Protein secondary structures representation

J. M. Burridge and S. J. P. Todd, /. Mol. Graphics, 4, 220 (1986). Protein Secondary Structural Representations Using Real-Time Interactive Computer Graphics. 

Sequences of the representative proteins are displayed in JOY protein sequence/ structure representation (http //www-cryst.bioc.cam.ac.uk/ joy/). The representations are uppercase for solvent inaccessible, lowercase for solvent accessible, red for a helix, blue for strand, maroon for 310 helix, bold for hydrogen bond to main chain amide, underline for hydrogen bond to main chain carbonyl, cedilla for disulfide bond, and italic for positive angle. The query sequence is displayed in all capital letters. The consensus secondary structure (a for a helix, b for strand, and 3 for 310 helix) as defined, if greater than 70% of the residues in a given position in that particular conformation, is given underneath. 

Figure 5.11 Stereo representation of a model of IFABP-PXK51. The overall protein structure is shown with C60 and the pyridoxal linked via a disulfide bond.The pyridoxal aldehyde group is bonded through a Schiff base to K51. Color scheme Protein secondary structure (green), carbon (white), oxygen (red), nitrogen (blue), sulfur (orange).

Figure 5.1 Common representations of the three-dimensional structures of proteins Three-dimensional graphics of hen s egg-white lysozyme as visualized with RasMol (first row, ILYZ.pdb) are displayed in wireframe (residue type), spacefill (atom type) and backbone (structure type). The Cj, mainchain with side chain residues is displayed with KineMage (second raw left). The secondary structure representations (a helices and P-sheets) are visualized with KineMage (lLYZ.kin) in ribbons and arrows (second raw center), and Cn3D (ILYZ.cnS) in cylinders and arrows (second raw right).

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

FIGURE 5.8 Two structural motifs that arrange the primary structure of proteins into a higher level of organization predominate in proteins the a-helix and the /3-pleated strand. Atomic representations of these secondary structures are shown here, along with the symbols used by structural chemists to represent them the flat, helical ribbon for the a-helix and the flat, wide arrow for /3-structures. Both of these structures owe their stability to the formation of hydrogen bonds between N—H and 0=C functions along the polypeptide backbone (see Chapter 6). 

Figure 26.5 (a) The o-helical secondary structure of proteins is stabilized by hydrogen bonds between the N—H group of one residue and the C=0 group four residues away, (b) The structure of myoglobin, a globular protein with extensive helical regions that are shown as coiled ribbons in this representation. 

Fig. 4.1.13 A ribbon representation of the crystal structure of recombinant acquorin molecule showing the secondary structure elements in the protein. Alpha-helices are denoted in cyan, beta-sheet in yellow, loops in magenta coelenterazine (yellow) and the side chain of tyrosine 184 are shown as stick representations. From Head et al., 2000, with permission from Macmillan Publishers.

The association of secondary structures to give super-secondary structures, which frequently constitute compactly folded domains in globular proteins, is completed by the a-a motifs in which two a-helices are packed in an anti-parallel fashion, with a short connecting loop (Figure 4.8c). Examples of these three structural domains, often referred to as folds, are illustrated in Figures 4.9—4.11. The schematic representation of the main chains of proteins, introduced by Jane Richardson, is used with the polypeptide backbone... 

Figure 10.4. Schematic representation of the Tat protein and its functional regions, highlighting the basic RNA binding domain. The secondary structure of its RNA target, TAR, is shown. Critical residues for Tat binding within the recognition domain (highlighted) are shown in bold.

Figure 10.7. Schematic representation of the Rev protein, emphasizing its two key functional domains. The secondary structure of the RRE, highlighting the Rev biding site, is shown. Residues essential for RRE are in bold. The intervening bulge contains two non-Watson-Crick base pairs, G48 G71 and G47 A73, and a bulged base U72. ...

The first surprise was that these molecules are much longer than seems necessary for the formation of adapters. In addition, 10-20% of their bases are modified greatly from their original form.171 Another surprise was that the anticodons are not all made up of "standard" bases. Thus, hypoxanthine (whose nucleoside is inosine) occurs in some anticodons. Conventional "cloverleaf" representations of tRNA, which display their secondary structures, are shown in Figs. 5-30 and 29-7. However, the molecules usually have an L shape rather than a cloverleaf form (Figs. 5-31 and 29-6),172 and the L form is essential for functioning in protein synthesis as indicated by X-ray and other data.173 Three-dimensional structures, now determined for several different tRNAs,174 175 are all very similar. Structures in solution are also thought to be... 

Sequence analysis is a core area of bioinformatics research. There are four basic levels of biological structure (Table 1), termed primary, secondary, tertiary, and quaternary structure. Primary structure refers to the representation of a linear, hetero-polymeric macromolecule as a string of monomeric units. For example, the primary structure of DNA is represented as a string of nucleotides (G, C, A, T). Secondary structure refers to the local three-dimensional shape in subsections of macromolecules. For example, the alpha- and beta-sheets in protein structures are examples of secondary structure. Tertiary structure refers to the overall three-dimensional shape of a macromolecule, as in the crystal structure of an entire protein. Finally, quaternary structure represents macromolecule interactions, such as the way different peptide chains dimerize into a single functional protein. 

Protein topology cartoons (TOPS) are two-dimensional schematic representations of protein structures as a sequence of secondary structure elements in space and direction (Flores et al, 1994 Sternberg and Thornton, 1977). The TOPS of trypsin domains as exemplified in Figure 4.9 have the following symbolisms ... 

Figure 4.11. Graphic representations of protein 3D structure. Three-dimensional graphics of hen s egg-white lysozyme as visualized with RasMol (first and second rows, ILYZ.pdb) and Cn3D (third row, ILYZ.val) are shown from left to right (color type) in wireframe (atom), spacefill (atom), dots (residue), backbone (residue), ribbons (secondary structure), strands (secondary structure), secondary structure (secondary structure), ball-and-stick (residue), and tubular (domain) representations.

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 II-2 Major elements of secondary structure of proteins. Left, the a-helix right, representation of the antiparallel pleated sheet structures for polypeptides. (After Pauling, L., and R. B. Corey (1951). Proc Natl Acad Sci USA 37 729).

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