Secondary structure, definition

Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R. RNA-Motif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 2001 29 4724-4735. 

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

Different side chains have been found to have weak but definite preferences either for or against being in a helices. Thus Ala (A), Glu (E), Leu (L), and Met (M) are good a-helix formers, while Pro (P), Gly (G), Tyr (Y), and Ser (S) are very poor. Such preferences were central to all early attempts to predict secondary structure from amino acid sequence, but they are not strong enough to give accurate predictions. 

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). 

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. 

The ICD of the dyes bound to saccharides through an ionic coupling or hydrophobic interaction may remain a conflicting problem. The side-chain chromophores covalently bound to saccharides permit CD bands in the far or near ultraviolet region. These side-chain chromophores can exhibit CD and thus provide more definitive information on the conformation of saccharide moieties. Thus, acetamide CD has been observed to reflect polymer secondary structure of glycosaminoglycans, which are the connective-tissue proteoglycans. 

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...

Fig. 16. Example of tree-like representation for RNA secondary structure. Each hairpin structure is shown next to its equivalent tree. With such representations, a graph theoretic measure can measure the distance between these trees and help generate fitness values for a fitness landscape. For example, the distance between two structures may be defined as the minimal number of elementary graph operations (insert a point, switch an edge, etc.) needed to convert one tree into the other. Note that there are many variants of tree representations for RNA secondary structures and many definitions of graph distance. In low-resolution tree representations, several secondary structures can map to the same graph.

In RmL the analysis of the structural features of the lid is simplified by the availability of structures of both native and complexed molecules this allows for clear identification of the mobile fragments. The lid is created by a long surface loop made up by residues 80—109. This fragment defies a classical definition of an H loop (Leszczynski and Rose, 1986) in that it exhibits well-defined secondary structure in its central helical fragment. Residues 82-96 (which include a short helix) directly obscure the entrance to the active site in the native enzyme. It is notable that between Arg-80 and Val-95 this fragment is not involved in any hydrogen bonds with any other parts of the molecule. Thus, the lid interacts with the main body of the protein only through hydrophobic interactions. 

The a-helix is one of the best-known regular conformational features as a subheading within the secondary structure of polypeptides and is frequently adopted in chains of six or more helicogenic amino acids (see Table 2.1 for a definition of terms and examples). The (3-sheet is another classic conformational structure that has been detected from the earliest days of X-ray crystallography of proteins. Local... 

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