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

• Published in: The journal of physical chemistry. B 2023-04, Vol.127 (13), p.2900-2908
• Main Authors: Nde, Jules, Zhang, Pengzhi, Waxham, M. Neal, Cheung, Margaret S.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; B: Biophysical and Biochemical Systems and Processes; Binding Sites; Calcium - chemistry; Calmodulin - chemistry; Computer Simulation; Protein Binding
• ISSN: 1520-6106; 1520-5207
• 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.