Lysozyme, secondary structure analysis

Figure 12.6. Secondary structure prediction of duck lysozyme at NPS . The predicted secondary structures of duck lysozyme at Network Protein Sequence Analysis (NPS ) with GOR IV method are depicted in different representations.

Figure 12,7. Secondary structure consensus prediction at NPS . Network Protein Sequence Analysis (NPS ) offers numerous methods for secondary structure prediction of proteins. The secondary structure consensus prediction (Sec.Cons.) of duck lysozyme is derived from simultaneous execution of predictions with more than one methods.

An example of this approach to protein analysis is illustrated by Figure 6.2c, which shows the amide I band of the enzyme lysozyme in D2O. The amide I band of this protein shows nine component bands. The band at 1610 cm is due to amino acid side-chain vibrations and does not contribute to the amide I band. The relative areas of the amide I components are listed in Table 6.2e, and these may be assigned to the various types of secondary structures. The bands at 1623 and 1632 cm... 

Figure 3 SAM-T02 results for the secondary structure prediction of bovine a-lactalbumin. The predicted secondary structure of proteins by SAM-T02 is reported using four different secondary structure evaluation methods. The relative size of the letters corresponds to the reliability of the predicted secondary structure. For bovine a-lactalbumin, it leads to residues with only one type of predicted secondary structure (specifically, large C s or H s) or residues with several secondary structure types (specifically, T s, S s, C s, and X s). The brackets under the residues signify the type of expected secondary structure given the predictions. The predicted secondary structure is reported in the STR (a), DSSP-EBGHSTL (b), STRIDE-EBGHTL (c), and DSSP-EHL2 (d) formats. Analysis of the results indicates the predicted secondary structure is similar to that of chicken lysozyme or human a-lactalbumin.

Perhaps one major uncertainty in the CD analysis of the secondary structures of proteins is choice of reference proteins which will adequately represent the protein to be analyzed [86Y1, 91V1]. In the early 1970s the selection was dictated by the then available X-ray structures such as myoglobin, lysozyme, ribonuclease, lactate dehydrogenase and papain. Today we have more than 300 proteins of known 3-dimensional structure at our disposal. What constitutes a representative set of reference proteins is still a subject to be investigated. Therefore, this problem may not be completely solved until different sets of reference proteins are extensively tested for the four classes of proteins. 

The first x-ray analysis of a protein, identifying the active site and giving details of secondary and tertiary structure, was that of lysozyme, carried out by Phillips [30] in 1966. The subsequent structure determinations of myoglobin [31] and haanoglobin [32] by Kendrew and Perutz represent great triumphs for both x-ray crystallography and protein science. 

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