Factor analysis scales of generalized amino acid information as applied in predicting interactions between the human amphiphysin-1 SH3 domains and their peptide Ligands

Factor analysis scales of generalized amino acid information (FASGAI) involving hydrophobicity, alpha-helix and beta-turn propensities, bulky properties, compositional characteristics, local flexibility, and electronic properties, was proposed to represent the structures of the decapeptides binding the human amphiphysin-1 SH3 domains. Parameters being responsible for the binding affinities were selected by genetic algorithm, and a quantitative structure-affinity relationship (QSAR) model by partial least square was established to predict the peptide-SH3 domain interactions. Diversified properties of the residues between P-2 and P-3 (including P-2 and P-3) of the decapeptide (P4P3P2P1P0P-1P-2P-3P-4P-5) may contribute remarkable effect to the interactions between the SH3 domain and the decapeptide. Particularly, electronic properties of P2 may provide relatively large positive contributions to the interactions, and reversely, hydrophobicity of P2 may be largely negative to the interactions. These results showed that FASGAI vectors can well represent the structural characteristics of the decapeptides. Furthermore, the model obtained, which showed low computational complexity, correlated FASGAI descriptors with the binding affinities as well as that FASGAI vectors may also be applied in QSAR studies of peptides.