Experiment and Simulation Reveal Residue Details for How Target Binding Tunes Calmodulin?s Calcium-Binding Properties

J Nde and PZ Zhang and MN Waxham and MS Cheung, JOURNAL OF PHYSICAL CHEMISTRY B, 127, 2900-2908 (2023).

DOI: 10.1021/acs.jpcb.2c08734

We aim to elucidate the molecular mechanism of the reciprocal relation of calmodulin's (CaM) target binding and its affinity for calcium ions (Ca2+), which is central to decoding CaM-dependent Ca2+ signaling in a cell. We employed stopped-flow experiments and coarse grained molecular simulations that learn the coordination chemistry of Ca2+ in CaM from first-principle calculations. The associative memories as part of the coarse-grained force fields built on known protein structures further influence CaM's selection of its polymorphic target peptides in the simulations. We modeled the peptides from the Ca2+/CaM-binding domain of Ca2+/CaM-dependent kinase II (CaMKII), CaMKIIp (293- 310) and selected distinctive mutations at the N-terminus. Our stopped flow experiments have shown that the CaM's affinity for Ca2+ in the bound complex of Ca2+/CaM/CaMKIIp decreased significantly when Ca2+/CaM bound to the mutant peptide (296-AAA-298) compared to that bound to the wild-type peptide (296-RRK-298). The coarse-grained molecular simulations revealed that the 296-AAA-298 mutant peptide destabilized the structures of Ca2+-binding loops at the C domain of CaM (c-CaM) due to both loss of electrostatic interactions and differences in polymorphic structures. We have leveraged a powerful coarse-grained approach to advance a residue- level understanding of the reciprocal relation in CaM, that could not be possibly achieved by other computational approaches.

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