Modern Polymer Spect..

5 Vibrational Spectroscopy of Polypeptides
S. Kriinm
5.1 Introduction
The polypeptide chain, (NHCH(R)CO),l, is the basic backbone chemical unit of
proteins, and knowledge of its possible structures and dynamics is crucial to an
understanding of the functions of these important biological macromolecules. In
synthetic polypeptides, all the side chains, R, are usually the same; in proteins, they
can be any of 20 ainino acid residues whose specific sequence is determined by the
base sequence in the DNA of the corresponding genome [I]. The unusual property
of these chains is their ability to adopt a wide range of three-dimensional structures
121, which accounts for the richness of biological functions that they can perforin [f].
This presents a special challenge to mastering the spectroscopy of these polymeric
molecules.
While vibratioiial spectroscopy is not capable of the structural resolution of X-
ray diffraction, it nevertheless has some important advantageous features. First, it
is not generally limited by physical state: samples can be in the form of powders,
crystals, films, solutions, membranous aggregates, etc. Second, a number of different
experimental methods probe the structure-dependent vibrational modes of the
system: infrared (IR), Raman (both visible and UV-excited resonance), vibrational
circular dichroism, and Raman optical activity, many of these with time-resolution
capabilities. Finally, in addition to providing structural information, vibrational
spectra are sensitive to intra- and intermolecular interaction forces, and thus they
also give information about these properties of the system.
To gain such insights, however, requires that we achieve the deepest possible
understanding of the vibrational spectrum. Correlations using characteristic band
frequencies, particularly with resolution-enhanced spectra [3], can be usefd, but it is
increasingly being recognized that this is a fundamentally limited approach [4]. For
the kind of understanding we seek it is necessary to determine the detailed normal
modes of the molecule. Only by achieving an accurate description of these modes
can we expect to explain fully all features of the vibrational spectrum and thereby to
validate the structure and force field inputs to the normal-mode calculation [S]. This
is now beginning to be possible for the polypeptide chain.
In this chapter we review the present state of the calculation of accurate normal
modes of polypeptides. Since the burden of such calculations falls primarily on the
quality of the force fields, we first review the state of present methods for obtain-