Wire model

Figure 2-121. The first brass-wire model of a macromolecule built by Kendrew et al. in 1958 [193],...

A carbon atom with four unfilled va lences (white) appears in the Spartan-Build window as a ball and wire model... 

All five models for ethane show roughly the same information. The Wire model looks like a line formula in your chemistry textbook, except that all atoms, not just earbons, are found at the end of a line or at the intersection of lines. (The only exception occurs where three atoms lie on a line. Here, a Wire model will not show the exact position of the center atom.) The Wire model uses color to distinguish different atoms, and one, two and three lines to indicate single, double and triple bonds, respectively. 

The Ball and Wire model is identical to the Wire model, exeept that atom positions are represented by small spheres. This makes it possible to identify all atom locations in all molecules. The Tube model is identical to the Wire model, except that bonds, whether single, double or triple, are represented by single colored tubes. The tubes are useful because they better eonvey the three-dimensional shape of a molecule. The Ball and Spoke model is a variation on the Ibbe model atom positions are represented by colored spheres, making it possible to see all atom locations in all molecules. 

Atoms are colored according to type (see table at right). Atoms may also be labelled by selecting Labels (labels may be turned off by selecting Labels a second time). Only wire and ball-and-wire models may be labelled. 

Figure 11. Wire model of human body used for walk Doppler signature analysis.

Wire models will make this and other features of the optical indicatrix clearer than plane diagrams can possibly do. 

Figure 2-13 (A) Stereoscopic view of the nucleotide binding domain of glyceraldehyde phosphate dehydrogenase. The enzyme is from Bacillus stearothermophilus but is homologous to the enzyme from animal sources. Residues are numbered 0-148. In this wire model all of the main chain C, O, and N atoms are shown but side chains have been omitted. The large central twisted P sheet, with strands roughly perpendicular to the page, is seen clearly hydrogen bonds are indicated by dashed lines. Helices are visible on both sides of the sheet. The coenzyme NAD+ is bound at the end of the P sheet toward the viewer. Note that the two phosphate groups in the center of the NAD+ are H-bonded to the N terminus of the helix beginning with RIO. From Skarzynski et al.llla (B) Structural formula for NAD+.

Figure 2-17 Wire model of the tailspike protein of bacteriophage P22 of Salmonella. Three of these fishshaped molecules associate as a trimer to form the spike. From Steinbacher et al.123...

Three nearest neighbors, indexed as 0, 6, and 11, are indicated. The axial slab shown represents 1% of the total length of the virion. From Marvin.31a (B) A 2.0 nm section through the virus coat with the helices shown as curved cylinders. The view is down the axis from the N-terminal ends of the rods. The rods extend upward and outward. The rods with indices 0 to -4 start at the same level, forming a five-start helical array. The rods with more negative indices start at lower levels and are therefore further out when they are cut in this section. (C) The same view but with "wire models" of the atomic structure of the rods. From Marvin et al 2... 

Figure 23-31 (A) Stereoscopic ribbon drawing of the photosynthetic reaction center proteins of Rhodopseudomonas viridis. Bound chromophores are drawn as wire models. The H subunit is at the bottom the L and M subunits are in the center. The upper globule is the cytochrome c. The view is toward the flat side of the L, M module with the L subunit toward the observer. (B) Stereo view of only the bound chromophores. The four heme groups Hel-He4, the bacteriochlorophylls (Bchl) and bacteriopheophytins (BPh), the quinones QA and QB/ and iron (Fe) are shown. The four hemes of the cytochrome are not shown in...

The adsorbance of NaBr, Ts, was large and negative. The Donnan exclusion factor rex = rs/rp was in fair agreement with that calculated from the wire model of Devore and Manning119 for the polyelectrolyte in salt solution. 

Wire models and ball-and-stick models are extremely useful because of the great detail they contain. They are particularly useful in connection with blow-ups of selected protein/nucleic acid molecules. 

Fig. 2.1. The backbone structures of authentic and recombinant goat a-lactalbumin in the crystal form. The backbone of Mol A of the authentic protein, represented by a wire model, was superimposed on the backbone of the recombinant protein. Gray and black wires represent the authentic and recombinant proteins, respectively. The C -atom RMSD value between the two proteins was 0.54 A. The PDB codes for the authentic and recombinant proteins are 1HFY and 1HMK, respectively...

FIGURE 11. Stereo diagram of the Qj site structure in chicken bc complex (structure IBCC), viewed parallel to the membrane with the matrix side on die top. The amphipathic helix a, transmembrane helices A, D, and E are shown in bold lines connecting a carbon atoms, while haem bn, ubiquinone (UQ) and selected residues are shown as diin wire models. The hydrogen bonds between ubiquinone and residues His202, Ser206 and Asp229 are drawn as dashed lines. 

The percolation model suggests that it may not be necessary to have a rigid geometry and definite pathway for conduction, as implied by the proton-wire model of membrane transport (Nagle and Mille, 1981). For proton pumps the fluctuating random percolation networks would serve for diffusion of the ion across the water-poor protein surface, to where the active site would apply a vectorial kick. In this view the special nonrandom structure of the active site would be limited in size to a dimension commensurate with that found for active sites of proteins such as enzymes. Control is possible conduction could be switched on or off by the addition or subtraction of a few elements, shifting the fractional occupancy up or down across the percolation threshold. Statistical assemblies of conducting elements need only partially fill a surface or volume to obtain conduction. For a surface the percolation threshold is at half-saturation of the sites. For a three-dimensional pore only one-sixth of the sites need be filled. 

Preparation of this article was supported by research grants (A-4349) and (A-3412) from the National Institutes of Health, United States Public Health Service. One of us (P. H. von Hippel) is indebted to the Public Health Service for a Senior Research Fellowship (SF-360). Thanks are also due Miss S. Himmelfarb and Mrs. M. Backer for help in the final preparation of the manuscript, and to Mr. H. Walton for construction of the wire models of poly-L-proline. 

They treated the system much like a CSTR, with the balance for the gas-phase concentration substituted by the coverage equation for the catalyst. Ray and Hastings then applied the analytical treatment that they had developed for the CSTR in this same publication. Stability analysis revealed that the critical Lewis numbers for oscillations were in a range that did not allow for oscillations on normal nonporous catalytic surfaces. However, as Jensen and Ray 243) showed, a certain model for catalytic surfaces, the fuzzy wire model, with the assumption of a very rough surface with protrusions is able to produce Lewis numbers in the proper range for the occurrence of oscillations. This model, however, included both mass and heat balances as well as coverage equations, thus combining the two classes of reactor-reaction models discussed above. 

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