Not all carboxylates are created equal: differences in interaction of carboxylated peptides with a CaCO₃ dimer

Abstract

The carboxylate group has been considered the "glue" for mineralizing proteins because of its ability to bind Ca(II). We propose the calcium salts of dicarboxylated dipeptides (Asp-Asp and Glu-Glu) as the smallest models of a mineralizing protein active site. Molecular dynamics/simulated annealing was used for conformational search of the dipeptide global minimum. Semiempirical blind docking was used for configurational search of all cluster-peptide complexes and structures were then optimized in the gas phase at the RI-MP2/SVP level of theory. Solvent effects were also taken into account. We found that the energy of interaction of the calcium carboxylates with a calcium carbonate dimer can be either favorable or unfavorable depending on side-chain length, so side-chain carboxylic groups belonging to different amino acids may show different affinities towards calcium carbonate.

Keywords: Aggregation; Asprich protein; Blind docking; Crystallization; Organic–inorganic interface.