Backbone representation

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

Fig. 2. Protein backbone representations of (a) the 2[4Fe-4S] ferredoxin from Peptococcus aerogenes, (b) the proposed structure of the FA/FB-binding protein of PSl based on the 4 A crystsd structure (25), and (c) the [3Fe-4S][4Fe-4S] ferredoxin from Sulfolo-bus acidocaldarius. Ligands to clusters Fa and Fb, important residues as well as the loop extension (see text) EU e highlighted in darker gray.

A step closer toward realism is taken by off-lattice models in which the backbone is specified in some detail, while side chains, if they are represented at all, are taken to be single, unified spheres [44-50]. One indication that this approach is too simplistic was given in [51], which proved that for a backbone representation in which only Ca carbons were modeled, no contact potential could stabilize the native conformation of a single protein against its nonnative ( decoy ) conformations. However, Irback and co-workers were able to fold real protein sequences, albeit short ones, using a detailed backbone representation, with coarse-grained side chains modeled as spheres [49, 52-54]. 

Fig. 5.6 Superposition of the backbone representation of the 20 lowest energy DYANA structures of NPY/DPC.

A ribbon backbone representation of the three-dimensional structure of turkey-skeletal-muscle troponin C according to Herzberg and James. The crystals were grown at pH 5 in the presence of excess Ca , and at this low pH only Ca ions bound to the high-affinity domain (the C-terminal domain) are observed. Note the high stmctural homology with calmodulin (Figure 3.17). 

Fig. 5. Backbone representation of the subunits L (upper left), M (upper right) and H (lower). The M-subunit has been superimposed on the L-subunit to emphasize the high degree of identity of these polypeptides, (ect helical segment between E and the C-terminal.)...

Figure 1.9. Observation of the waters of Thales of the Fj-motor of ATP synthase. The crystal structure of the Fi-motor of ATP synthase is shown in cross-eye stereo view from the top axis having all sites filled with ATP and with the rotor given by the fine lines of a backbone representation. A A spacefilling model of (aP)3 shows detected surface waters.

Figure 8.17. Stereo view of the components of the homodimer of yeast cytochrome bci —one molecule of cytochrome b in space-filling representation, one molecule of cytochrome Ci in space-filling representation, and both of the FeS-containing Reiske Iron Proteins present are shown with one in gray backbone representation and the other in space-filling representation. As usual for the space-filling representations, neutral residues are in light gray, hydrophobic residues in gray, aromatic residues in...

Figure 8.19. Stereo views of monomers of Complex III cytochrome bci complex of chicken with (A) and without (B) inhibitors. Protein in backbone representation with neutral residues in light gray, hydrophobics in gray, aromatics in black, and charged residues in white. (A) The tether is extended when the FeS is at Q site. (Prepared using the crystallographic results of Zhang et al. as obtained from...

The expected mechanics for relocation of the FeS center within the globular domain of the RIP come from the yeast Complex III depicted in Figure 8.17. One of the two RIP subunits occurs in backbone representation such that it is possible to see through to the underlying Qo site for hydrophobic association. Immediately below the extended tether resides a raised side chain of residue F169. The bulky F169 side chain is positioned to function as a fulcrum that... 

Figure 8.24. Rhodobacter sphaeroides Complex IV cytochrome c oxidase. Stereo view in backbone representation of subunits I and II showing the greater permeation of water through the region of the lipid layer of Complex IV than for that of Complex III in Figure 8.20. (A) Heme redox centers at the heart of...

Figure 8.52. The same perspective for the stereo view (cross-eye) of scallop cross-bridge (SI) as shown in Figure 8.51, except that it is in backbone representation and thereby allows better delineation of domain movements. In A the amino-terminal domain is shown as a flap over the head of the lever arm in the near-rigor state, whereas it separates as a free-standing pedicle in B, the ATP state. The amino-terminal domain movement also becomes apparent by the changing G53 location at its leading edge.

Figure 1 Atomic stracture of a (a) double-helical (Imic.pdb ) and (b) head-to-head (Imag.pdb ) conformation of Gramicidin A. The pictures to the left show the backbone representation perpendicular to the pore. The pictures to the right show a view parallel to the channel that includes the hydrophobic sidechains. The pictures were generated with VMD. ...

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