Tunnels, hydrophobic

The cyclooxygenase active site lies at the end of a long, narrow, hydrophobic tunnel or channel. Three of the u-helices of the membrane-binding domain lie at the entrance to this tunnel. The... 

Structural information about the oxygenases provided limited insight into the mechanism (Schmidt et al. 2006). The crystallized enzyme from Synechocystis sp. PCC6803 is membrane associated and the interaction with the membrane is believed to be mediated by a nonpolar patch on the surface of the enzyme. This hydrophobic patch is thought to provide the necessary access of the protein to the membrane-bound carotenoids. Following withdrawal from the membrane, the substrate moves through the hydrophobic tunnel toward the metal center. The substrate orients the... 

Fig. 12.15 Approach of amine molecules on the holes of Ti02 through the hydrophobic tunnels made by -O-n-Bu chains.

A fascinating self-assembly process is based on the spontaneous threading of cyclodextrins or crown ethers onto polyether polyamine" or polyurethane chains (Figure 5.30). The formed polyrotaxanes possess several cyclodextrin units which are trapped after appropriate capping of the ends. Polymerization of the threaded cyclodextrins and removal of the central thread then leads to molecular cyclodextrane tubules with an inner hydrophobic tunnel and a diameter of about 5 A. 

Figure 5 Diagram illustrating the hydrophobic tunnel and catalysis at the a and /3 active sites.

The salient features of this model involve the binding of the /3 subunit ligand serine and its activation through a PLP-dependent reaction to form a reactive enzyme-bound aminoacrylate (PLP AA) species that in turn triggers a conformational change that promotes the cleavage of IGP to indole at the a subunit. When a molecule of indole is formed it diffuses rapidly through the hydrophobic tunnel to the (3 subunit and reacts with the PLP AA, also very rapidly, to form the product tryptophan. This intersubunit communication keeps the a and /3 reactions in phase such that the intermediate indole does not accumulate. 

Mechanistic Implications. The native Zn(II)-substituted enzyme has been shown to undergo a conformational change from an open structure, where the active site clefts are solvent accessible, to a closed structure on formation of ternary complexes where the substrate binding cleft becomes a narrow hydrophobic tunnel from which solvent is excluded.The d d transitions of the Co(II)-substituted enzyme are sensitive both to the change from an open to a closed conformation and to the electronic properties of inner sphere coordinated ligands. It is likely that in the enzyme-NAD" complexes, the ionization of the coordinated ligand (water, benzyl alcohol, or trifluoroethanol) is accompanied by a change in protein conformation from the open conformation to the closed conformation. ... 

Tryptophan synthase (TS) catalyzes the conversion of IGP and serine to tryptophan. The well-characterized bacterial TS enzyme consists of a- and P-subunits that join to form two active sites with a hydrophobic tunnel between them. TS is an a P heterotetramer linked via the P-subunits. The individual subunits catalyze two independent reactions IGP is converted by the a-subunit to indole and glyceraldehyd-3-phosphate, and indole and serine are converted by the p-subunit to tryptophan and H2O. It has been shown for bacterial enzymes that the activity of the isolated subunits is very low in comparison to their activity in the intact TS complex (Table 4.1). Indole is not released from the TS complex but rather travels through the tunnel connecting the active sites of a and P (Fig. 4.2). There is evidence that plant TS, like the bacterial complex, functions as a P heteromers. " The a and P subunits are encoded by independent genes (7X4 and TSB) and the interaction of a and P was inferred from complementation experiments. 

Fig.1 Structure of [NiFe]-hydrogenase. A Polypeptide fold. The arrow indicates a hydrophobic tunnel network, shown in dark grey. Spheres highlight metal and inorganic sulfur sites three FeS clusters in the small subunit and a Mg-site as well as the Ni - Fe active site in the large subunit. B Zoomed depiction of the active site, shown as a ball-and-stick model. Dashed lines indicate putative H-bonds. Exogenous ligand binding sites are labeled El and E2...

Putative pathways have been characterized in C. hydrogenoformans CODH for the respective transit of CO/CO2 and the H2O product through hydrophobic and hydrophiUc tunnels, respectively [87]. The bi-functional CODH/ACS from M. thermoacetica contains several hydrophobic tunnels that connect the two CODH C-cluster active sites to each other and to the ACS active site named the A-cluster [90]. High-pressure, xenon-binding experiments carried out in a CODH/ACS crystal have shown that these tunnels can trap many xenon atoms [91]. In addition, putative proton transfer pathways connecting... 

Fig. 3 Structure of the carbon monoxide dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) hetero-tetramer. A Polypeptide fold of the CODH dimer (center) and of ACS in the closed (left) and open subunit conformation (right). Metal sites and inorganic sul-furs are shown as spheres an extensive hydrophobic tunnel network is highlighted in dark grey. B Zoomed depiction of the CODH active site. Dashed lines indicate putative H-bonds...

Three crystal structures of ACS have been reported, two of CODH/ACS from M. thermoacetica [90,91] and one of the monomeric ACS from C. hydrogeno-formans [104]. ACS consists of three globular domains with the catalytic A-cluster bound to domain 3 at its interface with domain 1. As mentioned above, CODH/ACS has a hydrophobic tunnel network that allows CO, the product of Eq. 2 catalyzed by the C-cluster, to diffuse to the A-cluster where it combines with the methyl group donated by CFeSP to form an acetyl group that, in turn, binds to coenzyme A (Eq. 4). The presence of a tunnel connecting the two active sites was predicted before the structure was determined because, under normal turnover conditions, no CO was detected in the reaction medium [9,10]. 

Several attempts were also made to increase the substrate scope of (S)-selective HNLs. The active sites of HfcHNL from R brasiliensis and MeHNL from M. esculenta are accessible via a narrow hydrophobic tunnel harboring a tryptophan residue (W128), which hampers the passage of large substrates. Replacement of W128 by smaller residues led to improved conversions of sterically hindered substrates [154] like the industrially interesting 3-phenoxybenzaldehyde, whose (S)-cyanohydrin is a pyrethroid precursor (Scheme 25.7). 

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