title: Opposing Intermolecular Tuning of Ca2+Affinity for Calmodulin by Neurogranin and CaMKII Peptides.
abstract: We investigated the impact of bound calmodulin (CaM)-target compound structure on the affinity of calcium (Ca2+) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca2+/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca2+signaling pathways in neurons. It was shown experimentally that Ca2+/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca2+-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca2+affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng13-49), 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-Ng13-49is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng13-49structures by matching the changes in the chemical shifts of CaM upon Ng13-49binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca2+affinity for CaM with and without binding targets in atomistic models using Jarzynski's equality. We discovered the molecular underpinnings of lowered affinity of Ca2+for CaM in the presence of Ng13-49by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca2+binding loops particularly at C-domain of CaM, enabling Ca2+release. In contrast, CaMKII peptide increases Ca2+affinity for the C-domain of CaM by stabilizing the two Ca2+binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng13-49and holoCaM-CaMKII delineates the importance of CaM's progressive mechanism of target binding on its Ca2+binding affinities.
authors.affiliation: Department of Physics, University of Houston, Houston, Texas.
authors.forename: Pengzhi
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Department of Physics, University of Houston, Houston, Texas.
authors.forename: Swarnendu
authors.initials: S
authors.lastname: Tripathi
authors.affiliation: Department of Physics, University of Houston, Houston, Texas.
authors.forename: Hoa
authors.initials: H
authors.lastname: Trinh
authors.affiliation: Department of Physics, University of Houston, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas. Electronic address: mscheung@uh.edu.
authors.forename: Margaret S
authors.initials: MS
authors.lastname: Cheung
mesh_terms: D000595:Amino Acid Sequence; D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D002118:Calcium / Q000378:metabolism*; D054732:Calcium-Calmodulin-Dependent Protein Kinase Type 2 / Q000737:chemistry*; D002147:Calmodulin / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D051579:Neurogranin / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D001059:Apoproteins; D002147:Calmodulin; D010446:Peptide Fragments; D051579:Neurogranin; D054732:Calcium-Calmodulin-Dependent Protein Kinase Type 2; D002118:Calcium