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 (Ca) by integrating coarse-grained models and all-atomistic simulations with nonequilibrium physics. We focused on binding between CaM and two specific targets, Ca/CaM-dependent protein kinase II (CaMKII) and neurogranin (Ng), as they both regulate CaM-dependent Ca signaling pathways in neurons. It was shown experimentally that Ca/CaM (holoCaM) binds to the CaMKII peptide with overwhelmingly higher affinity than Ca-free CaM (apoCaM); the binding of CaMKII peptide to CaM in return increases the Ca affinity for CaM. However, this reciprocal relation was not observed in the Ng peptide (Ng), 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 is unknown due to low binding affinity, therefore we computationally generated an ensemble of apoCaM-Ng structures by matching the changes in the chemical shifts of CaM upon Ng binding from nuclear magnetic resonance experiments. Next, we computed the changes in Ca 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 for CaM in the presence of Ng by showing that the N-terminal acidic region of Ng peptide pries open the β-sheet structure between the Ca binding loops particularly at C-domain of CaM, enabling Ca release. In contrast, CaMKII peptide increases Ca affinity for the C-domain of CaM by stabilizing the two Ca binding loops. We speculate that the distinctive structural difference in the bound complexes of apoCaM-Ng and holoCaM-CaMKII delineates the importance of CaM's progressive mechanism of target binding on its Ca binding affinities.

A mutually induced conformational fit underlies Ca2+-directed interactions between calmodulin and the proximal C terminus of KCNQ4 K+ channels

“…To properly interpret our data, we must consider the physiology of CaM molecules and Ca 2ϩ ions in the cytoplasm. Because the affinity of CaM for almost all of its cellular targets greatly increases upon Ca 2ϩ loading (neurogranin being a notable converse example (6,(72)(73)(74) (75)(76)(77), such as in response to strong neuronal stimulation and rapid firing. It is important to note that, unlike the case of CaM actions on VGCCs, for which highly local free [Ca 2ϩ ] at the inner mouth of the pore may approach millimolar concentrations (16,78,79), no Ca 2ϩ ions are flowing through open K ϩ channels, and so it is likely that, as for the analysis of CaM actions on SK K ϩ channels, it is global [Ca 2ϩ ] that should be most relevant for our thinking.…”

Physical Interactions Driving the Activation/Inhibition of Calcium/Calmodulin Dependent Protein Kinase II

“…Sutoo and Akiyama [35] studied the clinical effects of administering or to sleeping mice, and noticed a strong difference in their response, suggesting that the Ca 2+ cations have important effects in the brain, probably via interaction with CaM. Related, Zhang et al [36] found that the Ca 2+ /CaM complex binds with an overwhelmingly higher affinity to CaMKII than Ca 2+ -free CaM. Inspired by these ideas, we hypothesize that the ultimate explanation to CaMKII’s activation is the electrostatic interaction between the charged patches of the SUs, mentioned in Pullara et al [23] (negative patches in hub and kinase, and positive in linker), and the negative Ca 2+ /CaM molecules.…”

Metal cofactor modulated folding and target recognition of HIV-1 NCp7

“…Our results are consistent with previous experimental observations and demonstrated that the zinc binding is able to modulate the inter-domain conformations. Such inherent conformational flexibility may be functionally important, enabling adaptive binding of the NCp7 to different recognition elements [ 53 , 54 ].…”

“…Interestingly, although the free zinc fingers are unstable at apo condition as shown in Figs 2 and 6 , binding of the RNA makes the ZF1 well folded even without zinc binding ( Fig 8A and 8B ), which suggests that the target RNA tends to reshape the energy landscape of the zinc-finger domains by interface interactions, leading to increased stability. Such coupled binding and folding has been observed in the target recognition of a number of intrinsically disordered proteins [ 54 , 65 – 72 ]. The RNA binding induced stabilization can also be observed for the ZF2, as shown in Fig 8C and 8D .…”