Molecular Modeling of a Functionalized Aib-based Octapeptide by Molecular Mechanics calculations restrained by NMR and Fluorescence Data in DMSO

The structural features of the sequential octapeptide Boc-(Leu)2-Lys(P)-(Aib)2-(Leu)2-Lys(N)-OtBu, where P is protoporphyrin IX and N is naphthalene, were investigated in DMSO by NMR and fluorescence spectroscopy. Earlier IR, CD, and fluorescence results showed that this compound attains a 310-helical conformation in methanol or water/methanol (75/25, v/v). By contrast, the backbone structure in DMSO is destroyed, but the high helix propencity of the Aib residues forces the peptide to attain locally ordered arrangements, reminiscent of β-turn features. Both NMR coupling constant and NOE connectivity data allowed us to compute the structural features of part of the molecule, but only their combination with fluorescence results allowed us to build up the whole molecular model. Implications of fluorescence data on the dynamics of internal rotation of the chromophores are briefly discussed.