Vibrational analysis of the structure of gramicidin A. I. Normal mode analysis

Normal mode frequencies have been calculated for single-stranded beta 4.4 and beta 6.3 and for double-stranded increases decreases beta 5.6, increases decreases beta 7.2, increases increases beta 5.6, and increases increases beta 7.2 helices that are possible models for the structure of gramicidin A. The force field used in the calculations is one that reproduces the frequencies of model polypeptide chain structures to about +/- 5 cm-1, and is therefore expected to provide meaningful distinctions between these conformations. The calculations predict significant differences in the infrared and Raman spectra of these beta-helices, suggesting that they should be identifiable from their spectra (which is shown in the following paper to be the case). The most sensitive region is that of the amide I frequencies, where the predicted patterns of intense infrared mode, infrared splittings, and intense Raman mode provide a characteristic identification of each of the above structures.