Definition of Secondary Structure

An example of the use of chemical shifts to delineate residual secondary structure is given in Figure 3 for the molten globule state of apomyo-globin (Eliezer et al., 1998 Eliezer et al., 2000). Combined use of 13C , H , 13C, and 13CO secondary shifts gives a more precise definition of secondary structure boundaries than use of 13C shifts alone (Eliezer et al., 2000). 

Reliable secondary structures can enhance the prediction of higher order protein structure, and to a limited extent, secondary-structure motifs can even suggest specific fold structures. Sometimes these secondary structures provide insight into function. Definition of Secondary Structure of Proteins (DSSP), Integrated Sequence-Structure Database (ISSD), Protein Secondary Structure Database (PSSD), and CATH are covered in this section (see Table 2.2). 

NAD+-pyruvate is shown in Fig. 8. The enzyme has an extensive amount of secondary structure. Ramachandran diagrams are shown in Fig. 9. Estimates of the proportion of amino acid residues located in the helices depend on the precise definition of secondary structure and vary around 40%. Three different p structures are found in LDH and account for around 23% of all residues. The amino terminal half of the molecule contains a six-stranded parallel sheet whereas the carboxy terminal half of the subunit has two three-stranded antiparallel p structures. The parallel sheet which is mainly in the interior of the molecule, exposes two edges to the solvent and one to a subunit interface. Thus, most of the residues in this structure are hydrophobic. The high concentration of / -branched residues such as valine, isoleucine, and threonine as well as the twist present in all observed p structures 143) can be seen in Fig. 

Disulfide bridges are, of course, true covalent bonds (between the sulfurs of two cysteine side chains) and are thus considered part of the primary structure of a protein by most definitions. Experimentally they also belong there, since they can be determined as part of, or an extension of, an amino acid sequence determination. However, proteins normally can fold up correctly without or before disulfide formation, and those SS links appear to influence the structure more in the manner of secondary-structural elements, by providing local specificity and stabilization. Therefore, it seems appropriate to consider them here along with the other basic elements making up three-dimensional protein structure. 

Fig. 7.10. Plot of the PCA coefficients for the two most important basis functions for a set of 78 polypeptide, protein and virus ROA spectra. Definitions of the structural types analysed are all alpha, > 60% a-helix with little other secondary structure mainly alpha, > 35% a-helix and a small amount of (3-sheet ( 5-15%) alpha beta, similar significant amounts of a-helix and (3-sheet mainly beta, > 35% 13-sheet and a small amount of a-helix ( — 5—15%) all beta, > 45% (3-sheet with little other secondary structure mainly disordered/irregular, little secondary structure all disordered/irregular, no secondary structure...

D. Effects of Secondary Structure Definition and Truncation of Terminal Loops... 

Distances between C —C and a torsion angles (i.e., dihedral angles about virtual bonds C —C ) (see Chapter 4, Section 4.3.1.1) were also used to identify secondary structures (Srinivasan et al., 1975). Levitt and Greer (1977) proposed rules based on combination of three criteria, inter a carbon distances, a torsion angles, and hydrogen bond patterns. The authors have proposed this procedure as the first objective compilation of secondary structures in a large number of globular proteins. The automatic identification procedure is objective, but somewhat arbitrary definitions still remain... 

Growth and diet are subject to seasonal changes. The presence (or absence) and relative concentrations of secondary metabolites in the extracts of organisms are factors which chemists should document along with observations made during collection. Often, in preliminary experiments guided by bioassay, mixtures, rather than individual compounds, are tested. Association of a certain activity with structurally related compounds may serve as a lead for further tests, but should not be considered definitive. 

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