On the propensity of Asn-Gly-containing heptapeptides to form $β$-turn structures : comparison between ab initio quantum mechanical calculations and Molecular Dynamics simulations

Abstract: Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular dynamics simulations with previously reported results from quantum mechanical calculations. More specifically, three molecular dynamics simulations of 5 $\mu$s each in explicit water solvent were carried out for three Asn-Gly-containing heptapeptides, in order to study their folding and dynamics. Previous data, based on quantum mechanical calculations and the DFT methods have shown that these peptides adopt $\beta$-turn structures in aqueous solution, with type I' $\beta$-turn being the most preferred motif. The results from our analyses indicate that for the given system the two methods diverge in their predictions. The possibility of a force field-dependent deficiency is examined as a possible source of the observed discrepancy.