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

Abstract

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.

Dynamic structure of the polytheonamide B channel studied by normal mode analysis

“…However, when they studied the normal modes of gramicidin A, the 3D structure had not been determined yet and they assumed it to be a left-handed b-helix conformation instead of the correct right-handed b-helix. Naik and Krimm [27][28][29] have also reported on vibrational analyses of gramicidin A and other D,Lalternating polypeptides. However, their studies mainly focused on amide vibration at high frequencies (600 -1700 cm 21 ) that may not be directly relevant to channel functions.…”

Vibrational spectroscopic studies of L,D‐alternating phenylalanine peptides

“…This is most probably due to shorter chain lengths of PHE-8 and PHE-10 compared to PHE-15. As the calculations (21) were done on infinite chains, better agreement is expected with predicted frequencies in longer chains. The strong Raman amide I modes observed in all three The amide I1 (mainly NH in-plane motion and some CN stretching) modes appear as strong bands in the IR and are very weak in the Raman spectrum and frequently are not observed.…”

“…5 and 6. Since we are concerned primarily with the backbone conformation of these molecules, and the normal-mode calculations have been carried out in thc side-chain point-mass approximation (21), a complete assignment of the vibrational spectra is not attempted in this paper. Rather, only the conformationally sensitive amide A, B, I, 11, 111 and V bands are analyzed.…”

“…structure (from ref. 21) gramicidin A has a double-stranded ps6 structure (25), whereas a cesium ion complex adopts t l 86.4 structure (24). The 7 1 fi64 structure has the same hydrogen-bonding pattern as the one proposed for the model t l p72 structure, but it has a slightly different helical twist leading to 6.4 residues per turn of the helix.…”

“…In this paper the amide vibrations observed in PHE-8, PHE-10 and PHE-15 are compared with the calculated 126 frequencies of 71 p5.6 and 71 p7.? structures by Naik & Krimm (21). They have calculated the normal modes of these two and other single-and double-helical structures using alanine as the side chain.…”