Accurate determination of protein secondary structure content from raman and raman optical activity spectra

Raman spectroscopy measures molecular vibrations triggered by the inelastic scattering of light, while Raman optical activity (ROA) measures a small difference in the Raman scattering from chiral molecules using circularly polarized light. We used Raman or ROA spectra to determine the secondary structure contents (helix, sheet, or other) of proteins. Forty-four ROA and 24 Raman protein spectra were converted into mean intensities within 10 cm -1 width bins. The partial least squares algorithm with 5-fold cross-validation was used to construct models to give secondary structure contents from spectral data. The optimized algorithm gives highly accurate secondary structure contents, with R 2 and rmsd values of 0.99, and 0.6-1.7%, respectively, for second derivative Raman data when comparing predicted to experimental data. Using ROA data from 620 to 1850 cm -1 is almost as accurate. Analysis of amide I, II, and III and backbone spectral regions reveals the importance of each of these regions for secondary structure assignment. Raman and ROA may be the methods of choice for rapid measurement of protein secondary structure contents, since they have unprecedented accuracy. © 2010 American Chemical Society.