Site-based binding

The operator locus (the presumptive repressor binding site). Bases are numbered +1 for the first base transcribed and — 1 for the base before that. Regions showing dyad symmetry are underlined and overlined. Arrows indicate point mutations leading to the constitutive phenotype (oc). Circled bases are those groups that are strongly... 

When the incubations were performed in the presence of WGA (sufficient lectin was added to provide at least one equivalent of binding sites, based on the amount of sialic acid formed in the control experiments) the product distribution was observed to change dramatically over time (Figure... 

Another equally attractive empirical approach is the design of new metal-binding sites based on protein homology. This approach depends strongly on the degree of sequence or... 

Fig. 5.24. Model of the L-PA binding site based on NMR and chromatographic data and the relation between structure and retention.

Corelli F, Manetti F, Tafi A, Campiani G, Nacci V, Botta M. Diltiazem-like calcium entry blockers A hypothesis of the receptor-binding site based on a comparative molecular field analysis model. J Med Chem 1997 40 125-31. 

If an X-ray structure of a protein is not available, we are thrown back to designing a theoretical binding site based on the structures of the compounds which interact with it. This, of course, introduces the uncertainty of which conformations are adopted by flexible molecules. One cannot assume that the most stable conformation is adopted, since the energy gained from bonding interactions between protein and drug may be... 

Figure 12 Schematic model of Dps binding site based on the X-ray structure of iron-bound Dps from B. brews ...

PCIB can therefore be either due to, a) a disruption of endogenous auxin transport, b) an inhibition of auxin synthesis and or accumulation, and c) competition for auxin-binding sites. Based on data available at present, these alternatives cannot be distinguished. 

A systematic approach is presented below for the structure prediction of an antigen binding site based on the crystallographic data of the HLA-DRl molecule [171]. The approach examines each of the binding sites separately and involves the following steps ... 

Finally, we would like to show two examples where this approximation was used to predict the interaction of molecular oxygen with metallic copper clusters. It has been shown that one can make useful predictions of the binding sites, based on the knowledge of the donor local reactivity of the cluster, by using the condensed Fukui function,. In this way, it was reported that CU3, CU5, and Cus have the highest reactivity toward molecular oxygen. In Fig. 8.5, the results for CU3 (panel a) and for CuJ (panel b) are shown. These results are similar to those reported in Ref. [57]. 

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