Active sites calculating number

Figure 8-7. A. Binding energy (AEMP2, circles, and AEel, squares) as a function of inhibitory activity for the model comprising LAP active site residues. Numbers of particular points correspond to inhibitors designation introduced in right panel. B. Structures of LAP inhibitors included into binding energy calculations presented in left panel...

Figure 2-9. Reaction scheme for the complete catalytic cycle in glutathione peroxidase (left). Numbers represent calculated reaction barriers using the active-site model. The detailed potential energy diagram for the first elementary reaction, (E-SeH) + H2O2 - (E-SeOH) + H2O, calculated using both the active-site (dashed line) and ONIOM model (grey line) is shown to the right (Adapted from Prabhakar et al. [28, 65], Reprinted with permission. Copyright 2005, 2006 American Chemical Society.)...

Theoretical calculations have been carried out on a number of zinc-containing enzymatic systems. For example, calculations on the mechanism of the Cu/Zn enzyme show the importance of the full protein environment to get an accurate description of the copper redox process, i.e., including the electronic effects of the zinc ion.989 Transition structures at the active site of carbonic anhydrase have been the subject of ab initio calculations, in particular [ZnOHC02]+, [ZnHC03H20]+, and [Zn(NH3)3HC03]+.990... 

Estimated based on published protein expression (19) and converted to total number of subunit active sites per g of liver tissue. The Michaelis-Menton parameters for ethanol oxidation at pH 7.5 were utilized to calculate individual isozyme activities as a total activity per g of tissue and then normalized as a percent of total activity per pg of tissue following summation of all isozyme activities... 

To complete the calculation we must assume values for Cgi and the total number of molecules migrating over the surface, not related to the number of active sites. For our calculation we assume Cg, = c 2 = 10 molecules cm . Using these values and converting masses to molecular weights, Eq. (39) becomes... 

In the late 1950s it was shown that imidazole catalyzes the hydrolyses of />-nitrophenyl acetate (7, 76) and that histidine was at the active site of a-chymotrypsin (2). These findings led Katchalski ei al. (39) to synthesize a number of histidine-containing polymers for evaluation as catalysts. Second-order rate constants were calculated on the basis of the concentration of neutral imidazole, that is, k2 = (A bs — .)/a[IM], where k , is the rate constant in the absence of catalyst and a is the fraction ionized. Some of these rate constants appear in Table I. All of the polymers possess less than... 

There are at least three possibile ways in which the inhibitor can bind to the active site (1) formation of a sulfide bond to a cysteine residue, with elimination of hydrogen bromide [Eq. (10)], (2) formation of a thiol ester bond with a cysteine residue at the active site [Eq. (11)], and (3) formation of a salt between the carboxyl group of the inhibitor and some basic side chain of the enzyme [Eq. (12)]. To distinguish between these three possibilities, the mass numbers of the enzyme and enzyme-inhibitor complex were measured with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI). The mass number of the native AMDase was observed as 24766, which is in good agreement with the calculated value, 24734. An aqueous solution of a-bromo-phenylacetic acid was added to the enzyme solution, and the mass spectrum of the complex was measured after 10 minutes. The peak is observed at mass number 24967. If the inhibitor and the enzyme bind to form a sulfide with elimination of HBr, the mass number should be 24868, which is smaller by about one... 

The two parameters Pmi and m control the properties of the decay function defined in eq. (7), and thus the reaction dynamics. The reaction events occurring at each site on the surface are recorded by counting the number of visits by the reacting particle and the reaction probability is calculated at each site. It was observed that the number of active sites increases with an increase in Pmi, and the number of reaction events whereas it decreases with an increase in m and the surface roughness. 

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