Is the peptide bond formation activated by Cu(2+) interactions? Insights from density functional calculations

• Published in: The journal of physical chemistry. B 2007-05, Vol.111 (20), p.5740-5747
• Main Authors: Rimola, A, Rodríguez-Santiago, L, Ugliengo, P, Sodupe, M
• Format: Article
• Language: English
• Subjects: Binding Sites; Computer Simulation; Copper - chemistry; Models, Molecular; Molecular Structure; Peptides - chemistry; Protein Binding; Thermodynamics
• ISSN: 1520-6106
• DOI: 10.1021/jp071071o

The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.