Backbone models

Figure 18-23 (A) Stereoscopic oc-carbon backbone model of cytochrome P450cam showing the locations of the heme and of the bound camphor molecule. (B) View in the immediate vicinity of the thiolate ligand from Cys 357. From Poulos et al.i9S...

X-ray model of the fish muscle myosin filament shown in Fig. 18C along with the backbone model from Squire (1986) and Chew and Squire (1995). (B) View down the fiber axis of one full myosin 429 A repeat in the fish muscle A-band unit cell, in which two actin filaments have been included. The head perturbations create a local environment of acdn-binding sites (blue) on the myosin heads (yellow) around the actin filaments (green). 

Table 5 Total energies per diacetylene unit in four different PDA backbones (model I to IV as defined in Table 4) obtained with balanced lattice sum truncation using one and sixteen interacting neighbours (N— 1, N= 16), respectively (values from ref 11)...

Table 6 Ionization potentials (IP), electron affinities (EA), and fundamental gaps (A Eg) of four PDA backbones (model I and IV as defined in Table 4) calculated with the correct lattice sum truncation using sixteen interacting neighbours (N= 16, ref. 77). All quantities in eV...

The ionization energies obtained can be reasonably compared with experiment in the following way. From PDA cluster calculations we have learned80 that the valence levels obtained in the STO-3G basis have to be shifted downwards by 1.5 eV to mimic the effect of extension of the atomic basis beyond the minimal level. Applying the same correction to the valence bands obtained in CO calculations, the upper edges of the n-type valence bands for the PTS-backbone (Model II) and for the TCDU-backbone (Model III) will lie at —6.7 and —5.5 eV, respectively, while the corresponding experimental values are — 7.3 1 and — 6.6 1 eV, respectively. 

For more complex structures, it is possible to combine electron cryomicroscopy structures with sequence-based secondary structure predictions to interpret the observed secondary structure elements. In the outer shell protein P8 of rice dwarf virus (RDV), where nine helices were predicted in the domain formed by the N and C termini, it was possible to match the lengths of the helices identified in the 3-D density map to those predicted from a consensus secondary structure analyses (Fig. 13a see Color Insert). The connections between the helical densities can be seen in the lower domain of P8, allowing us to establish a rough backbone model for the lower domain of P8 (Zhou et at, 2001). 

Fig. 39. (A) The ribbon diagram of subunit c and (B) peptide backbone model of a dodecameric ring of c-subunits of E. coli Fq viewd toward the membrane from the F, side. The C-terminal a-heiices are arranged in the inner ring and the N-terminal a-heiices in the peripheral ring. Residue Asp-61 located in the middle of the C-terminal sequence is indicated by a dot. Figure source (A) Fillingame, Girvin and Zhang (1995) Correlations of structure and function in subunit c of Escherichia coli FqF, ATP synthase. Biochem Soc Trans 23 763 (B) Groth and Walker (1997) Model of the c-subunit oligomer in the membrane domain ofF-A TPases. FEBS Lett 410 118.

Scientists have developed powerful techniques for the determination of protein structures, as will be considered in Chapter 3. In most cases, these techniques allow the positions of the thousands of atoms within a protein structure to be determined. The final results from such an experiment include the x, y, and z coordinates for each atom in the structure. These coordinate files are compiled in the Protein Data Rank (http //www. rcsb.org/pdb/) from which they can be readily downloaded. These structures comprise thousands or even tens of thousands of atoms. The complexity of proteins with thousands of atoms presents a challenge for the depiction of their structure. Several different types of representations are used to portray proteins, each with its own strengths and weaknesses. The types that you will see most often in this book are space filling models, bail-and-stick models, backbone models, and ribbon diagrams. Where appropriate, we note structural features of particular importance or relevance in an illustration s legend. 

Because space-filling and ball-and-stick models depict protein structures at the atomic level, the large number of atoms in a complex structure makes it difficult to discern the relevant structural features. Thus, representations that are more schematic—such as backbone models and ribbon diagrams—have been developed for the depiction of macromolecular structures. In these representations, most or all atoms are not shown explicitly. 

Backbone models show only the backbone atoms of a molecule s polypeptide or even only the a-carbon atom of each amino acid. Atoms are linked by lines representing bonds if only a-carbon atoms are depicted, lines connect a-carbon atoms of amino acids that are adjacent in the amino acid sequence (Figure 2.71). In this book, backbone models show only the lines connecting the a-carbon atoms other carbon atoms are not depicted. 

A backbone model shows the overall course of the polypeptide chain much better than a space-filling or ball-and-stick model does. However, secondary structural elements are still difficult to see. 

The above findings and proposals about the location and function of the Rpb4/7 complex were generally confirmed and extended by recent crystallographic backbone models of the complete Pol II that includes the... 

Fig. 10. Stereoview of the 5 -d(GIGGATCICG)2-SJG-136 intrastrand adduct. DNA strands are colored blue, and SJG-136(4) is shown in atom colors. Watson-Grick base pairing has been maintained, and there is minimal distortion to the P-helical structure of the DNA backbone. Models were produced in the SYBYL modeling suite and images produced using UCSF Chimera. [ 1...

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