Ribbon model

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. 

Fig. 4. Ribbon model of protein kinase with peptide substrate and Mn2ATP (left) and protein phosphatase (right)...

Figure 2-124. The most common molecular graphic representations of biological molecules (lysozyme) a) balls and sticks b) backbone c) cartoon (including the cylinder, ribbon, and tube model) and of inorganic molecules (YBajCujO , d) polyhedral (left) and the same molecule with balls and sticks (right),...

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 14.2 Models of a collagen-like peptide with a mutation Gly to Ala in the middle of the peptide (orange). Each polypeptide chain is folded into a polyproline type II helix and three chains form a superhelix similar to part of the collagen molecule. The alanine side chain is accommodated inside the superhelix causing a slight change in the twist of the individual chains, (a) Space-filling model, (b) Ribbon diagram. Compare with Figure 14.1c for the change caused by the alanine substitution. (Adapted from J. Bella et al.. Science 266 75-81, 1994.)...

FIGURE 22.18 Model of the R. viridis reaction center, (a, b) Two views of the ribbon diagram of the reaction center. Mand L subunits appear in purple and blue, respectively. Cytochrome subunit is brown H subunit is green. These proteins provide a scaffold upon which the prosthetic groups of the reaction center are situated for effective photosynthedc electron transfer. Panel (c) shows the spatial relationship between the various prosthetic groups (4 hemes, P870, 2 BChl, 2 BPheo, 2 quinones, and the Fe atom) in the same view as in (b), but with protein chains deleted. 

Figure 26.9 X-ray crystal structure of citrate synthase. Part (a) is a space-filling model and part (b) is a ribbon model, which emphasizes the a-helical segments of the protein chain and indicates that the enzyme is dimeric that is, it consists of two identical chains held together by hydrogen bonds and other intermolecular attractions. Part (cl is a close-up of the active site in which oxaloacetate and an unreactive acetyl CoA mimic are bound.

Fig. 2. Ribbon diagram of the structures of (a) the water-soluble Rieske fragment from bovine heart bci complex (ISF, left, PDB file IRIE), (b) the water-soluble Rieske fragment from spinach b f complex (RFS, middle, PDB file IRFS), and (c) the Rieske domain of naphthalene dioxygenase (NDO, right, PDB file INDO). The [2Fe-2S] cluster is shown in a space-filling representation, the ligands as ball-and-stick models, and residues Pro 175 (ISF)/Pro 142 (RFS)/Pro 118 (NDO) as well as the disulfide bridge in the ISF and RFS as wireframes.

Fig. 7. Comparison of the cluster binding fold of the water-soluble Rieske fragment from bovine heart 6ci complex (ISF, left PDB file IRIE) with the structure of ru-bredoxin (middle PDB file 7RXN) and with the zinc-ribbon motif (right PDB file ITFl). The metal binding loops are shown as ball-and-stick models of the backbone atoms.

Fig. 2. The structure of the Fe protein (Av2) from Azotobacter vinelandii, after Geor-giadis et al. (1). The dimeric polypeptide is depicted by a ribbon diagram and the Fe4S4 cluster and ADP by space-filling models (MOLSCRIPT (196)). The Fe4S4 cluster is at the top of the molecule, bound equally to the two identical subunits, Emd the ADP molecule spans the interface between the subunits with MoO apparently binding in place of the terminal phosphate of ATP.

Fig. 3. The tetrameric structure of the MoFe protein (Kpl) from Klebsiella pneumoniae (7). The two FeMoco clusters and the P clusters are depicted by space-filling models and the polypeptides by ribbons diagrams (MOLSCRIPT (196)). The FeMoco clusters are bound only to the a subunits, whereas the P clusters span the interface of the a and j8 subunits.

Fig. 10. The putative transition-state complex formed between the Fe protein MgADP AlFj and the MoFe protein. For simplicity only one a/3 pair of subunits of the MoFe protein is shown. The polypeptides are indicated by ribbon diagrams and the metal-sulfur clusters and MgADP AlFi" by space-filling models (MOLSCRIPT (196)). The figure indicates the spatial relationship between the metal-sulfur clusters of the two proteins in the complex.

Fig. 10 (a-f) Hierarchical self-assembly model for chiral rod-like units A curly tape (c ), a twisted ribbon (d ), a fibril (e ) and a fibre (f). Adapted from Aggeli et al. [20], Copyright 2001 National Academy of Sciences, USA... 

For technological applications it is highly desirable to be able to design self-assembling systems to have particular physico-chemical properties under a given set of experimental conditions. Using computer simulation, it is possible to construct an atomistic model of tapes, ribbons and fibrils to study all of the interatomic interactions within the system in a quantitative manner. Figure 13 shows atomistic... 

Fig. 30 Model for the self-assembly of structure 2 into a double helix comprised of two ribbons, each of which consists of two parallel sheets. Reproduced with permission from Jahnke et al. [70].

FIGURE 2.1 A side view of the structure of the prototype G-protein-coupled, 7TM receptor rhodopsin. The x-ray structure of bovine rhodopsin is shown with horizontal gray lines, indicating the limits of the cellular lipid membrane. The retinal ligand is shown in a space-filling model as the cloud in the middle of the structure. The seven transmembrane (7TM) helices are shown in solid ribbon form. Note that TM-III is rather tilted (see TM-III at the extracellular and intracellular end of the helix) and that kinks are present in several of the other helices, such as TM-V (to the left), TM-VI (in front of the retinal), and TM-VII. In all of these cases, these kinks are due to the presence of a well-conserved proline residue, which creates a weak point in the helical structure. These kinks are believed to be of functional importance in the activation mechanism for 7TM receptors in general. Also note the amphipathic helix-VIII which is located parallel to the membrane at the membrane interface. 

Fig. 1 The w-stack of double helical DNA. In this idealized model of B-DNA the stack of heterocyclic aromatic base pairs is distinctly visible within the sugar-phosphate backbone (schematized by ribbons) a view perpendicular to the helical axis b view down the helical axis. It is the stacking of aromatic DNA bases, approximately 3.4 A apart, that imparts the DNA with its unique ability to mediate charge transport. Base stacking interactions, and DNA charge transport, are exquisitely sensitive to the sequence-depen-dent structure and flexibility of DNA...

Figure 18 Structural model for A0 (1-40) protofilaments, derived by energy minimization with constraints based on solid-state NMR data, (a) Ribbon representation of residues 8-40, viewed down the long axis of the protofilament, (b) Atomic representation of residues 1-40. From Ref. 141.

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