Thermodynamic and kinetic scenarios of cooperative allosteric ligand binding in calmodulin

Conformational dynamics are essential to a protein’s ability to control regulatory functions through
allosteric interactions between a binding site and a distal region of the protein. Calmodulin (CaM)
is a well-characterized allosteric protein that undergoes a conformational transition between closed
and open conformations upon binding two calcium ions to each of its two domains. This induced con-
formational change provides an effective coupling between the binding sites essential for fine-tuned
molecular control. We study the thermodynamics and kinetics of calcium binding to CaM through a
coupled molecular dynamics/Monte Carlo simulation scheme. Here, the protein dynamics is simulated explicitly,
while ligand binding/unbinding are treated implicitly with a ligand concentration
treated within the grand canonical ensemble. Binding thermodynamics are analyzed in terms of
the classic Monod-Wyman-Changeux model of allostery. Within this framework, we characterize
the free energy of each ligation state and identify the contribution of microscopic cooperativity to
its stability. The kinetic binding mechanism of CaM is described through quantifying the kinetic
flux of pathways through this heterogeneous ligation space as a function of ligand concentration.