Theoretical study of the contribution of aromatic side chains to the circular dichroism of basic bovine pancreatic trypsin inhibitor.

Circular dichroism (CD) spectroscopy is frequently employed to determine the secondary structure composition of a protein. However, this assumes that the far-UV region of the spectrum, which is used for these analyses, is due only to contributions from the polypeptide backbone. Basic bovine pancreatic trypsin inhibitor (BPTI) possesses an unusual far-UV CD spectrum, which has made such an analysis difficult. One possible reason for the discrepancy is that other chromophores, such as the aromatic side chains (four tyrosines, four phenylalanines), might be responsible. The CD spectrum of BPTI was calculated by employing a variation of the matrix method. Including only the peptide backbone gave poor agreement between theory and experiment. This was shown to be independent of the quality of the calculation performed. Subsequent inclusion of tyrosine contributions did little to improve the fit. However, further inclusion of the phenylalanine chromophores provided a good fit between the calculated and experimental far-UV spectrum. The important contributions arise from the cluster of aromatic amino acids formed by two tyrosines (Tyr21 and Tyr23) and three phenylalanines (Phe22, Phe4, and Phe45). Consideration of both types of side chains and the entire peptide backbone is essential to produce an accurate description of the CD curve. Overall, these results indicate that contributions from aromatic amino acids can significantly perturb the far-UV CD spectrum of a protein, making secondary structure analysis difficult. This is particularly true in systems like BPTI, with low amounts of alpha-helical structure and clusters of aromatic amino acids.