Active sites definition

H atom addition, protonation state, active site definition, His tautomers, structural water, pharmacophore definition etc. 

Definitive identification of lysine as the modified active-site residue has come from radioisotope-labeling studies. NaBH4 reduction of the aldolase Schiff base intermediate formed from C-labeled dihydroxyacetone-P yields an enzyme covalently labeled with C. Acid hydrolysis of the inactivated enzyme liberates a novel C-labeled amino acid, N -dihydroxypropyl-L-lysine. This is the product anticipated from reduction of the Schiff base formed between a lysine residue and the C-labeled dihydroxy-acetone-P. (The phosphate group is lost during acid hydrolysis of the inactivated enzyme.) The use of C labeling in a case such as this facilitates the separation and identification of the telltale amino acid. 

A difference between the two systems is that in NEMCA experiments the spillover-backspillover rate can be accurately measured and controlled by simply measuring the imposed current or potential. Another difference is that in electrochemical promotion experiments backspillover provides a promoting species, not an active site, to the catalyst surface. This latter difference can however be accommodated by a broader definition of the active site . 

Table 1 provide definitive evidence that the redon surrounding the site is, indeed, the pectinolytic active site as first hypothesized from the localization of the surface charges on tne PelC structure. 

Attempts to determine how the activity of the catalyst (or the selectivity which is, in a rough approximation, the ratio of reaction rates) depends upon the metal particle size have been undertaken for many decades. In 1962, one of the most important figures in catalysis research, M. Boudart, proposed a definition for structure sensitivity [4,5]. A heterogeneously catalyzed reaction is considered to be structure sensitive if its rate, referred to the number of active sites and, thus, expressed as turnover-frequency (TOF), depends on the particle size of the active component or a specific crystallographic orientation of the exposed catalyst surface. Boudart later expanded this model proposing that structure sensitivity is related to the number of (metal surface) atoms to which a crucial reaction intermediate is bound [6]. 

Thus from Equation (2.13) we see that a working definition of KM is the substrate concentration that yields a velocity equal to half of the maximum velocity. Stated another way, the Ku is that concentration of substrate leading to half saturation of the enzyme active sites under steady state conditions. 

Another property relevant to the current discussion is the distribution of water in the active site. Specifically, we characterize the population of various water wires connecting the zinc-bound water/hydroxide and His 64 found in the SCC-DFTB/MM simulations. These wires were identified following a definition of hydrogen-bond in terms of both distance (O—O < 3.5 A) and angle (O—H—O > 140°) and care... 

In this paper, we presented new information, which should help in optimising disordered carbon materials for anodes of lithium-ion batteries. We clearly proved that the irreversible capacity is essentially due to the presence of active sites at the surface of carbon, which cause the electrolyte decomposition. A perfect linear relationship was shown between the irreversible capacity and the active surface area, i.e. the area corresponding to the sites located at the edge planes. It definitely proves that the BET specific surface area, which represents the surface area of the basal planes, is not a relevant parameter to explain the irreversible capacity, even if some papers showed some correlation with this parameter for rather low BET surface area carbons. The electrolyte may be decomposed by surface functional groups or by dangling bonds. Coating by a thin layer of pyrolytic carbon allows these sites to be efficiently blocked, without reducing the value of reversible capacity. 

Fe 2S], a [4Fe-4S] and a [3Fe-4S] center. The enzyme catalyzes the reversible redox conversion of succinate to fumarate. Voltammetry of the enzyme on PGE electrodes in the presence of fumarate shows a catalytic wave for the reduction of fumarate to succinate (much more current than could be accounted for by the stoichiometric reduction of the protein active sites). Typical catalytic waves have a sigmoidal shape at a rotating disk electrode, but in the case of succinate dehydrogenase the catalytic wave shows a definite peak. This window of optimal potential for electrocatalysis seems to be a consequence of having multiple redox sites within the enzyme. Similar results were obtained with DMSO reductase, which contains a Mo-bis(pterin) active site and four [4Fe 4S] centers. 

In the absence of definitive information about the structure of the active site theoretical modeling of enzyme catalyzed reactions is difficult but not impossible. These difficulties are caused by the extremely large size of the enzyme-substrate-solvent system which typically comprises thousands or tens of thousands of atoms so that direct theoretical treatment at the microscopic quantum mechanical level is not yet practical. The computational demand is simply too enormous. As a compromise, a scheme generally referred to as QM/MM (quantum mechanics/molecular mechanics) has been devised. In QM/MM calculations, the bulk of the enzyme-solvent system (i.e. most of the atoms) is treated at a low cost, usually at the molecular mechanics (MM) level, while the more nearly correct and much more expensive quantum level (QM) computation is applied only to the reaction center (active site). 

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