Divalent Cation Adsorption on the Actin Monomer

Binding energies for calcium adsorption on the actin monomer have been computed from molecular dynamics simulation using the CHARMM22 force field. Relative binding free energies were evaluated from Poisson−Boltzmann computations. For large values of the dielectric constant (i.e., > 4), binding affinity is highest at the adsorption site near the nucleotide in the cleft region of the monomer, and the binding free energies of five other calcium adsorption sites are statistically comparable. For small values of the dielectric constant (i.e., unity) for the ion−protein complex, all six binding sites exhibit comparable binding affinity. Replacing the ADP nucleotide with ATP has only a small effect on the binding potential energy change for calcium at the six crystallographic adsorption sites. Likewise, the presence of charged residues at the N-terminus of the monomer only modestly affects the binding potential energy at the crystallographic calcium sites. Molecular simulation snapshots reveal that calcium ions at the cystallographic sites are coordinated by one or two acidic side chains and three or four water molecules. Free energy perturbation methods were used to compute the selectivity between zinc and calcium ion binding in the cleft region. In the cleft region, the exchange of bound Zn2+ for bound Ca2+ incurs a free energy change of −12.3 (3.4) kcal/mol for solvated actin. This agrees with experimental observations that calcium exhibits a higher binding affinity than zinc at the primary divalent cation binding site of the actin monomer.