Quantitative structure-activity relationship modeling of peptide and protein behavior as a function of amino acid composition

A quantitative structure-activity relationship (QSAR) modeling approach bas ed on the location of each amino acid along three axes obtained by principa l component analysis (called z scores) was extended to physical and functio nal properties of proteins, where the proportion of particular amino acids rather than a precise sequence is the determining factor. Coomassie Brillia nt Blue spectral responses to amino acid homopolymers (R = 0.926) and prote ins, either as a function of their contents of six basic and aromatic amino acids (R = 0.976) or as a function of the contributions of these amino aci ds to the three z scores (R = 0.935), were modeled. The ultraviolet absorba nce of proteins was modeled in terms of the z scare contributions of tyrosi ne, tryptophan, and cysteine (R = 0.995). Modeling many protein functional properties in this manner appears to be possible. An approach to modeling p eptide behaviors that depend on short sequences of amino acids was also con sidered.