Impact of divalent metal cations on the catalysis of peptide bonds: a DFT study

Within the ATP-grasp family of enzymes, divalent alkaline earth metals are proposed to chelate terminal ATP phosphates and facilitate the formation of peptide bonds. Density functional theory methods are used to explore the impact of metal ions on peptide bond formation, providing an insight into experimental metal substitution studies. Calculations show that alkaline earth and transition metal cations coordinate with an acylphosphate reactant and aid in the separation of the phosphate leaving group. The critical biochemical reaction is proposed to proceed through the formation of a six-membered transition state in the relatively nonpolar active site of human glutathione synthetase, an ATP-grasp enzyme. While the identity of the metal ion has a moderate impact on the thermodynamics of peptide bond formation, kinetic differences are much sharper. Simulations indicate that several transition metal ions, most notably Cu²⁺, may be particularly advantageous for catalysis. The detailed mechanistic study serves to elucidate the vital role of coordination chemistry in the formation of peptide bonds.