Theoretical investigation on the binding of lysine-containing peptides with dodecyl sulfate ion using semi-empirical calculations

Electrostatic part of the free energy plays an important role in the interaction of proteins with charged molecules. In addition, changes in the charge distribution on protein structure due to this interaction cause conformational changes in protein. Since investigations of these processes are difficult experimentally, the prediction methods using semi-empirical calculations have been extensively considered recently. In the present study, the electrostatic energy and conformational changes of di-, tri- and some oligo-peptides containing Lys were estimated after interaction with dodecyl sulfate ions by the semi-empirical method using PM3 calculations of Hyperchem 5.02. At non-aqueous media most DS−-peptide complexes are preferred to β-sheet structure. In addition, the energy of interaction is considerably dependent on the amino acid next to the Lys residue. The positively charge amino acids favor the interaction while the negatively charged amino acids weaken it.