Turn, Protein Secondary Structures Identification

Resolution enhancement of the amide I band allows for the identification of various structures present in a protein or peptide. Derivatives and deconvolution can be used to obtain such information. The best method used for the estimation of protein secondary structure involves band-fitting the amide I band. The parameters required, and the number of component bands and their positions, are obtained from the resolution-enhanced spectra. The fractional areas of the fitted component bands are directly proportional to the relative proportions of structure that they represent. The percentages of helices, -structures and turns may be estimated by addition of the areas of all of the component bands assigned to each of these structures and expressing the sum as a fraction of the total amide I area. The assumption is made that the intrinsic absorptivities of the amide I bands corresponding to different structures are identical. 

A description of the protein-structure hierarchy is incomplete without a discussion of structural motifs, which are critical to an understanding of protein structure [17]. Identification of recurring motifs in protein structures has refined our knowledge of the protein-structure hierarchy these motifs occur at all levels from primary to tertiary. The Phe-Asp-Thr-Gly-Ser sequence found in the active site of all aspartic acid proteinases, and the Gly-Gly-X-Leu sequence (where X represents any amino acid residue) that predicts a 3-strand for the last two residues [17], are examples of sequence motifs a-helices, P-strands, and turns are examples of secondary-structural motifs PaP and PxP units, P-hairpins, and Greek keys are examples of supersecondary-structural motifs and four-a-helix bundles and TIM barrels are examples of tertiary-structural motifs. The tertiary fold of a protein is characterized by its tertiary-structural motif. 

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