Protein structure analysis randomized region

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

The final session demonstrates how to characterize a protein region as random-izable. For a set of solvent-exposed residues of an immunoglobulin structure, 103 mutants are randomly generated. We examine how many of these mutants are destabilized with respect to the wild type. The analysis is repeated with an alternative set of residues that correspond to part of the natural epitope of the immunoglobulin structure. 

Secondary structure predictions for human poly(ADP-ribose) polymerase. A computer-derived secondary structure prediction for the polymerase based on a Chou-Fasman analysis predicts a very low p-sheet (< 9%), a high content of random coil (38%), a large number of p-tums and approximately 25% helical content. The stmcture shows several regions of helix-tum-helix (i.e. centered at residues 82, 97, 232, 258 and 275) which is characteristic of a number of DNA binding proteins (Fig. 3). The predicted stmcture does not show a B-A-B stmcture, which is characteristic of NAD binding domains. 

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