Conformational Ensembles of an Intrinsically Disordered Protein pKID with and without a KIX Domain in Explicit Solvent Investigated by All-Atom Multicanonical Molecular Dynamics

The phosphorylated kinase-inducible activation domain (pKID) adopts a helix–loop–helix structure upon binding to its partner KIX, although it is unstructured in the unbound state. The N-terminal and C-terminal regions of pKID, which adopt helices in the complex, are called, respectively, α(A) and α(B). We performed all-atom multicanonical molecular dynamics simulations of pKID with and without KIX in explicit solvents to generate conformational ensembles. Although the unbound pKID was disordered overall, α(A) and α(B) exhibited a nascent helix propensity; the propensity of α(A) was stronger than that of α(B), which agrees with experimental results. In the bound state, the free-energy landscape of α(B) involved two low free-energy fractions: native-like and non-native fractions. This result suggests that α(B) folds according to the induced-fit mechanism. The α(B)-helix direction was well aligned as in the NMR complex structure, although the α(A) helix exhibited high flexibility. These results also agree quantitatively with experimental observations. We have detected that the α(B) helix can bind to another site of KIX, to which another protein MLL also binds with the adopting helix. Consequently, MLL can facilitate pKID binding to the pKID-binding site by blocking the MLL-binding site. This also supports experimentally obtained results.