Richardson diagram

Figure 2.10 Examples of schematic diagrams of the type pioneered by Jane Richardson. Diagram (a) illustrates the structure of myoglobin in the same orientation as the computer-drawn diagrams of Figures 2.9b-d. Diagram (b), which is adapted from J. Richardson, illustrates the structure of the enzyme triosephosphate isomerase, determined to 2.5 A resolution in the laboratory of David Phillips, Oxford University. Such diagrams can easily be obtained from databases of protein structures, such as PDB, SCOP or CATH, available on the World Wide Web.

Figure 14.15 Stmcture of the SI fragment of chicken myosin as a Richardson diagram (a) and a space-filling model (b). The two light chains are shown in magenta and yellow. The heavy chain is colored according to three proteolytic fragments produced by trypsin a 25-kDa N-terminal domain (green) a central 50-kDa fragment (red) divided by a cleft into a 50K upper and a 50K lower domain and a 20-kDa C-terminal domain (blue) that links the myosin head to the coiled-coil tail. The 50-kDa and 20-kDa domains both bind actin, while the 25-kDa domain binds ATP. [(b) Courtesy of 1. Rayment.]...

To illustrate protein conformations in a clear (but extremely simplified) way, Richardson diagrams are often used. In these diagrams, a-helices are symbolized by red cylinders or spirals and strands of pleated sheets by green arrows. Less structured areas of the chain, including the p-turns, are shown as sections of gray tubing. 

Similar Ellingham-Richardson diagrams for the formation of nitrides and sulfides can be constructed and are available in the Uteratme. 

Figure 2.26 Ellingham-Richardson diagram for some common metal oxides. Reprinted, by permission, from D. R. Gaskell, Introduction to the Thermodynamics of Materials, 3rd ed., p. 370. Copyright 1973 by Taylor Francis.

Figure 4 Richardson diagram of various transition metal mononitrides (together with other nitrides) giving the free energy of formation as a function of temperature. (Ref 4. Reproduced by permission of Wiley VCH)...

Fig.1 Plot of Gibbs energy of formation per mole O2 versus temperature, for some important oxides (Ellingham-Richardson diagram). Lines of constant p02, PH2O/PH2, and pCOi/pCO are drawn by connecting the point at 0 K with the mark at the auxiliary scale.

Figure 4. "Richardson diagrams" [29] of five proteins illustrating four classes of tertiary-fold motifs typically found in globular proteins, (a) AU-a hemoglobin, P subunit, (b) AU- Immunoglobulin variable domain, (c) o/p tnose phosphate isomerase. (d) ot/p alcohol dehydrogenase, domain 2. (e) a+ Stai ylococcal nuclease.

In a shorthand method for drawing complex peptide structures, P-strands are shown as thick arrows, an a-helix is a spiral ribbon, and nonrepetitive structures are shown as ropes. These shorthand structures are called ribbon drawings or Richardson diagrams, after Jane S. Richardson (United States 1941-). To illustrate this method, ribonuclease A131 is shown in Figure 27.4, along with the helical ribbon and tube used to represent a helix. The wide arrow used to represent a P-strand in a ribbon structure is also shown. 

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

Figure 4.1 Alpha/beta domains are found in many proteins. They occur in different classes, two of which are shown here (a) a closed barrel exemplified by schematic and topological diagrams of the enzyme trlosephosphate isomerase and (b) an open twisted sheet with helices on both sides, as in the coenzymebinding domain of some dehydrogenases. Both classes are built up from p-a-p motifs that are linked such that the p strands are parallel. Rectangles represent a helices, and arrows represent p strands in the topological diagrams, [(a) Adapted from J. Richardson, (b) Adapted from B. Furugren.j...

Figure 4.19 Schematic and topological diagrams for the structure of the enzyme carboxypeptidase. The central region of the mixed p sheet contains four adjacent parallel p strands (numbers 8, 5, 3, and 4), where the strand order is reversed between strands 5 and 3. The active-site zinc atom (yellow circle) is bound to side chains in the loop regions outside the carboxy ends of these two p strands. The first part of the polypeptide chain is red, followed by green, blue, and brown. (Adapted from J. Richardson.)...

Figure 4.21 The polypeptide chain of the arabinose-binding protein in E. coli contains two open twisted a/P domains of similar structure. A schematic diagram of one of these domains is shown in (a). The two domains are oriented such that the carboxy ends of the parallel P strands face each other on opposite sides of a crevice in which the sugar molecule binds, as illustrated in the topology diagram (b). [(a) Adapted from J. Richardson.)...

Figure 8.21 Richardson-type diagram of the structure of one suhunit of the lac repressor. The polypeptide chain is arranged in four domains, an amino terminal DNA-hinding domain (red) with a helix-tum-helix motif, a hinge helix (purple), a large core domain which has two subdomains (green and hlue) and a C-terminal a helix. (Adapted from M. Lewis et al.. Science 271 1247-1254, 1996.)...

Figure 8.19 F.llingham diagram for the free energy of formation of metallic oxides. (After F. D. Richardson and J. H. F. Jeffes, J. Iron Steel Inst. 160, 261 (1948).) The oxygen dissociation pressure of a given M - MO system at a given temperature is obtained by joining on the lop left hand to the appropriate point on the M-MO frec-energy line, and extrapolating to the scale on the right hand ordinate for POi (atm).

By comparing this simple diagram with the conventional continuous countercurrent decantation circuit, shown in Fig. lb (Coulson and Richardson, 1968, 1978 Treybal, 1955, 1968, 1980) for carrying out the same duty, it is easy to deduce the following characteristics for fluidized leaching and washing ... 

By combining the various observations obtained from the G-T diagrams in different P conditions, we can build up a P-P diagram plotting the stability fields of the various polymorphs, as shown in figure 2.5. The solid dots in figures 2.4 and 2.5 mark the phase transition limits and the triple point, and conform to the experimental results of Richardson et al. (1969) (A, R, B, C ) and Holdaway (1971) (A, H, B, C). The dashed zone defines the uncertainty field in the... 

Richardson-style diagram of the polypeptide backbone of the individual structure of AP-A [46] that is closest to the average over the whole molecule. The locations of the sulfurs in the three disulfide bonds (4-46, 6-36, and 29-47) are shown in CPK format. The locations of reverse turns found in more than half the NMR-derived structures (6-9, 25-28, and 30-33) are indicated by darker backbone shading. 

Fig. 34. Diagram illustrating the arrangement of strands and helices in triose-phosphate isomerase. (B designed by J. Richardson). From the work of Branden and colleagues [72],...

Figure 5. Ribonuclease A (a) schematic diagram (/>) diagram showing heavy atoms with small radii (c) diagram showing all heavy atoms with van der Waals radii. [Part (a) was prepared by J. Richardson (b) and (c) were prepared by A. Briinger from coordinates supplied by G. Petsko.]...

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