Quantitative prediction of protein secondary structure —Where is the lacuna?

Secondary structure of the entomocidal toxin from Bacillus thuringiensis subsp. kurstaki HD-73

The secondary structure of the toxin from Bacillus thuringiensis subsp. kurstaki (Btk) HD-73 was estimated by Raman, infrared, and circular dichroism spectroscopy, and by predictive methods. Circular dichroism and infrared spectroscopy gave an estimate of 33-40% alpha-helix, whereas Raman and predictive methods gave approximately 20%. Raman and circular dichroism spectra, as well as predictive methods, indicated that the toxin contains 32-40% beta-sheet structure, whereas infrared spectroscopy gave a slightly lower estimate. Thus, all of these approaches are in agreement that the native conformation of Btk HD-73 toxin is highly folded and contains considerable amounts of both alpha-helical and beta-sheet structures. No significant differences were detected in the secondary structure of the toxin either in solution or as a hydrated pellet.

Secondary structure of 11 S globulin in aqueous solution investigated by FT-IR derivative spectroscopy

Secondary structure of 11 S globulin, a major storage protein of soybean seeds, has been investigated in aqueous solution by FT-IR spectroscopy. Conformational changes in the native protein upon thermal and chemical denaturation have been monitored by observing changes in the frequency position and peak intensity of the various bands. The frequency of the Amide I band of the native protein shifts by 4 cm-1 from 1,643 cm-1 to 1,647 cm-1 when denatured, while the corresponding intensity of the Amide I band compared to the native protein, decreases by 30 and 67%, respectively, for the urea and thermally denatured proteins, indicating gross conformational changes in the secondary structure. Trifluoroethanol, an alpha-helix promoter shifts the Amide I band from 1,643 cm-1 to 1,651 cm-1, typical of alpha-helix, with a corresponding increase in intensity by 14% relative to the native protein. Derivative spectroscopy, allowing resolution of overlapping bands, shows that the native protein mainly consists of beta-sheet, beta-turns and disordered structure with very little alpha-helix. On denaturation, beta-sheet disappeared almost completely with urea, while this is less so with thermal denaturation.