Edited by José N. Onuchic, Rice University, Houston, TX, and approved June 9, 2014 (received for review March 28, 2014)
Understanding how proteins are regulated through the binding of an effector molecule at a nonoverlapping site is a central problem in protein allostery. However, connecting the changes in structural dynamics to changes in the binding affinity can be challenging. Here, we investigate the allosteric mechanism involving a promiscuous protein that serves as a hub for a variety of intrinsically disordered proteins (IDPs). By using a coarse-grained model to simulate the interactions between the protein and two IDPs, we were able to recapitulate experimental binding affinities, capture relevant structural dynamics, and provide a thermodynamic and kinetic description of the allosteric mechanism. It is presumable that the features identified in this allosteric mechanism are conserved between the central protein and other IDPs.
The kinase-inducible domain interacting (KIX) domain of the CREB binding protein (CBP) is capable of simultaneously binding two intrinsically disordered transcription factors, such as the mixed-lineage leukemia (MLL) and c-Myb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Myb is approximately doubled when KIX is in complex with MLL, which suggests a positive cooperative binding mechanism, and the affinity for MLL is also slightly increased when KIX is first bound by c-Myb. Expanding the scope of recent NMR and computational studies, we explore the allosteric mechanism at a detailed molecular level that directly connects the microscopic structural dynamics to the macroscopic shift in binding affinities. To this end, we have performed molecular dynamics simulations of free KIX, KIX-c-Myb, MLL-KIX, and MLL-KIX-c-Myb using a topology-based Gō-like model. Our results capture an increase in affinity for the peptide in the allosteric site when KIX is prebound by a complementary effector and both peptides follow an effector-independent folding-and-binding mechanism. More importantly, we discover that MLL binding lowers the entropic cost for c-Myb binding, and vice versa, by stabilizing the L12-G2 loop and the C-terminal region of the α3 helix on KIX. This work demonstrates the importance of entropy in allosteric signaling between promiscuous molecular recognition sites and can inform the rational design of small molecule stabilizers to target important regions of conformationally dynamic proteins.
Author contributions: S.M.L., A.K.M., and C.L.B. designed research; S.M.L. and J.K.G. performed research; S.M.L. contributed new reagents/analytic tools; S.M.L., J.K.G., A.K.M., and C.L.B. analyzed data; and S.M.L., J.K.G., A.K.M., and C.L.B. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1405831111/-/DCSupplemental.
