Interaction of Short Homopeptides of Glycine and L-Alanine with Fullerene C60

We analyzed theoretically the behavior of simple homopeptides (up to decapeptides, starting with the parent amino acid) derived from glycine and L-alanine, arranged into alpha helix and beta sheet, when interacting non-covalently with fullerene C-60. The main goal was to study how the increase of peptide chain length influences the geometry and formation energy of peptide + C-60 complex. We employed a series of computational techniques, including two DFT functionals (BLYP GGA and VWN LDA implemented in the DMol3 module of Materials Studio) and two force fields (AMBER and MM + available in the HyperChem package). Of the two DFT functionals tested, BLYP in a number of cases produced positive energies of the complex formation, as well as strongly overestimated intermolecular separations (sometimes exceeding 4 angstrom). VWN calculations produced reasonable and consistent values for the closest intermolecular contacts between amino acids/peptides and fullerene, along with likely overestimated absolute values of (all negative) binding energies; therefore, the VWN data are preferable to be taken as a reference to compare with the results obtained with other computation techniques. Of the two force fields used, AMBER produced stronger interactions (even stronger than those obtained by VWN DFT) in terms of binding energies and complexation-induced conformational changes in peptide molecules. On the other hand, the results of MM + calculations are in much closer agreement with the data obtained by VWN DFT. The general trend in which all the calculation techniques employed coincide is a remarkable rigidity of alpha helix peptides and a considerable flexibility of their beta sheet counterparts, when interacting with C-60 molecule. The degree of conformational changes observed in beta sheet peptides depends on the parent amino acid, length of peptide, and computational method used.