We report on structural and dynamic properties in water of all the isomers of both peptides related to the trans and cis conformations of the peptide bonds preceding the proline (Pro) residues. Free-energy calculations indicate that the isomers having the Pro closer to the N-terminus (Pro1) in trans and the Pro2 in cis conformations are the most populated. Furthermore, the backbone is more flexible for APGPR than for VPDPR, and its conformation is more stable in the hydrophilic C-terminal moiety than in the hydrophobic N-terminal region. (C) 2007 Elsevier B.V. All rights reserved.