Helix formation, spectral

A major limitation of the above studies of calmodulin-peptide interactions was that spectral evidence to support helix formation was limited to predictive algorithms and measurements of the difference in the circular dichroism of peptides and calmodulin in free solution and the CD in 1 1 complexes. Interpretation of such experiments was severely limited by the fact that calmodulin probably undergoes conformational changes upon binding peptides (Klevit et al., 1985). One elegant NMR study has been reported on a complex of melittin and bacterial-derived perdeuter-ated calmodulin the results were consistent with helix formation by the peptide in the complex (Seeholzer et al., 1986). 

The spectral changes accompanying helix formation in proteins can be generalized... 

Ho et al. were able to verify the a-helical shape of the polymer by circular dichroism (CD) spectra. No structural elements were observed until the formation of the double helical DNA at which point they observed a right-handed a-helix in the polythiophene backbone. Their work demonstrates the power of fluorometric detection as they noted a seven order of magnitude increase in detection sensitivity (20 fM in 200 pi) simply through the use of fluorometric detection as opposed to UV-vis absorption. The polymer in solution has a high fluorescence yield with a maximum at 530 nm (Fig. 11a). Upon formation of the duplex the fluorescence is significantly quenched (Fig. lib), while with the addition of the complementary DNA and triplex formation, the fluorescence intensity is enhanced by a factor of 5 (Fig. 11c). The inherent sensitivity of the spectral shift even allowed distinction between DNA with only one and two mismatched bases (Fig. lOBd, e). 

Helical heptad repeat sequences have been reported to be well behaved although they are difficult to characterize by NMR spectroscopy due to spectral overlap. The motifs that have been shown to have native-like properties, and are not highly repetitive, have cores composed of aromatic amino acid side chains of, for example, phenylalanine and tryptophan. In four-helix bundle motifs [1, 2], the /1/la-motif BBAl [5] and the /1-sheet protein Betanova [9], the formation of the folded structure appears to be strongly dependent on such residues although the energetics have not been calculated by substitution studies. As a tentative rule, therefore, the probability of success in the design of a new protein is probably much higher if residues are included that can form aromatic clusters in the core (Fig. 5). 

The first isomerization step from enantiomerically pure (P, P)-trans-l to (M, M)-cis-l (Figure 44j) was observed upon UV irradiation at 20 °C. The observed CD spectral changes (Figure 44e) are typically associated with the P, P to M, M helix inversion. The second isomerization, which is a thermal isomerization step, resulted in the formation... 

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