Experiment and simulations reveal residue details for how target binding tunes calmodulin's calcium binding properties

Calmodulin (CaM) is the main calcium (Ca²⁺) binding protein that transduces the calcium signal to numerous downstream proteins including Ca²⁺-CaM dependent protein kinase II (CaMKII). The affinity of CaM for CaMKII increases by over 3000-fold as Ca²⁺ binds to CaM and in turn the affinity of Ca²⁺ for CaM increases by many folds as a result of CaM interactions with CaMKII. This reciprocal effect between Ca²⁺, CaM, and CaMKII has been shown by many research groups; however, the basic mechanism underlying such complex process is still not well understood. In this work, we used the experimental and non-equilibrium coarse-grained molecular dynamics simulations to study the dynamics of CaM and its interactions with a family of three peptides (wildtype, 1-residue mutation, and 3-residue mutation) from the CaM-binding domain of CaMKII. Our results show that CaM interactions with CaMKIIp (wildtype and 1-residue mutation) lead to a large increase in Ca²⁺ affinity for CaM whereas CaM interactions with CaMKIIp (3-residue mutation) show over 50-fold decrease in Ca²⁺ affinity for CaM relative to the wildtype. Additionally, these differences occur specifically in the C-domain of CaM, where the Ca²⁺ binding sites are highly disturbed for the CaM/CaMKII (3-residue mutation). These observations highlight the contribution of specific residues, 296-RRK-298, of the wildtype peptide to the high Ca²⁺ affinity for CaM. We then propose that residues 296-RRK-298 of the peptide interact with the negatively charged residues in the Ca²⁺ binding sites of the C-domain of CaM through electrostatic interactions which lead to the reduced Ca²⁺ release rate from the C-domain of CaM.