Proteins regions, model building

The mechanism of the lysozyme reaction is shown in Figures 16.36 and 16.37. Studies using O-enriched water showed that the Ci—O bond is cleaved on the substrate between the D and E sites. Hydrolysis under these conditions incorporates into the Ci position of the sugar at the D site, not into the oxygen at C4 at the E site (Figure 16.36). Model building studies place the cleaved bond approximately between protein residues Glu and Asp. Glu is in a nonpolar or hydrophobic region of the protein, whereas Asp is located in a much more polar environment. Glu is protonated, but Asp is ionized... 

Figure 3-25 (A) Alpha-carbon plot of the structure of ribosomal protein L30 from E. coli as deduced by NMR spectroscopy and model building. (B) Combined COSY-NOESY diagram for ribosomal protein L30 used for elucidation of dm connectivities (see Fig. 3-27). The upper part of the diagram represents the fingerprint region of a COSY spectrum recorded for the protein dissolved in H20. The sequential assignments of the crosspeaks is indicated. The lower part of the diagram is part of a NOESY spectrum in H20. The dm "walks" are indicated by (->—) S11-A12 (—) H19 to L26 (-------)...

Bradbury and Norton (1975), on the basis of the model building studies by Browne et al. (1969) and by Warme et al. (1974), were able to make assignments of specibc resonances in the proton NMR spectrum of bovine a-lactalbumin to the three His residues. These resonances, after reaction of the protein with iodoacetate under conditions that were nearly specific for the His residues, disappeared from the native frequency positions, but did so in a differential manner, consistent with differences in the degrees of exposure to the solvent. This was predicted by the model building studies, particularly those by Browne et al., which were subsequently confirmed by X-ray analysis. Thus, His-68 is the most exposed His-32, being involved in a helical region (according to Browne et al., but not to Warme et al.), is less exposed, while His-107 is the least exposed. 

Alignment of the MetH sequence between residues 366 and -610 with a methyltetrahydrofolate corrinoid iron-sulfur protein methyltransferase (AcsE) reveals 22% identity and 43% homology between these proteins (6) the same region of MetH is more distantly related to pteroate synthase (6, 31). Structures for pteroate synthase (52, 55) and the recently determined structure of AcsE (6) predict that the folate binding module will be a (Pa)g barrel. Model-building (6)... 

Backbone generation is the first step in building a three-dimensional model of the protein. First, it is necessary to find structurally conserved regions (SCR) in the backbone. Next, place them in space with an orientation and conformation best matching those of the template. Single amino acid exchanges are assumed not to affect the tertiary structure. This often results in having sections of the model compound that are unconnected. 

Figure 7.2 (a) Schematic representation of the structure of B. subtilis ferrochelatase. Domain I is coloured green and domain II blue. The parts of the chain in red build up the walls of the cleft, and the region in yellow makes the connection between the domains. The N- and C-termini are marked, (b) The proposed active site of ferrochelatase with protoporphyrin IX molecule (red) modelled into the site. The backbone atoms of the protein are in purple, the side-chains in blue. Reprinted from Al-Karadaghi et ah, 1997. Copyright (1997), with permission from Elsevier Science. 

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