IDP-protein interaction, and emphasizes the importance of understanding how IDPs manage to fold efficiently upon (nonspecific) binding. Success of the current study also further supports the notion that, with careful calibration, topology-based models can be effective tools for mechanistic study of IDP interaction and regulation, especially when combined with physicsbased atomistic simulations and experiments.2

Fast Association and Slow Transitions in the Interaction between Two Intrinsically Disordered Protein Domains

“…Such binding mechanism is consistent with the observed structural plasticity of IDP complexes, where disordered regions search the most stable conformation with specific interactions after the initial encounter event. The presence of intermediate states is also in agreement with recent molecular dynamics simulation studies (17,23) on NCBD/ACTR, where it was suggested that productive on-pathway intermediates may arise through two different pathways. One intermediate was formed by docking of the C-terminal helices and stabilized by the highly conserved and buried salt bridge between Asp-1068 in ACTR and Arg-2104 in NCBD, whereas formation of the second intermediate was found to be initiated by interactions between the N-terminal helices.…”

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

“…75 An earlier simulation study using a single-Gō model, with carefully calibrated secondary structure, similarly predicted an initial formation of inter-protein contacts prior to folding of the NCBD, when binding to ACTR, consistent with our results. 53 The results we obtain with our double-Gō model are completely consistent with the conclusions of our earlier all-atom study of the isolated NCBD. 38 In that work, we found that although the unbound state was still significantly disordered, there was evidence that some features of the binding interface were already present.…”

“…46 Gō models have been successful 47 in describing a range of phenomena, from protein folding mechanisms 48 to protein association, 49 domain swapping, 50 protein misfolding, 51 and association of IDPs with their binding partners. 18,19,52,53 However, these models each describe only one folded (and one unfolded) free energy minimum (excepting nativelike intermediates), and would therefore not be appropriate for describing the association of an IDP with two different binding partners where it binds them in very different structures. To address this shortcoming, we have constructed a double-Gō variant which combines Gō potentials derived from different structures into a hybrid system whose partition function at a defined mixing temperature T mix is equal to the sum of the partition functions of the separate Gō potentials at T mix .…”

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein

“…Therefore, we introduced additional energetic parameters to match the experimental observations, including structural fluctuations, binding affinity, residual structure, and ionic strength. Overall, our model is substantially different from previous physics-based models (24)(25)(26)(27)(28) and structure-based models (10,11,13,(29)(30)(31)(32)(33)(34)(35) used in the studies of IDPs.…”

“…Among these 96 replicas in REMD simulations, we focused on investigating the thermodynamic properties at 298 K, which is comparable to the experimental conditions. There are multiple methods to define the formation of a helix in a peptide segment (13,26,28,34). Here, we used three different definitions (SI Appendix) to guarantee the robustness of the analysis.…”