Peptide alignment, calculation

The peptide alignment is calculated by a / -analysis of the F-NMR chemical shifts as a function of r and p (using Smoi = 1 as there is no wobble), as previously explained [18,19,22,23]. Figure 5A,B shows the allowed regions in the r-p maps for GS-3/3 and GS-l/T, respectively. The overlap of the allowed regions suggests a peptide tilt angle r between 70° and 90°, but the value of the azimuthal rotation p is not well defined. 

Fig. 7 Solid state N-NMR spectra of GS-3/3 at 1 40 in oriented DMPC bilayers. The arrow indicates the new resonance emerging at high peptide concentration, from which the upright alignment of gramicidin S in the membrane was calculated. The dashed line corresponds to the respective powder pattern of the lyophilized peptide...

In 1958, Beer et al. re-examined the infrared dichroism situation and remeasured the dichroic ratio for several of the peptide bands in collagen. On the basis of studies on model compounds, they calculated the directions of the transition moments for the principal bands in the peptide link and, using the atomic coordinates for various proposed collagen models, the inclination of these transition moment vectors to the fiber axis. Since Beer (1956) had shown that the dichroism of a partially oriented polymer may be considered equivalent to that of a sample containing fully aligned and completely random portions, a disorientation parameter (/) characteristic of the degree of order of the sample could be calculated for each band. The spread of the values obtained for this parameter, which is characteristic of the sample only and not of the bands used to determine it,... 

For DNA sequences, (local) sequence similarity can be calculated at the nucleotide level, at the peptide level and at both levels with the mixed-alignment option as previously explained. If the peptide-level or mixed-alignment option is used, it is possible to translate sequence segments only at the forward strand or to have the program look at both, the forward strand and the reverse complement. 

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