Experimental design molecule targets

In order to examine whether this sequence gave a fold similar to the template, the corresponding peptide was synthesized and its structure experimentally determined by NMR methods. The result is shown in Figure 17.15 and compared to the design target whose main chain conformation is identical to that of the Zif 268 template. The folds are remarkably similar even though there are some differences in the loop region between the two p strands. The core of the molecule, which comprises seven hydrophobic side chains, is well-ordered whereas the termini are disordered. The root mean square deviation of the main chain atoms are 2.0 A for residues 3 to 26 and 1.0 A for residues 8 to 26. 

Characterization of amide vibrational modes as seen in IR and Raman spectra has developed from a series of theoretical analyses of empirical data. The designation of amide A, B, I, II, etc., modes stem from several early studies of the (V-methyl acetamide (NMA) molecule vibrational spectra which continues to be a target of theoretical analysis. 15 27,34 162 166,2391 Experimental frequencies were originally fitted to a valence force field using standard vibrational analysis techniques and subsequently were compared to ab initio quantum mechanical force field results. 

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