Molecular mechanical study of the stability of the Lys-Ala-Ala tripeptide dimer

A molecular mechanical study of two Lys-Ala-Ala tripeptide chains in interaction is presented. The study was carried out to explore the feasibility of dimer formation and explain some features of the crystal structure not completely understood. The role of the counterions present in the crystal structure on the conformation has been included in this study by investigating the effect of removing the charges on the lysyl side chains. The results of the present molecular mechanical study explains well the structural features found by X-ray crystallography, complementing that study.