Random-coil conformations spectra

Fresh solutions of pustulan, which are presumably in a random-coil conformation, have a positive c.d. at 180 nm (see Fig. 8). The c.d. spectrum... 

It is common today to consider a peptide or an unfolded protein to be random coil —i.e., a blend of conformations—if their CD spectra resemble the traditionally accepted random coil CD spectrum (Blanco and Serrano, 1995 Dyson et al., 1992 Jimenez et al., 1993 Luisi et al., 1999 Munoz et al., 1995 Najbar et al., 2000 Viguera etal., 1996). As we argue here, this CD spectrum does not correspond to random coil at all. Theoretical calculated spectra representing blends of different conformations have been published by Krimm s group (Ronish and Krimm, 1972, 1974). While the results are uncertain because of the unknown compositional coefficients for each conformation in the blend, these spectra are clearly unrelated to that of Pn and many unfolded peptides and proteins. We need to reconsider what kind of CD spectrum is an appropriate representative for a true random coil. 

As an example chosen in the macromolecular field the C NMR spectrum of syndiotactic polypropylene might be mentioned In solution (averaged random coil conformation, molecular model corresponding to 7) it presents three signals in the crystal state, where a chiral rigid conformation exists [(2/1)2 helix], it shows four signals (Figure 17). 

Figure 10.1 -NMR spectrum of thioredoxin, reducedform. Labels show chemical-shift values typical of various hydrogen types in protein chains having random coil conformation. Some signals lie outside these ranges because of specific interactions not present in random coils. Atom labels are as found in PDB coordinate files. Spectrum generously provided by Professor John M. Louis.

Figure 2 shows 1 3C NMR spectra of curdlan(DPn 540) of an water suspension and alkaline solution reported by Saito et al. 8). It is noteworthy that at a concentration of 0.22M NaOH the broad 1 3C NMR signals decrease to less than one-tenth of those of the aqueous suspension. This sharp spectrum is characteristic of random-coil conformation. This is consistent with the results of Ogawa et They determined the dependence of optical... 

The structures of spiropyran-modified poly(L-glutamate)s are strongly affected by light or dark conditions, as demonstrated by the CD spectra in Figure 10. Before irradiation, the colored solutions show the CD spectrum of a random coil conformation. After exposure to sunlight, the colorless solutions display the typical CD pattern of the a-helix, thus indicating that the isomerization of the side chains causes a transition from coil to helix in the polypeptide chains. The photoinduced conforma-... 

Finally, the shift toward higher wavenumbers of the zero crossing of the negative-positive VCD spectrum is better reproduced by the extended helix than the left-handed a-helix. Thus, we favor the interpretation that the observed spectra of the "random coil" conformation can best be described by an extended helical structure, and that a truly random coil peptide will exhibit virtually no VCD. Dukor and Keiderling [39] reached very similar conclusions about the nature of the "random coil" conformation of homo-polyamino acids based on an extensive study of a number of left- and right handed helical segments, and fully supports the conclusion reached earlier by Krimm [42,43] about the extended helix discussed above. All evidence points to the fact... 

Fig. 24.15B), 16.9 and 15.9 ppm, which are unequivocally ascribed to six Ala residues at the C-terminus the peak at 16.9 ppm is assigned to Ala 245-248 taking random coil conformation at the terminal end, whereas 15.9 ppm is assigned to Ala 228 and 233 taking the au-helix conformation [70, 76]. Especially, the signal from Ala 246 and 247 is also assigned, in view of the difference spectrum between carboxypeptidase A- and papain-cleaved bR... 

The other extreme of the conformation spectrum that may be assumed by the polymer chain is the completely random coil. Polymers that are in solution, in melt, or amorphous in the solid state assume this conformation. Between these two extremes (planar zigzag and random coil conformation) the number of conformation shapes that a polymer chain can assume is virtually limitless. This, of course, assumes that there is free rotation about single bonds. In practice, however, there is no such thing as completely free rotation. All bonds have to overcome certain rotational energy barriers whose magnitude depends on such factors as steric hindrance, dipole forces, etc. (Figure 3.7). 

Determination of the average DP for the peptide grafts involves quantitation of the backbone and peptide resonances. These measurements were made in 10 v/v% TFA/CDCI3 because the most accurate comparisons were obtained with the peptide in a random coil conformation. A typical spectrum is shown in Figure 2. The resonances associated with the poly-(arylene ether sulfone) backbone are reasonably well resolved with the exception of an overlap in the aromatic region with the aromatic protons attached to the benzyl ester and the amide protons of the peptide backbone. The average DP was calculated from the ratio of the ratio of the benzyl CH2 protons to the geminal CH3 protons in the backbone polymer. 

Figure 11.2 shows the UV-Visible absorption spectrum of a P3HT/THF solution [5b]. On dissolution, a major shift of the n-% absorption band is observed (see Figures 11.1 and 11.2), Dissolution causes localization of the electronic wavefunctions as a result of the disorder brought about by the (random) coil conformation. Based on the similar spectral shifts observed for the P3ATs, it seems that the chains of the yellow P3AT in solution are in a disordered conformation, whereas casting into solid film restores the more ordered crystalline phase with an associated more extensive delocalization of the n-electron wavefunctions. 

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