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.