Protein folding ribbon diagrams

Figure 17.16 Ribbon diagram representations of the structures of domain B1 from protein G (blue) and the dimer of Rop (red). The fold of B1 has been converted to an a-helical protein like Rop by changing 50% of its amino acids sequence. (Adapted from S. Dalai et al.,...

Fig. 3. (A) Ribbon diagram of ribosomal L9 protein from B. stearothermophilus. The N- and C-terminal domains are labelled. The C-terminal construct consisting of residues 58-149 is shaded. (B) Ribbon diagram of the C-terminal domain showing the location of the three histidine residues. Reprinted from J. Mol. Biol., Vol. 318, S. Sato and D. P. Raleigh, pH-dependent stability and folding kinetics of a protein with an unusual alpha-beta topology The C-terminal domain of the ribosomal protein L9 , pp. 571-582, Copyright 2002, with permission from Elsevier Science.

Schematic illustration of the icosahedral rhinovirus 14. (a) Shown is the icosahedron comprised of 60 copies each of VP1 (light gray), VP2 (black), and VP3 (gray). The shaded circles around each five-fold axis indicate the canyon positions. Also indicated is the approximate position of the VP1 hydrophobic pocket that lies underneath the surface of the virion, (b) An icosahedral pentamer is expanded with one viral protomer shown as a protein ribbon diagram, (c) This pentamer is seen in a cutaway view. Here VP1 is white, VP2 and VP4 black, and VP3 gray. A capsid-binding compound is depicted as black spheres inside the VP1 ribbon diagram. The cross hatched regions on the (c) schematic (right) indicate areas that disorder when HRV14 crystals are exposed to acid.

Figure 31-4 Schematic structure of one-fifth of an IgM molecule. From Putnam et al A (A) Covalent structure. (B) Schematic three-dimensional representation. (C) Ribbon diagram of an IgG molecule. From Cochran et al,64a (D) Folding patterns of one chain in a constant and a variable domain of a Bence-Jones protein. From Schiffer et al.66 Green arrows indicate hypervariable regions. (E) MolScript drawing of the common core structure of Ig-like domains. The lighter shaded strands (b, c, e, f) form the core common to all Ig-like domains, which is surrounded by structurally more varied additional strands (darker). The front sheet has up to five strands (a, f, c, e, c") and the back sheet up to four (a, b, e, d). Strand c" is very flexible and is not always a part of the (3 sheet. From Bork, Holm, and Sander.65 See also Fig. 2-16.

Fig. 4. Ribbon diagram (81) of the polypeptide chain fold of the A. vinelandii Fe protein (15). The nucleotide binding sequence at the amino terminus of Fe protein is red. The 4Fe 4S cluster, ADP, and molybdate are represented by atomic models. 

Ribbon diagrams. These diagrams are highly schematic and most commonly used to accent a few dramatic aspects of protein structure, such as the a helix (a coiled ribbon), the P strand (a broad arrow), and loops (simple lines), so as to provide simple and clear views of the folding patterns of proteins. 

Human pancreatic lipase is a protein consisting of 445 amino acids. It folds in two domains with the larger N-terminal containing the catalytic site. The overall folding is represented in a ribbon-diagram in Fig. 17. This crystallographic structure of the human pancreatic lipase represents an inactive form of the enzyme [17]. The active site is totally buried by a loop and... 

Figure 2.48 Three-dimensional structure of myoglobin. (A) A ribbon diagram shows that the protein consists largely of a helices. (B) A space-filling model in the same orientation shows how tightly packed the folded protein is. Notice that the heme group is nestled into a crevice in the compact protein with only an edge exposed. One helix is blue to allow comparison of the two structural depictions. [Drawn from lA6N.pdb.]...

The two protein folds associated with glycosyl transferases (a) GTA and (b) These greyscale ribbon diagrams were kindly provided... 

Figure 16-3 Structure of the protein shell of ferritin (apoferritin). (A) Ribbon drawing of the 163-residue monomer. From Crichton.62 (B) Stereo drawing of a hexamer composed of three dimers. (C) A tetrad of four subunits drawn as a space-filling diagram and viewed down the four-fold axis from the exterior of the molecule. (D) A half molecule composed of 12 subunits inscribed within a truncated rhombic dodecahedron. B-D from Bourne et al.7i...

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