20S active sites

Another noteworthy difference between core- and periphery-functionalized dendrimers is that much higher costs are involved in the application of core-functionalized dendrimers due to their higher molecular weight per catalytic site. Furthermore, applications may be limited by the solubility of the dendrimer. (To dissolve 1 mmol of catalyst/L, 20 g/L of core-functionalized dendrimer is required (MW 20 000 Da, 1 active site) compared to 1 g/L of periphery-functionalized dendrimer (MW 20 000 Da, 20 active sites). On the other hand, for core-functionalized systems, the solubility of the dendritic catalyst can be optimized by changing the peripheral groups. 

Figure 6.20 Active sites of phosphatases with a dimetallic diamond core.

The protonated oxazolidines are comparatively strong acids (2-methyl-A -oxazoline has a pifa of 5.5, which the electron-withdrawing substituents in the sugar will lower), and in GH and GH 20 active site aspartates... 

Figure 6.20 Active site electron density for (A) native and (B) H143M rusticyanin. 2006 American Chemical Society.

Active site (Section 27 20) The region of an enzyme at which the substrate is bound... 

Metallocene (Section 14 14) A transition metal complex that bears a cyclopentadienyl ligand Metalloenzyme (Section 27 20) An enzyme in which a metal ion at the active site contributes in a chemically significant way to the catalytic activity... 

Figure 4.20 Detailed view of the zinc environment in carboxy-peptidase. The active-site zinc atom is bound to His 69 and Glu 72, which are part of the loop region outside P strand 2. In addition, His 196, which is the last residue of P strand 5, also binds the zinc.

The a/p-barrel structure is one of the largest and most regular of all domain structures, comprising about 250 amino acids. It has so far been found in more than 20 different proteins, with completely different amino acid sequences and different functions. They are all enzymes that are modeled on this common scaffold of eight parallel p strands surrounded by eight a helices. They all have their active sites in very similar positions, at the bottom of a funnel-shaped pocket created by the loops that connect the carboxy end of the p strands with the amino end of the a helices. The specific enzymatic activity is, in each case, determined by the lengths and amino acid sequences of these loop regions which do not contribute to the stability of the fold. 

Figure 6.20 Space-filling diagram illustrating the structural changes of CDK2 upon cyclin binding, (a) The active site is in a cleft between the N-terminal domain (blue) and the C-terminal domain (purple). In the inactive form this site is blocked by the T-loop.

X-ray structures are determined at different levels of resolution. At low resolution only the shape of the molecule is obtained, whereas at high resolution most atomic positions can be determined to a high degree of accuracy. At medium resolution the fold of the polypeptide chain is usually correctly revealed as well as the approximate positions of the side chains, including those at the active site. The quality of the final three-dimensional model of the protein depends on the resolution of the x-ray data and on the degree of refinement. In a highly refined structure, with an R value less than 0.20 at a resolution around 2.0 A, the estimated errors in atomic positions are around 0.1 A to 0.2 A, provided the amino acid sequence is known. 

Baird is the 20-acre site of a former chemical mixing and batching company. Poor waste disposal practices resulted in the contamination of groundwater, soil, the municipal water supply, and a brook adjacent to the site. Over one hundred contaminants, including chlorinated and nonchlorinated volatile organics, heavy metals, pesticides, herbicides, and dioxins, had been identified in site soil and groundwater. Remediation activities included soil excavation and incineration, and groundwater treatment (the audit focused on the soil excavation and incineration... 

Citrate synthase in mammals is a dimer of 49-kD subunits (Table 20.1). On each subunit, oxaloacetate and acetyl-CoA bind to the active site, which lies in a cleft between two domains and is surrounded mainly by a-helical segments (Figure 20.6). Binding of oxaloacetate induces a conformational change that facilitates the binding of acetyl-CoA and closes the active site, so that the reactive carbanion of acetyl-CoA is protected from protonation by water. 

FIGURE 20.7 (a) The aconitase reaction converts citrate to cis-aconitate and then to isocitrate. Aconitase is stereospecific and removes the pro-/ hydrogen from the pro-/ arm of citrate, (b) The active site of aconitase. The iron-sulfur cluster (red) is coordinated by cysteines (yellow) and isocitrate (white). 

FIGURE 20.10 (a) The isocitrate dehydrogenase reaction, (b) The active site of isocitrate dehydrogenase. Isocitrate is shown in green, NADP is shown in gold, with Ca" in red. 

The mechanism of succinyl-CoA synthetase is postulated to involve displacement of CoA by phosphate, forming succinyl phosphate at the active site, followed by transfer of the phosphoryl group to an active-site histidine (making a phosphohistidine intermediate) and release of succinate. The phosphoryl moiety is then transferred to GDP to form GTP (Figure 20.13). This sequence of steps preserves the energy of the thioester bond of succinyl-CoA in a series of high-energy intermediates that lead to a molecule of ATP ... 

Rubisco exists in three forms an inactive form designated E a carbamylated, but inactive, form designated EC and an active form, ECM, which is carbamylated and has Mg at its active sites as well. Carbamylation of rubisco takes place by addition of COg to its Lys ° e-NHg groups (to give e—NH—COO derivatives). The COg molecules used to carbamylate Lys residues do not become substrates. The carbamylation reaction is promoted by slightly alkaline pH (pH 8). Carbamylation of rubisco completes the formation of a binding site for the Mg that participates in the catalytic reaction. Once Mg binds to EC, rubisco achieves its active CM form. Activated rubisco displays a Ai, for CO2 of 10 to 20... 

Substrate RuBP binds much more tightly to the inactive E form of rubisco (An = 20 nM) than to the active ECM form (A, for RuBP = 20 ixM). Thus, RuBP is also a potent inhibitor of rubisco activity. Release of RuBP from the active site of rubisco is mediated by rubisco activase. Rubisco activase is a regulatory protein it binds to A-form rubisco and, in an ATP-dependent reaction, promotes the release of RuBP. Rubisco then becomes activated by carbamylation and Mg binding. Rubisco activase itself is activated in an indirect manner by light. Thus, light is the ultimate activator of rubisco. 

Equations (3.16) and (3.17) describe the dissociative adsorption and, recombination of oxygen on a donor D. The transfer between the donor D and acceptor A is described by eq. (3.18). The spillover oxygen (O) is a mobile species which is present on the acceptor surface without being associated with a particular surface site. The mobile spillover species can interact with a particular surface site B forming an active site C (eq. 3.19). Eq. (3.20) represents the deactivation of the active site C by interaction with a reactant E. 

Equation (1.20) is frequently used to correlate data from complex reactions. Complex reactions can give rise to rate expressions that have the form of Equation (1.20), but with fractional or even negative exponents. Complex reactions with observed orders of 1/2 or 3/2 can be explained theoretically based on mechanisms discussed in Chapter 2. Negative orders arise when a compound retards a reaction—say, by competing for active sites in a heterogeneously catalyzed reaction—or when the reaction is reversible. Observed reaction orders above 3 are occasionally reported. An example is the reaction of styrene with nitric acid, where an overall order of 4 has been observed. The likely explanation is that the acid serves both as a catalyst and as a reactant. The reaction is far from elementary. 

Concerning the role of the active site Fe ion, it has been argued that the observed FTIR band shifts (typically 20 cm ) resulting from one-electron redox changes are too small to correspond to metal-based redox processes, whose band shifts should amount to about 100 cm per electron (90, 101). There is, however, one example where the shift in f(CN ) upon one-electron reduction of a Fe(III) center is only of... 

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