Secondary structure assignments

Frishman, D., and Argos, P. (1995). Knowledge-based protein secondary structure assignment. Proteins 23, 566-579. 

Structural Alignment of the Switch-1 and Switch-2 Regions of Kinesin Motor Domains with Secondary Structure Assignments and Classification of the Switch-2 Cluster and Neck/Neck Linker Conformations... 

Code used for secondary structure assignments determined by PROCHECK v.3.5. (Laskowski el al., 1993) using the extended Kabsch/Sander classification (Kabsch and Sander, 1983) ... 

Raman spectroscopy provides structure-sensitive bands for distinguishing these secondary structures. Assignments of the —CO—NH— group vibrations were first made via normal coordinate analysis on jV-methylacetamide by Miyazawa et al. (11). 

A state-of-the-art assessment of predictions requires an up-to-date set of secondary structure assignments and a measure to compare predictions with the correct assignments. Evaluation sets of non-homologous domains with secondary structure assignments have been proposed by Barton et al. [166, 326], This dataset is an extension of other proposed test sets [155, 167]. It contains 496 non-homologous (SD cutoff of 5, which is more stringent than mutually less than 25% sequence identity) domains. The database contains 82 847 residues, 28678 alpha-helix (H), 17 741 beta-strand (E), and 36 428 coil (C) residues. 

Fig. 3. A working example of NdPASA identifying template sequences for the query, cytochrome C from the purple phototropic bacterium, using PSI-BLAST searches. The selected template is 1GQA-D, cytochrome C from Rhodobacter Spheriodes, which shares 44 % sequence identity with the query. The output of the alignment includes secondary structure assignments of the template.

The DSSP database is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) [29]. The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does not predict protein structure [29]. 

Fig. 15.18. Schematic hydrogen-bonding diagrams of all the examples of y/ loops in unrelated proteins. The diagrams are based on the secondary structures assigned using a modified version of the Kabsch Sander [55] algorithm [56]...

Table 6.2c Amide I band frequencies and secondary structure assignments for standard proteins...

Infrared spectroscopy has been used in a large number of studies of proteins over a range of different environments. Some examples of the proteins that have been analysed are listed in Table 6.2c, which details the deconvolved amide I frequencies and secondary structure assignments that have been made for a series of proteins in D2O. These assignments are based on the fact that the secondary structures of these globular proteins have been very well characterised by X-ray crystallography. 

From the spectra shown in the figures and following the discussion in the text the secondary structure assignments for the five groups of proteins are summarized in Table 2. From this table is can be observed that for the Amide I vibration the major structural components dictates the Amide I frequency, but it also indicates that one structure influences the frequencies of the other. For example, the a-Amide I frequency falls at 1656 cm , but as more and more B-structure is present the frequency shifts from 1656 cm (a ) to 1652 cm l ( a+ low B ) to 1644 cm l (a + B ). In the Amide III region the a-helix frequency shifts from 1298 cm to 1315 cm whenever some B Sheet structure is present. Similarly, the B-sheet Amide III shifts from 1235 cm" to 1241 cm" when enough a-helix structure is present. 

Figure 11.4. Comparison of secondary structure predictions by various methods. The sequence of flavodoxin was used as the query and is shown on the first line of the alignment. For each prediction, H denotes an a-helix, E a 3-strand, and T a 3-turn all other positions are assumed to be random coil. Correctly assigned residues are shown in inverse type. The methods used are listed along the left side of the alignment and are described in the text. At the bottom of the figure is the secondary structure assignment given in the PDB file for flavodoxin (10FV, Smith et al., 1983).

The work is still in progress. However, it seems clear that the variability in secondary structure assignments in the PDB is so great that it will probably be impossible to reproduce completely the assignments which have been made by previous workers. That said, our results to date show that it is possible to identify all of the alpha-helix and beta-strand structures with a precision of about 75% and 35% respectively the results for the 3-10 stretch and turn secondary structures are very much worse, with the precision typically being less than 20%. Full details of this work will be reported elsewhere. 

Knowledge-Based Secondary Structure Assignment. Available http //wolf.bi.umist.ac.uk/... 

Secondary Structure Assignment from Known Atomic Coordinates of Proteins. Available http //webclu.bio.wzw.tum.de/stride/. 

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