Opposing Intermolecular Tuning of Ca(2+) Affinity for Calmodulin by Neurogranin and CaMKII Peptides

We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca(2+)) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca(2+)/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca(2+) signaling pathways in neurons. It was shown experimentally that Ca(2+)/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca(2+)-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca(2+) affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng(13–49)), which binds to apoCaM or holoCaM with binding affinities of the same order of magnitude. Unlike the holoCaM-CaMKII peptide, whose structure can be determined by crystallography, the structural description of the apoCaM-Ng(13–49) is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng(13–49) structures by matching the changes in the chemical shifts of CaM upon Ng(13–49) binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca(2+) affinity for CaM with and without binding targets in atomistic models using Jarzynski’s equality. We discovered the molecular underpinnings of lowered affinity of Ca(2+) for CaM in the presence of Ng(13–49) by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca(2+) binding loops particularly at C-domain of CaM, enabling Ca(2+) release. In contrast, CaMKII peptide increases Ca(2+) affinity for the C-domain of CaM by stabilizing the two Ca(2+) binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng(13–49) and holoCaM-CaMKII delineates the importance of CaM’s progressive mechanism of target binding on its Ca(2+) binding affinities.