Peptide representation

Left side of Fig. 4 shows a ribbon model of the catalytic (C-) subunit of the mammalian cAMP-dependent protein kinase. This was the first protein kinase whose structure was determined [35]. Figure 4 includes also a ribbon model of the peptide substrate, and ATP (stick representation) with two manganese ions (CPK representation). All kinetic evidence is consistent with a preferred ordered mechanism of catalysis with ATP binding proceeding substrate binding. 

Where helical secondaiy structures are represented by the cylinder model, the /i-strand. structures are visualized by the ribbon model (see the ribbons in Figure 2-124c). The broader side of these ribbons is oriented parallel to the peptide bond. Other representations replace the flat ribbons with flat arrows to visualize the sequence of the primary structure. 

Figure 5.27 Schematic representation of a model for the conformational change of hemagglutinin that at low pH brings the fusion peptide to the same end of the molecule as the receptor binding site. The fusion peptide (purple) is at the end of heUx A about 100 A away from the receptor binding site in the high pH form. In the low pH fragment this region of helix A has moved about 100 A towards the area where the receptor binding sites are expected to be in the intact hemagglutinin molecule. (Adapted from D. Stuart, Nature 371 19-20, 1994.)...

Figure 15.19 Schematic representation of the peptide-binding domain of a class I MHC protein. The al and a2 domains are viewed from the top of the molecule, showing the empty antigen-binding site as well as the surface that is contacted by a T-cell receptor. (Adapted from P.J. Bjdrkman et al.. Nature 329 506-512, 1987.)...

Figure 9.10 Three-dimensional representation of the data volume of a tryptic digest of ovalbumin. Series of planar slices through the data volume produce stacks of disks in order to show peaks. Reprinted from Analytical Chemistry, 67, A. W. Moore Jr and J. W. Jorgenson, Comprehensive three-dimensional separation of peptides using size exclusion chromatogra-phy/reversed phase liquid chromatography/optically gated capillary zone electrophoresis, pp. 3456-3463, copyright 1995, with permission from the American Chemical Society.

Figure 28.7 A representation of protein biosynthesis. The codon base sequences on mRNA are read by tRNAs containing complementary anticodon base sequences. Transfer RNAs assemble the proper amino acids into position for incorporation into the growing peptide.

Fig. 2.14 Formulae of /5-peptides 81 and 82 forming stable 3,4-helical structures in aqueous solution and schematic representation of the position of the amino acid side-chains looking down the 3,4-helix axis [128, 165]...

Fig. 2.39 Schematic representation of the projection of idealized ji- and y-peptide helices in a plane perpendicular to the helix axis and comparison with the helical wheel of the natural a-helix...

Fig. 2.40 Sequences and helical wheel representation of amphiphilic 2.5,2-helical jS-pep-tide 17-mers evaluated for antimicrobial activity [234, 248]. These peptides are exclusively composed of hydrophobic trans-ACPC...

Fig. 2.41 Schematic representation of type II peptides and unlike-y dipeptide illustrating...

Figure 38-8. Diagrammatic representation of the peptide elongation process of protein synthesis. The small circles labeled n - 1, n, n -I-1, etc, represent the amino acid residues of the newly formed protein molecule. EFIA and EF2 represent elongation factors 1 and 2, respectively. The peptidyl-tRNA and aminoacyl-tRNA sites on the ribosome are represented by P site and A site, respectively.

Figure 3. Schematic representation of the PGII, PGI, PGC [13] and PGE proteins from A. niger, indicating the putative processing sites for the signal peptide ( ) and the mono- and dibasic processing site for the propeptide ( ). The position of introns (lA, IB and IC) are indicated ( [) and variation of amino acids number is shown in different parts of protein. The putative N-glycosylation sites are marked ( ).

PI. 3.1 A MUP peptide backbone ribbon representation, shown in two orthogonal projections (left p-sheet framework right binding-cavity, highlighted) (from Luckc et at., 1999). 

Fig. 27. A schematic representation of the seven transmembrane helical peptide chains (A-G) viewed from inside the cell. The numbering denotes the first and last amino acid residues. The proton channel is believed to be the volume between helices C, D, F and G...

Fig. 8. Lck SH2 domain-peptide complex (Ac-cmF-Glu-Glu-Ile-OH, 12) revealing the twopronged plug engaging a two-holed socket 1 binding mode, reminiscent of the majority of SH2 domains (Protein Databank entry code 1BHF.PDB [118]). The protein is depicted in a Connolly surface mode, the ligand is given in a ball-and-stick representation. The cmF residue is deeply buried in its binding pocket (left)...

FIGURE 1.20 Abbreviated designations of substituted amino acids and peptides. Examples of incorrect representations are given. 

FIGURE 5.4 Schematic representation of a continous-flow system for the solid-phase synthesis of peptides. Solvent is forced through the system by a pump. The support is in the form of a column that is stationary. A reaction is monitored by measuring the change in absorbance of the solvent stream. 

Scheme 14 Schematic representations of the assay for nucleases and protease detection based on the complex of ACP, DNA-TR and peptide-H...

A nice example of an indirect structure determination using the trNOE method is the study of the conformation of a loop of the membrane protein bacteriorhodopsin (BR) [28]. Antibodies were raised against BR, and subsequently the complex of a heptapetide derived from BR was studied in complex with the antibody by trNOE. The bound conformation is a reasonably good representation of the conformation of the peptide in its native state in BR. 

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