Binding site orientation

Information Ligand conformation Pharmocophore model Bound ligand conformation Binding site/ orientation 3D structures Dynamics... 

The generation of molecular imprints at surfaces is an obvious solution to the problems of mass transfer and accessibility, and potentially affords control over more subtle parameters such as binding site orientation and local solvation state. While a standard general protocol does not as yet exist for surface imprinting, a number of strategies that create the required recognition cavities at a surface or interface have now been developed and selected examples of these are considered in this chapter. 

A primordial catalytic function could develop in a protein, perhaps by the chance juxtaposition of serine and histidine (imidazole) moieties. Improvements in the spatial arrangement can be made by random mutations of amino acids removed from the catalytic site. Similarly, improvements in binding-site orientation with respect to proximity of the substrate molecules to one another and to enzyme functional groups could occur by small degrees, which would then be fixed by selection. Thus, orientation and proximity, the crucial factors for binding interaction and entropic effects, are ideally suited for evolutionary optimization. 

Fig. IB shows that in all preparations an excess RC s exists having their cytochrome binding site oriented towards the exterior of the vesicles, particularly in vesicles prepared from LDAO-depleted RC s. However, a complete unidirectional orientation is not obtained under these conditions (contrast Pachence et al., 1979). This becomes more evident when one realizes that at the two lowest lipid/RC ratio s the amount of RC s that are not incorporated into a bilayer, increases significantly. Under these conditions maximally a ratio of 70 to 30 of RC s with opposite orientation occurs. A higher net-orientation can be obtained by lowering the salt concentration.

A unique feature of the interaction of the hormone and PLR is at the beginning of the F-G loop in the C-terminal domain. In HGR the sequence is Arg-Asn-Ser whereas in PLR it is Asp-His-deletion. This loop interacts with His 18 and Glu 174 of the hormone. In PLR the orientation of this loop is such that the Asp and His residues, in combination with His and Glu from the hormone, form a strong binding site for a zinc atom that links the hormone and the receptor (Figure 13.23b). The presence of zinc increases the affinity of the hormone for the receptor in vitro by a factor of 10,000. As shown by mutagenesis studies His 18 and Glu 174 of the hormone are important for the tight binding to PRL but not to GHR. 

The variable domains associate in a strikingly different manner. It is obvious from Figure 15.11 that if they were associated in the same way as the constant domains, via the four-stranded p sheets, the CDR loops, which are linked mainly to the five-stranded p sheet, would be too far apart on the outside of each domain to contribute jointly to the antigen-binding site. Thus in the variable domains the five-stranded p sheets form the domain-domain interaction area (Figure 15.11). Furthermore, the relative orientation of the p strands in the two domains is closer to parallel than in the constant domains and the curvature of the five-stranded p sheets is such that they do not pack... 

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