Molecular dynamics simulation of protein-mediated biomineralization of amorphous calcium carbonate

Abstract

The protein-mediated biomineralization of calcium carbonate (CaCO₃) in living organisms is primarily governed by critical interactions between the charged amino acids of the protein, solvent, calcium (Ca²⁺) and carbonate (CO₃²⁻) ions. The present article investigates the molecular mechanism of lysozyme-mediated nucleation of amorphous calcium carbonate (ACC) using molecular dynamics and metadynamics simulations. The results reveal that, by acting as nucleation sites, the positively charged side chains of surface-exposed arginine residues form hydrogen bonds with carbonates and promote aggregation of ions around them leading to the formation and growth of ACC on the protein surface. The newly formed ACC patches were found to be less hydrated due to ion aggregation-induced expulsion of water from the nucleation sites. Despite favorable electrostatic interactions of the negatively charged side chains of aspartate and glutamate with calcium ions, these residues contribute minimally to the growth of ACC on protein surface. The activation barrier for the growth of partially hydrated ACC patches on lysozymes was determined from the free energy profiles obtained from metadynamics simulations.