Hydrophobic binding pocket

Figure 17.3 Anatomy of a redox enzyme representation of the X-ray crystallographic structure of Trametes versicolor laccase III (PDB file IKYA) [Bertrand et al., 2002]. The protein is represented in green lines and the Cu atoms are shown as gold spheres. Sugar moieties attached to the surface of the protein are shown in red. A molecule of 2,5-xyhdine that co-crystallized with the protein (shown in stick form in elemental colors) is thought to occupy the broad-specificity hydrophobic binding pocket where organic substrates ate oxidized by the enzyme. Electrons from substrate oxidation are passed to the mononuclear blue Cu center and then to the trinuclear Cu active site where O2 is reduced to H2O. (See color insert.)...

It has already been mentioned that metal complexes with confined binding pockets often display unusual chemical reactivities (see Section II). Thus, complexes of substituted hydrotris (pyrazolyl)borates, in which the substituents serve to from a hydrophobic binding pocket, have already been shown to exhibit enhanced chemical reactivity when compared with their unmodified analogs (282,283). Likewise, cyclodextrin and calixarene-based metallocavitands have been used as catalysts for selective organic transformations, and even as catalysts for reactions that... 

Clearly, the strength of hydrogen bonds depends on the reaction medium. In practice, the nonpolar solvent toluene is routinely used. It can be considered to mimic a hydrophobic binding pocket of an enzyme and clearly supports the formation of moderate (1.5-2.2A) and even strong (1.2-1.5 A) hydrogen bonds [42]. 

Finally, three groups have reported the preparation of artificial enzymes with catalytic activity. Stewart and co-workers [73] incorporated a catalytic triad from the serine proteases into a designed four a-helix protein (80). In their design, they incorporated one of the amino acids involved in the catalytic function at the N-terminal side of the a-helices that are linked together by their C-terminal position (Fig. 29). The authors proposed that the oxyanion hole and the hydrophobic binding pocket are created by the three-dimensional structure formed by the folding of 80. Compared to the spontaneous reaction, impressive... 

The modified GK domain of the P subunit forms a hydrophobic binding pocket with which the AID of the a, subunit interacts. Surprisingly, at least in the conformation that was crystallized, the BID region is found buried within the P subunit protein. It is therefore unlikely to be involved directly in such protein-protein interactions as binding to the AID. However, as Chen et al. (2004) have discussed, the BID still appears to play an essen-... 

Hydrophobic binding pocket protectors (phenols, anilines) 10... 

Fig. 9 The hydrophobic binding pocket for T -Taxol on beta tubulin. Color on the surface model ranges from most lipophilic (brown) to most hydrophilic (blue). The ribbon view of beta tubulin is colored by secondary structure with red - alpha helices and blue - beta sheets...

Figure 19.1 Hydrophobic binding pockets in mesoporous materials. This biomimetic approach takes advantage from both the extraction of the guest from water by finely tuned polarity and size, and the selective reaction of the guest with the binding site.

Comparison of 34E4 with a less proficient catalyst shows that merely positioning a carboxylate in a hydrophobic binding pocket does not result in efficient general base catalysis. Antibody 4B2, generated against cationic amidinium salt 14 (Scheme 4.5),... 

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