# Fitting and comparison of calcium-calmodulin kinetic schemes to a common data set using non-linear mixed effects modelling

## TL;DR

This study compares different models of calcium-calmodulin binding using a shared dataset and finds that a model with unique binding sites fits best, suggesting new insights into calmodulin's role in signaling.

## Contribution

The study introduces a novel approach by fitting and comparing calcium-calmodulin models using a common dataset and non-linear mixed effects modeling.

## Key findings

- A kinetic scheme with independent lobes and unique binding sites fit the data best.
- Published parameters for calmodulin models were found to be suboptimal based on Akaike information criterion values.
- Partially bound calmodulin and distinct calcium binding sites within a lobe are important for cellular signaling.

## Abstract

Calmodulin is a calcium binding protein that is essential in calcium signalling in the brain. There are many computational models of calcium-calmodulin binding that capture various calmodulin features. However, existing models have generally been fit to different data sets, with some publications not reporting their training and validation performance. Moreover, there is no model comparison using a common benchmark data set as is common practice in other modeling domains. Finally, some calmodulin models have been fit as a part of a larger kinetic scheme, which may have resulted in parameters being underdetermined. We address these three limitations of previous models by fitting the published calcium-calmodulin schemes to a common calcium-calmodulin data set comprising equilibrium data from Shifman et al. and dynamical data from Faas et al. Due to technical limitations, the amount of uncaged calcium in Faas et al. data could not be predicted with certainty. To find good parameter fits, despite this uncertainty, we used non-linear mixed effects modelling as implemented in the Pumas.jl package. The Akaike information criterion values for our reaction rate constants were significantly lower than for the published parameters, indicating that the published parameters are suboptimal. Moreover, there were significant differences in calmodulin activation, both between the schemes and between our reaction rate and those previously published. A kinetic scheme with independent lobes and unique, rather than identical, binding sites fit the data best. Our results support two hypotheses: (1) partially bound calmodulin is important in cellular signalling; and (2) calcium binding sites within a calmodulin lobe are kinetically distinct rather than identical. We conclude that more attention should be given to validation and comparison of models of individual molecules.