Orientation of the infrared transition moments for an alpha-helix

Appropriate values for the orientation of the amide transition dipoles are essential to the growing use of isotopically edited vibrational spectroscop y generally in structural biology and to infrared dichroism measurements on membrane-associated alpha-helices, in particular. The orientations of the transition moments for the amide vibrations of an alpha-helix have been det ermined from the ratio of intensities of the A- and E-1-symmetry modes in t he infrared spectra of poly(gamma-methyl-L-glutamate)(x)-co-(gamma-n-octade cyl-L-glutamate)(y) oriented on silicon substrates. Samples possessing a hi gh degree of alignment were used to facilitate band fitting. Consistent res ults were obtained from both attenuated total reflection and transmission e xperiments with polarized radiation, yielding values of Theta(I) = 38 degre es, Theta(II) = 73 degrees, and Theta(A) = 29 degrees, relative to the heli x axis, for the amide I, amide II, and amide A bands, respectively. The mea surements are discussed both in the context of the somewhat divergent older determinations, and in relation to the helix geometry and results on model amide compounds, to resolve current uncertainties in the literature.