Competitive tuning: Competition's role in setting the frequency-dependence of Ca2+-dependent proteins

Abstract

A number of neurological disorders arise from perturbations in biochemical signaling and protein complex formation within neurons. Normally, proteins form networks that when activated produce persistent changes in a synapse’s molecular composition. In hippocampal neurons, calcium ion (Ca2+) flux through N-methyl-D-aspartate (NMDA) receptors activates Ca2+/calmodulin signal transduction networks that either increase or decrease the strength of the neuronal synapse, phenomena known as long-term potentiation (LTP) or long-term depression (LTD), respectively. The calcium-sensor calmodulin (CaM) acts as a common activator of the networks responsible for both LTP and LTD. This is possible, in part, because CaM binding proteins are “tuned” to different Ca2+ flux signals by their unique binding and activation dynamics. Computational modeling is used to describe the binding and activation dynamics of Ca2+/CaM signal transduction and can be used to guide focused experimental studies. Although CaM binds over 100 proteins, practical limitations cause many models to include only one or two CaM-activated proteins. In this work, we view Ca2+/CaM as a limiting resource in the signal transduction pathway owing to its low abundance relative to its binding partners. With this view, we investigate the effect of competitive binding on the dynamics of CaM binding partner activation. Using an explicit model of Ca2+, CaM, and seven highly-expressed hippocampal CaM binding proteins, we find that competition for CaM binding serves as a tuning mechanism: the presence of competitors shifts and sharpens the Ca2+ frequency-dependence of CaM binding proteins. Notably, we find that simulated competition may be sufficient to recreate the in vivo frequency dependence of the CaM-dependent phosphatase calcineurin. Additionally, competition alone (without feedback mechanisms or spatial parameters) could replicate counter-intuitive experimental observations of decreased activation of Ca2+/CaM-dependent protein kinase II in knockout models of neurogranin. We conclude that competitive tuning could be an important dynamic process underlying synaptic plasticity.

Competitive Tuning Among Ca2+/Calmodulin-Dependent Proteins: Analysis of In Silico Model Robustness and Parameter Variability

“…These assumptions have been used regularly in the modeling literature by us and others [9, 19–21] and have been shown to be experimentally validated [22]. For the Ca 2+ /CaM-dependent enzymes AC, PDE1, and CaN the catalytic activity is assumed to scale with the amount of Ca 2+ bound to CaM, similar to what has been shown with CaMKII [17].…”

“…Similar to our previous work [9], we constructed models of CaM binding to a number of downstream CBPs and allowed the CBPs to compete for the various states of Ca 2+ /CaM. CaM has four binding sites for Ca 2+ ions, two in EF-hand domains in the amino (N) terminus, and two in EF-hand domains in the carboxy (C) terminus.…”

“…a protein’s concentration) could cause a shift in competition that influences the signaling outcomes of other proteins in the system, perhaps leading to non-intuitive effects. We have previously shown that simulated knockout of the CaM buffer neurogranin (Ng) shifts the competition for CaM, non-intuitively decreasing Ca 2+ /CaM-dependent kinase II (CaMKII) activation and concomitantly increasing adenylyl cyclase (AC) activation [9]. Our previous results may explain a surprising experimental observation by Krucker et al .…”

“…The binding of CaM to its many downstream binding partners [5–8] depends on the kinetic rates with which different CaM species bind CBPs, such that each CBP is preferentially activated by, or “tuned” to, different input Ca 2+ signals. Aside from binding dynamics, other mechanisms that regulate this tuning include feedback loops, spatial localization, and a recently described phenomenon called competitive tuning [9–11]. We have recently reported that competitive tuning is sufficient to recreate, in silico , the in vivo Ca 2+ frequency-dependence of several CBPs [9].…”

“…Aside from binding dynamics, other mechanisms that regulate this tuning include feedback loops, spatial localization, and a recently described phenomenon called competitive tuning [9–11]. We have recently reported that competitive tuning is sufficient to recreate, in silico , the in vivo Ca 2+ frequency-dependence of several CBPs [9]. One prediction from competitive tuning is that, in the absence of other mechanisms, signaling outcomes may strongly depend on the abundance and binding dynamics of individual CBPs; parameters susceptible to perturbation either by genetic regulation or by post-translational modification.…”