Prepaying the entropic cost for allosteric regulation in KIX.

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 (WILL) and c-Wlyb peptides, at isolated interaction sites. In vitro, the affinity for binding c-Wlyb is approximately doubled when KIX is in complex with WILL, which suggests a positive cooperative binding mechanism, and the affinity for WILL is also slightly increased when KIX is first bound by c-Wlyb. Expanding the scope of recent NWIR 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, KlX-c-Wlyb, WILL-KIX, and WILL-KIX-c-Myb using a topology-based Go-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 WILL binding lowers the entropic cost for c-Wlyb 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. [ABSTRACT FROM AUTHOR]