Protein secondary structure from FT-IR spectroscopy: correlation with dihedral angles from three-dimensional Ramachandran plots

Abstract

The frequency of the so-called "amide I" band (amide C=O stretching vibration, vC=O) of proteins is discussed in terms of the dihedral angles of the various secondary structures present within proteins. We propose that in the case of intra- or intermolecular hydrogen-bonded amide carbonyl groups the frequency of this absorption can be directly related to the [Formula: see text], ψ angles of the amide moieties for the major secondary structures. Amide I bands at frequencies above those found for non-hydrogen bonded amide carbonyl groups are rationalized in terms of a change in the third dihedral angle, ω. Rotation around the amide C—N bond in sterically demanding structures, such as turns where ω deviates from 180°, is expected to cause an increase in the electron density of the amide carbonyl groups and so increase vC=O to frequencies greater than that seen for unperturbed carbonyl groups. Key words: FT-IR spectroscopy, proteins, structure, dihedral angles.