A Vibrational Analysis of Ld-Peptides (Infrared, Raman, Gramicidin).

Abstract

Theoretical calculations of the vibrational spectra of various single and antiparallel double-helical structures formed by poly(LD-alanine) have been performed with the side chain pproximated by a point mass equal to that of a -CH(,3) group. Synthetic LD-oligovalines and LD-oligophenylalanines have been studied in crystalline and solution states using IR and Raman spectroscopy. Naturally occurring antibiotic gramicidin A (GA) has also been studied in its native, various ion-bound forms, and in membranes using IR and Raman spectroscopy. The theoretically calculated amide A, I, II, III and V frequencies for (beta)('4.4), (beta)('6.3), (UPARR)(DARR)(beta)('5.6), and (UPARR)(DARR)(beta)('7.2) structures are used in studying the conformations of synthetic LD-peptides and GA. The synthetic LD-peptides, Boc-(L-Val-D-Val)(,n)-OMe, with n = 4, 6, and 8, HCO-L-Phe-(D-Phe-L-Phe)(,3)-OMe, and Boc-(L-Phe-D-Phe)(,4)-OMe exist in a (UPARR)(DARR)(beta)('5.6) structure in the crystalline state. In solution LD-valine with n = 4 and 8, and octaphenylalanine retain the (UPARR)(DARR)(beta)('5.6) structure while the other two peptides studied exist in a mixture of conformations. The structure of GA is found to be cation-size dependent. The experimental observations and the calculations strongly suggest a (UPARR)(DARR)(beta)('5.6) structure for ion-free GA and a (UPARR)(DARR)(beta)('7.2) structure in the ion-bound form. These results are in agreement with preliminary x-ray results. In liposomes GA forms a head-to-head dimer formed by the association of the two (beta)('6.3) helices. Because of the near coincidence of the IR amide I frequency for the (beta)('6.3) and (UPARR)(DARR)(beta)('5.6) structures, the Raman amide I frequency is found to be useful in discriminating the structures. The calculated Raman-active amide I frequency together with the splittings in the amide frequencies strongly suggest a head-to-head dimer in membranes. In dried liposomes GA exists in the (UPARR)(DARR)(beta)('5.6) structure but the location of GA remains to be determined. Our calculations also explain very well the observed amide I frequencies and their dichroic ratios of poly((gamma)-benzyl-D-L-glutamate) in various conformations.