Fourier transform infrared analysis of amide III bands of proteins for the secondary structure estimation

Protein secondary structure has been analyzed using a Fourier transform infrared spectroscopic method in the amide III region. Although extensive work has been done on protein secondary structure using the amide I region (1700 - 1600 cm⁻¹), the amide III region has not been utilized in the past for its potential in protein structural analysis. One of the major reasons for non-use of the amide III vibrations is perhaps the very weak signal in the amide III frequency region (1200 - 1350 cm⁻¹). However, benefits of using the amide III region are substantial. For example, water vibrations do not interfere with the protein spectrum unlike in the amide I region. In the amide III region, the protein spectrum is better resolved into individual bands than in the amide I region. This feature allows for a greater ease in peak definement of the protein spectra. In the amide III region, the bands for the individual secondary structures ((alpha) -helix, (beta) -sheet and random coils) do not overlap as much as they do in the amide I region. This lack of overlapping allows for easier and a more reliable means of peak assignment, and secondary structure band positions are easier to determine. Amide III region of protein IR spectra appears to be a valuable tool in estimating the amount of secondary structure present in proteins.