Active sites defined

Native CHS is a homodimer with subunits of 40 to 44kDa. The structure of the protein produced from the CHS2 cDNA of M. sativa has been determined and the residues of the active site defined. It belongs to the polyketide synthase (PKS) group of enzymes that occur in bacteria, fungi, and plants, and is a type III PKS. All the reactions are carried out at a single active site without the need for cofactors. 

Example Yon can monitor improper torsion angles to determine wh ich side of a substrate m olecn le faces the active site of a protein. Select three atoms on the substrate molecule and a fourth in the active site. These atom s define an improper torsion angle. Save th is selection as a named selection. Then observe a plot of this improper torsion angle (in the Molecular Dynam ics Results dialog... 

Nonrepetitive but well-defined structures of this type form many important features of enzyme active sites. In some cases, a particular arrangement of coil structure providing a specific type of functional site recurs in several functionally related proteins. The peptide loop that binds iron-sulfur clusters in both ferredoxin and high potential iron protein is one example. Another is the central loop portion of the E—F hand structure that binds a calcium ion in several calcium-binding proteins, including calmodulin, carp parvalbumin, troponin C, and the intestinal calcium-binding protein. This loop, shown in Figure 6.26, connects two short a-helices. The calcium ion nestles into the pocket formed by this structure. 

Recenl work has defined more carefully ihe nature of active sites. Metal surfaces are thought to contain three main types of sites terraces, ledges (or steps) and kinks, which correspond to one, two. and three coordinatively unsaturated sites of organometallic chemistry. These sites display differing activities toward saturation, isomerization, and CKChiingQ 7 J0,68 JO 1.103,104,105). 

In general, enzymes are proteins and cany charges the perfect assumption for enzyme reactions would be multiple active sites for binding substrates with a strong affinity to hold on to substrate. In an enzyme mechanism, the second substrate molecule can bind to the enzyme as well, which is based on the free sites available in the dimensional structure of the enzyme. Sometimes large amounts of substrate cause the enzyme-catalysed reaction to diminish such a phenomenon is known as inhibition. It is good to concentrate on reaction mechanisms and define how the enzyme reaction may proceed in the presence of two different substrates. The reaction mechanisms with rate constants are defined as ... 

It is not the catalytic activity itself that make zeolites particularly interesting, but the location of the active site within the well-defined geometry of a zeolite. Owing to the geometrical constraints of the zeolite, the selectivity of a chemical reaction can be increased by three mechanisms reactant selectivity, product selectivity, and transition state selectivity. In the case of reactant selectivity, bulky components in the feed do not enter the zeolite and will have no chance to react. When several products are formed within the zeolite, and only some are able to leave the zeolite, or some leave the zeolite more rapidly, we speak about product selectivity. When the geometrical constraints of the active site within the zeolite prohibit the formation of products or transition states leading to certain products, transition state selectivity applies. 

The advantages of microreactors, for example, well-defined control of the gas-liquid distributions, also hold for photocatalytic conversions. Furthermore, the distance between the light source and the catalyst is small, with the catalyst immobilized on the walls of the microchannels. It was demonstrated for the photodegradation of 4-chlorophenol in a microreactor that the reaction was truly kinetically controlled, and performed with high efficiency [32]. The latter was explained by the illuminated area, which exceeds conventional reactor types by a factor of 4-400, depending on the reactor type. Even further reduction of the distance between the light source and the catalytically active site might be possible by the use of electroluminescent materials [19]. The benefits of this concept have still to be proven. 

As an introductory example we take one of the key reactions in cleaning automotive exhaust, the catalytic oxidation of CO on the surface of noble metals such as platinum, palladium and rhodium. To describe the process, we will assume that the metal surface consists of active sites, denoted as We define them properly later on. The catalytic reaction cycle begins with the adsorption of CO and O2 on the surface of platinum, whereby the O2 molecule dissociates into two O atoms (X indicates that the atom or molecule is adsorbed on the surface, i.e. bound to the site ) ... 

Before deriving the rate equations, we first need to think about the dimensions of the rates. As heterogeneous catalysis involves reactants and products in the three-dimensional space of gases or liquids, but with intermediates on a two-dimensional surface we cannot simply use concentrations as in the case of uncatalyzed reactions. Our choice throughout this book will be to express the macroscopic rate of a catalytic reaction in moles per unit of time. In addition, we will use the microscopic concept of turnover frequency, defined as the number of molecules converted per active site and per unit of time. The macroscopic rate can be seen as a characteristic activity per weight or per volume unit of catalyst in all its complexity with regard to shape, composition, etc., whereas the turnover frequency is a measure of the intrinsic activity of a catalytic site. 

Zeolites are used in various applications such as household detergents, desiccants and as catalysts. In the mid-1960s, Rabo and coworkers at Union Carbide and Plank and coworkers at Mobil demonstrated that faujasitic zeolites were very interesting solid acid catalysts. Since then, a wealth of zeolite-catalyzed reactions of hydrocarbons has been discovered. Eor fundamental catalysis they offer the advantage that the crystal structure is known, and that the catalytically active sites are thus well defined. The fact that zeolites posses well-defined pore systems in which the catalytically active sites are embedded in a defined way gives them some similarity to enzymes. 

The crystal structure of the HNL isolated from S. bicolor (SbHNL) was determined in a complex with the inhibitor benzoic acid." The folding pattern of SbHNL is similar to that of wheat serine carboxypeptidase (CP-WII)" and alcohol dehydrogenase." A unique two-amino acid deletion in SbHNL, however, is forcing the putative active site residues away from the hydrolase binding site toward a small hydrophobic cleft, thereby defining a completely different active site architecture where the triad of a carboxypeptidase is missing. 

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