Molecular dynamic simulations of glycine amino acid association with potassium and sodium ions in explicit solvent

Abstract

Salt solutions are the natural environment in which biological molecules act, and dissolved ions are actively involved in biochemical processes. With metal ions, the membrane potentials are maintained. Ions are crucial for the activity of many enzymes, and their ability to coordinate with chemical groups modulates protein-protein interactions. Here we present a comparative study of sodium and potassium coordination with zwitterionic glycine, by means of explicit solvent molecular dynamics. We demonstrated that contact ion pair of cations and carboxylate group splits into two distinct coordination states. Sodium binding is significantly stronger than for potassium. These results can shed light on the different roles of sodium and potassium ions in abiogenic peptide synthesis.