Computational Study: Noncovalent Interaction of Cys-Ala Peptide with Alkaline Earth Metal Ions and its Conformation Changes

Abstract

The study of the intermolecular interactions is important to explain the phenomenon occurred on the human body. One of the most important processes that can be studied is the interaction of the peptide with metal ions. In this study, a computational approach was harnessed to predict the interaction and the changes in peptide’s conformation between Cys-Ala peptide which is one of the important amino acids in e-cadherin with some of alkaline earth metal ions. Cys-Ala peptide (Ac-CA-NH2) was used as a molecular model in this calculation. All the molecular structure involved in the interaction was optimized by density functional theory DFT/M06-2X, and basis set 6-31G** to obtain minimum energy, the interaction energies, and the changes in its conformation. The results showed that the interaction energy of Ac-CA-NH2 with alkaline earth metal ions from top to bottom based on the Periodic table is getting higher in a row. The interaction energies of Ac-CA-NH2 with Be2+, Mg2+ and Ca2+ ions are -2.393kcal, -17.489 kcal, and -25.938 kcal respectively. These energies were obtained from the interaction of the peptide with ions in a water solvent. The changes in the peptide's bond length and dihedral angle indicate a conformational change in the Cys-Ala peptide, but it still maintains the trans conformation in its peptide bonds. The results and evaluations of this study may be used for further research considerations and may be applied to enzymes or other peptides that have the Cys-Ala residue.