Modern Polymer Spect..

218 5 Vibratioid Spectroscopy oj Pollyeprides
In addition to frequencies, dichroic properties can be altered by small structural
changes. Since the peptide group in the uII-helix is more inclined to the helix axis
than it is in the a,-helix, the DRs of amide modes are expected to differ significantly
between the two structures. To calculate the DR of, for example, ainide I of an
a-helix we need to know (?g/dQ~),, and (l@/?Q,),, which involves knowing the L,,
and dc/dS, (see Eq. (5-5)). Since the L,r are known from the normal mode calculation
and the d$/ciSl have been obtained from ab azirio calculations [63], it becomes
possible to synthesize a band intensity profile for a given (even finite) ol-helix structure.
Such a calculation has been done for the oll-helix and the a11-helix for amide I
and aniide I1 by computing the IR intensity profiles for the two polarization components
of these two bands [141]. The results show that the DRs are significantly
different enough to pennit identification of these structures from this property.
The ability to predict a band intensity profile opens up an important additional
dimension in vibrational analysis. It means that we will be able to relate subtle
spectral differences to small structural changes with a greater degree of confidence.
Thus, it has been possible to confirm that an observed three-component contour of
the amide I band of tropomyosin is indeed expected for a coiled-coil a-helix [142].
Extensions to understanding the normal modes of proteins become possible [ 1431.
The systematic incorporation in an SDFF of dipoles and dipole fluxes to calculate
IR intensities [ 1441 will finally bring to the vibrational analysis of polymeric niolecules
the completeness and flexibility needed to make it a much more powerful
structural tool.
5.4.2.3 3lo-Helix
The 3lo-helix represents a different topology than the a-helix, being 4 - I rather
than 5 - 1, and is therefore of importance in studying the vibrational dynamics
of polypeptide helices. At present, its only clear identification has been in PAIB, so
its characterization from this polypeptide may lack soine generality. On the other
hand, the excellence of the experimental data [I 101 makes its vibrational analysis
secure.
Since the structure of PAIB has not been determined in detail by diffraction
methods, the normal-mode studies [110] were based on a 310 structure obtained
from conforniational analysis [l 1 11 (Figure 5-7). The vibrational studies compared
experimental data with predictions for two helices, and the results clearly favored
the 310- over the a-helix. The threefold screw symmetry of this structure results in
El and E2 species modes reducing to doubly degenerate E species modes. The main
chain force field was the same as that for oll-PLA, with additional force constants
refined for the (CH3)2 group. Some inodes from the full analysis [110] are compared
with those of q-PLA in Table 5-1 1.
The observed amide I frequencies are slightly lower for the 3lo-helix than for
the cq-helix because of the slightly stronger hydrogen bond (N...O = 2.83 A versus
2.86 A, respectively). The increased splitting is undoubtedly due to the different
TDC interactions as a function of conformation. This probably also accounts for
the large change in the A-E splitting of the aniide 11 modes. The nominal aniide 111
modes (they contain no CN s and NH ib dominates only in the 1312 cn-' mode!