Mechanistic insights into the role of calcium in the allosteric regulation of the calmodulin-regulated death-associated protein kinase

Calcium (Ca(2+)) signaling plays an important role in the regulation of many cellular functions. Ca(2+)-binding protein calmodulin (CaM) serves as a primary effector of calcium function. Ca(2+)/CaM binds to the death-associated protein kinase 1 (DAPK1) to regulate intracellular signaling pathways. However, the mechanism underlying the influence of Ca(2+) on the conformational dynamics of the DAPK1−CaM interactions is still unclear. Here, we performed large-scale molecular dynamics (MD) simulations of the DAPK1−CaM complex in the Ca(2+)-bound and-unbound states to reveal the importance of Ca(2+). MD simulations revealed that removal of Ca(2+) increased the anti-correlated inter-domain motions between DAPK1 and CaM, which weakened the DAPK1−CaM interactions. Binding free energy calculations validated the decreased DAPK1−CaM interactions in the Ca(2+)-unbound state. Structural analysis further revealed that Ca(2+) removal caused the significant conformational changes at the DAPK1−CaM interface, especially the helices α1, α2, α4, α6, and α7 from the CaM and the basic loop and the phosphate-binding loop from the DAPK1. These results may be useful to understand the biological role of Ca(2+) in physiological processes.