Cytochrome enzyme cavity

The Pathfinder approach was used to compare the CYP cavities of CYP2C9 [8], 2D6 [9], and 3A4 [10], the most important human cytochrome enzymes. CYP2C9 and 3A4 were available as protein crystal structures whilst an homology model was used for 2D6. Frequency distribution plots (Fig. 5.8) were obtained from non-superposed CYP structures, selecting the iron in the heme moiety as a root departure path. 

Enzymes are known for their exquisite shape selectivity and regio- and stereoselectivity with respect to their substrates [16,17], For example, different versions of the cytochrome P-450 enzyme family catalyze the hydroxylation of substrates as diverse as P-naphthylamine and vitamin D [18,19], The specificity of the P-450 enzymes derives from the shape of the substrate-binding cavity, which is contiguous with the active site. (Unfortunately, in heterogeneous catalysis, substrate is often the term used to describe the stratum or support upon which the catalyst is mounted. The analog of the enzymatic substrate in heterogeneous catalysis is called the feed or reactant.)... 

It has been suggested [95] that the synthesis of structured porphyrins with controllable steric ambience is a strategic direction in the reproduction of enzyme protein cavities, which control the selectivity and stability of biochemical reactions such as cytochrome P-450. Such an approach to the synthesis of biomimics has considerable potential, especially in their application on mineral matrices silicon dioxide, alumina and zeolites. Data exist on the synthesis of a biomimic [96] with a complex porphyrin complex (5-pentafluorophenyl-10,15,20-tri(2,6-dichlorophenyl)porphyrin (FeMPFDCPP)) covalently linked to aminopropyl silicon dioxide, which is applied in oxidation of ds-cyclooctene, cyclohexene, cyclohexane and adamantane with participation of iodosylbenzene dissolved in dichloromethane. 

The rate and the site of metabolism for xenobiotics are due to a complex mixture of recognition, shape and chemical reactivity. The human cytochrome P450 shape in proximity to the reactive heme plays a fundamental role in molecular recognition and orientation. Thus, the CYP cavity shape modulates the likelihood of a compound reacting with the enzyme, since it has to enter into the cavity, reach the reactive site (the heme), adopt a stable orientation to allow the reaction to occur and subsequently exit from the cavity. Different cytochromes show different cavity shape, and in silico prediction cannot neglect their key role. 

With the enzyme sidechains in fixed positions, the active site volumes computed by the GRID hydrogen probe ranged from 1500 for CYP3A4 to 640 for CYP1A2. With flexible sidechains, the accessible cavity volumes increased from 5% to 10%, probably due to the release of steric hindrance and consequent reduction in steric interaction between the chemical probe and the lateral chains. The explanation put forward is that the cytochromes may use sidechain flexibility to allocate more space when necessary, making sub-pockets or small charmels accessible without changing the structure of the protein backbone. 

When healthy volunteers were exposed by inhalation to 100 or 400 ppm tetrahydrofuran in air, the percentage of expired tetrahydrofuran was 25-35%. The elimination half-life of tetrahydrofuran was 30 min in individuals exposed to 200 ppm for 3h. Some tetrahydrofuran is absorbed in the nasal cavity due to its solubility and inspiratory flow rate. Tetrahydrofuran uptake in the nasal tissue is dependent on its reaction with tissue substrates. Some tetrahydrofuran can be metabolized in the nasal cavity. Tetrahydrofuran blood concentrations were higher at 1 h postexposure than immediately after cessation of exposure. In vitro studies indicated that tetrahydrofuran was first hydroxylated by microsomal enzymes. High concentrations (lO molH ) of tetrahydrofuran inhibited the in vitro activity of rat hepatic cytochrome P450 by 80%. Tetrahydrofuran has been noted to enhance the toxic action of a number of compounds and stimulate the rapid absorption of reactive metabolites. Some of the tetrahydrofuran is excreted in the exhaled breath, while the various metabolites of tetrahydrofuran are excreted in the urine. 

Transition metal complexes of phthalocyanine encaged in faujasite type zeolites have been reported as efficient catalysts in the oxidation of alkanes at room temperature and atmospheric pressure [6-13]. These catalysts constitute potential inorganic mimics of remarkable enzymes such as monooxygenase cytochrome P-450 which displays the ultimate in substrate selectivity. In these enzymes the active site is the metal ion and the protein orientates the incoming substrate relative to the active metal center. Zeolites can be used as host lattices of metal complexes [14, 15]. The cavities of the aluminosilicate framework can replace the protein terciary structure of natural enzymes, thus sieving and orientating the substrate in its approach to the active site. Such catalysts are constructed by the so-called ship in a bottle synthesis the metal phthalocyanine complexes are synthesized in situ within the supercages of the zeolite... 

Abresch et aL, 1998] and of the lumen-side domain of cytochrome/[Martinez et al., 1996]. Finally, in cytochrome c oxidase, two independent theoretical studies have predicted the hydration of buried cavities implicated in the uptake of protons [Riistama et al, 1997 Hofacker and Schulten, 1998]. Although these water molecules were not resolved in published crystallographic structures of the P. denitrificans [Iwata et al, 1995] and bovine heart [Tsukihara et al, 1996] enzymes, many of them are well-defined in a new structure of the Rb, sphaeroides enzyme [M. Svensson-Ek, personal communication]. Understanding the molecular properties giving rise to proton transport in hydrogen-bonded networks containing water molecules is therefore an important step towards the elucidation of proton-pumping mechanisms. 

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