Circular dichroism helical structure

Recently, peptoid-based mimics of both SP-C and SP-B have been designed to adopt helical secondary structures, and also mimic (to varying degrees) the sequence patterning of hydrophobic and polar residues found in the natural surfactant proteins. Peptoid-based SP-C mimics of up to 22 monomers in length, were synthesized and characterized by in vitro experimental methods [67, 68] (Fig. 1.8). The secondary structure of all molecules was assessed by circular dichroism and found to be helical. The surface activities of these peptoids, in comparison to the actual SP peptides described above, were characterized by surfactometry using... 

Tab. 2.3 Probing the 3,4-helical structure of j8-peptides by circular dichroism in MeOH (identification of the 3,4-helix CD signature and mean-residue ellipti-city (in deg cm dmoC ) of the extremum at 1, = ca. 215 nm)... 

The conformational changes which have been described so far are probably all relatively small local changes in the structure of H,K-ATPase. This has been confirmed by Mitchell et al. [101] who demonstrated by Fourier transform infrared spectroscopy that a gross change in the protein secondary structure does not occur upon a conformational change from Ei to 3. Circular dichroism measurements, however [102,103], indicated an increase in a-helical structure upon addition of ATP to H,K-ATPase in the presence of Mg and... 

Analyses by native polyacrylamide gel electrophoresis and circular dichroism (CD) spectroscopy revealed that spontaneous coiled-coil associations between EGF-E5-His and EGF-K5-His promoted heterodimer (dEGF-His) formation. The CD spectroscopic analysis suggested that the E5 peptide in monomeric EGF-E5-His had a disordered structure. However, the ot-helical structure was induced in the E5 peptide when it associated with EGF-K5-His. These findings are shown schematically in Fig. 6. 

The influence of adsorption on the structure of a -chymotrypsin is shown in Fig. 10, where the circular dichroism (CD) spectrum of the protein in solution is compared with that of the protein adsorbed on Teflon and silica. Because of absorbance in the far UV by the aromatic styrene, it is impossible to obtain reliable CD spectra of proteins adsorbed on PS and PS- (EO)8. The CD spectrum of a protein reflects its composition of secondary structural elements (a -helices, / -sheets). The spectrum of dissolved a-chymotrypsin is indicative of a low content of or-helices and a high content of //-sheets. After adsorption at the silica surface, the CD spectrum is shifted, but the shift is much more pronounced when the protein was adsorbed at the Teflon surface. The shifts are in opposite directions for the hydrophobic and hydrophilic surfaces, respectively. The spectrum of the protein on the hydrophilic surface of silica indicates a decrease in ordered secondary structure, i.e., the polypeptide chain in the protein has an increased random structure and, hence, a larger conformational entropy. Adsorption on the hydrophobic Teflon surface induces the formation of ordered structural elements, notably an increase in the content of O -helices (cfi, the discussion in Sect. 3.1.4). 

The optically active poly(TrMA) shows a large optical activity and intense circular dichroism (CD) due both to the triphenylmethyl group, indicating that this group has a chiral propeller structure, and to the helicity. Poly(TrMA) of degree of polymerization (DP) over 80 is insoluble in common organic solvents. 

As the concentration increases, the circular dichroism spectra show more and more helical structures (Dicko et al., 2004c). 

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). 

Infrared and circular dichroism (CD) measurements (Moss et al., 1976b) are both consistent with a sizable fraction of the tetramer being in the a-helical configuration, —29% a-helix with negligible j3 structure. This is rather similar to the 25% a-helix and —0% /3 structure obtained for the tetramer prepared from acid-extracted histones (D Anna and Isenberg, 1974b). 

Circular dichroism studies show that up to 50% of EPO s secondary structure is a-helical. The predicted tertiary structure is that of four anti-parallel helices formed by variable-sized loops, similar to many other haemopoietic growth factors. 

The next three sections (Sections 7.7.1, 7.7.2, and 7.7.3) cover fluorescence spectroscopy, I15-18 infrared, and circular dichroism, three powerful approaches to characterize the structure and conformational considerations of synthetic peptides. Section 7.7.1 deals with the use of fluorophores and broad aspects of fluorescence spectroscopy to characterize conformational aspects of peptide structure. In a similar manner, Section 7.7.2 covers a broad aspect of the uses of infrared (IR) techniques to study peptide conformations 19-22 Many IR techniques are discussed, as are approaches for the study of specific peptidic structures including amyloid, p-turn, and membrane peptides. Finally, there is a section on circular dichroism (Section 7.7.3) that covers the major issues of concern for peptide synthetic chemists such as the assignments of a-helix, 310-helix, -sheets and P-turns, and polyproline helices 23-25 There is also a brief description of cyclic peptides. 

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