Helix content, average

The helix contents of five peptide fragments from the protein thermolysin have been determined by CD and NMR in both water and 30% TFE. 85 The helix content was obtained from CD by the method of Chen et a I.162 and the NMR method utilized chemical shifts. 84 Four of the five peptides correspond to helical regions in the intact protein, and one corresponds to an Q-loop. 86 The rms difference between CD and NMR helix contents for the five peptides under the two conditions is 7.5%. One peptide shows the largest deviations (0 vs 13% in water, 45 vs 62% in 30% TFE). If it is excluded, the rms deviation decreases to 4%. The peptide showing the largest deviation, residues 258-276 from the thermolysin sequence, has two Tyr and one Phe (with the Phe adjacent to one of the Tyr in the sequence), and therefore it has an above-average content of aromatic amino acids, which can perturb both the CD spectrum and NMR chemical shifts. Of the other four peptides, three have a single aromatic residue and the fourth has two aromatics. 

Helical hydrophobic moment ratios, I , are evaluated for 34 polypeptides under conditions where the helix content is dictated solely by the short-range interactions operative in aqueous media. The mean-square helical hydrophobic moment is denoted by , and is the averaged of the squared hydrophoblcltles. This ratio would be one in absence of any correlation in the hydrophoblcltles of amino acid residues in helices. 

For paramyosin [ra ]232 and the Moffitt parameters a0 and b0 are colinear for the entire helix-coil transition see Figure 5), but since b0 represents an averaging of rotatory contributions at many wavelengths and is relatively insensitive to the environment, it is the preferable parameter for the estimation of helix content. 

Both approaches are empirical. They depend on comparing unknown spectra with spectra which represent presumably known structures. They give relatively accurate percentages of helix, P-sheet, reverse turn, and unfolded structure, but quantitate only the average secondary structure content [108]. The relative success of these spectroscopic methods gives confidence that more detailed information about specific vibrational characteristics of peptides and proteins will provide valuable and useful contributions to the study of these problems. The developments... 

We prepared three bifunctional redox protein maquettes based on 12 16-, and 20-mer three-helix bundles. In each case, the helix was capped with a Co(III) tris-bipyridyl electron acceptor and also functionalized with a C-terminal viologen (l-ethyl-V-ethyl-4,4 -bipyridinium) donor. Electron transfer (ET) was initiated by pulse radiolysis and flash photolysis and followed spectrometrically to determine average, concentration-independent, first-order rates for the 16-mer and 20-mer maquettes. For the 16-mer bundle, the a-helical content was adjusted by the addition of urea or trifluoroethanol to solutions containing the metal-loprotein. This conformational flexibility under different solvent conditions was exploited to probe the effects of helical secondary structure on ET rates. In addition to describing experimental results from these helical systems, this chapter discusses several additional metalloprotein models from the recent literature. 

The optical activity of helical segments in proteins can vary considerably with helix length, conformation and nature of side chains. The Cotton effects at 198 and 207 mn are sensitive to hehx geometry, while the 233 nm Cotton effect is not, therefore [m]233 measurement gives better average helical contents than do measurements at other wavelengths. The ORD of perfect helices should be relatively independent of solvent because the tightly packed hehx structure provide the uniform local environment for the n tt transition, while distorted hehces will be more environment dependent. 

At 233 nm, ORD spectrum of a-helix has a negative Cotton effect while P-sheet and random-coil structures have an average [m]233 value of-2520degcm dmor, thus [m]233 can be used to estimate the a-helical content by... 

The CD Spectra of P-sheet and random-coil conformations are isodichroic (identical elUp-ticity values) at 208 nm with an average effipticity of OOOdegcm dmor. The observed ellipticity at 208 nm for a-helix is -32600 4000deg cm dmoC. Thus the a-helical content (fraction of a-helical structure, of proteins can be estimated according to... 

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