Molecular dynamics simulations of conserved Hox protein hexapeptides II. Folded structures in water solution

MD simulations of Hox protein N-terminal hexapeptides TFDWMK (Hox B1) and LFPWMR (Hox B8) are performed in water solution and complemented with simulations where the aromatic residues phenylalanine (F) and tryptophan (W) are successively replaced by alanine (A). Results from this study give support that different hexapeptides can form similar folded structures in water, stabilized mainly by internal hydrogen bonding where the arrangement of the aromatic side chains together with the methionine (M) side chain forming a hydrophobic core covers and protects the internal hydrogen bonds from water. Replacement of the aromatic side chains with Alanine did not lead to unfolding, but rather the hexapeptides were slightly changing their conformations where the Methionine side chain together with the peptide backbone protected the internal hydrogen bonds and the hexapeptides remain folded. Our results give support that these hexapeptides are able to remain folded to some extent even without the aromatic side chains.