Cavity, binding

Figure 15.14 Schematic representation of the specific interactions between phosphoryicholine (orange) and the protein side groups (green) in Fab. The binding cavity is in a cleft between the light and the heavy chains. Choiine binds in the interior while the phosphate group is toward the surface. (Adapted from E.A. Padlan et al., Immunochemistry 13 945-949, 1976.)...

The above two models together with Tabushi s cyclodextrin bis(histamine)23) are really elabolate ones, each having a substrate binding cavity, but their catalytic activities are yet far behind of those of natural enzymes. They suggest the difficulties associated with the design of a metal ion center inside of a cavity which activates both substrate and catalytic groups. 

Several model systems related to metalloenzymes such as carboxypeptidase and carbonic anhydrase have been reviewed. Breslow contributed a great deal to this field. He showed how to design precise geometries of bis- or trisimidazole derivatives as in natural enzymes. He was able to synthesize a modified cyclodextrin having both a catalytic metal ion moiety and a substrate binding cavity (26). Murakami prepared a novel macrocyclic bisimidazole compound which has also a substrate binding cavity and imidazole ligands for metal ion complexation. Yet the catalytic activities of these model systems are by no means enzymic. 

PI. 3.1 A MUP peptide backbone ribbon representation, shown in two orthogonal projections (left p-sheet framework right binding-cavity, highlighted) (from Luckc et at., 1999). 

Scheme 13. Directing and protecting effect of the binding cavity.

This and the fact that the Diels-Alder adducts 103a,b do not isomerize in the binding pocket of the complexes can be attributed to the directing and protecting effect of the binding cavity as schematically represented in Scheme 13. 

The development, synthesis, and the coordination chemistry of novel metal complexes with deep binding cavities have been described. It was demonstrated that the doubly deprotona-ted forms of the macrocycles (LR)2 support the formation of... 

In this article, all species with a binding cavity (open or closed) are referred to as container molecules. 

Members of the different SERM families bind to the ligand-binding domain (LBD) of the ER, whose particular crystal structure has been revealed for estradiol and for raloxifene (Brzozowski et al. 1997). Once inserted into the binding cavity, estradiol makes direct hydrogen bonds bewteen its A-ring and... 

The information of Tables 4.3 and 4.4 indicates that a water molecule is found in the binding cavity of a chains of hemoglobin A (HbA) even though this cavity has been called hydrophobic. Indeed, although many hydrophobic groups such as... 

Identification of energetically favorable sites for water molecules and molecular fragments within the binding cavity, facilitating the design of novel ligands... 

Because of this photoisomerisation, structural changes occur within the confines of the binding cavity, which in turn produce changes in the opsin and the attached cell-membrane protein. This results in functional changes to the cell membrane, culminating in generation of a signal impulse which is sent to the brain. 

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