SITES, CATALYTIC FUNCTION

Yet another distinction is between intermolecular catalysis, in which the catalytic function and the reaction site are on different molecules, and intramolecular catalysis, in which the catalytic function and the reaction site are within the same molecule. All of the above examples constitute intermolecular catalyses. The following reaction, the hydrolysis of a monomaleate ester, is an intramolecular nucleophilic catalysis. 

Uncovering of the three dimentional structure of catalytic groups at the active site of an enzyme allows to theorize the catalytic mechanism, and the theory accelerates the designing of model systems. Examples of such enzymes are zinc ion containing carboxypeptidase A 1-5) and carbonic anhydrase6-11. There are many other zinc enzymes with a variety of catalytic functions. For example, alcohol dehydrogenase is also a zinc enzyme and the subject of intensive model studies. However, the topics of this review will be confined to the model studies of the former hydrolytic metallo-enzymes. 

Hydrodenitrogenation (HDN) is an important process in petroleum refining. It removes nitrogen from oil distillates, so that less NOx pollutes the air when oil is burned and poisoning of the subsequent refining catalysts is reduced when the oil is processed further. Although HDN has been studied intensively and different reaction mechanisms, catalytic active sites, and functions of the catalytic components have been proposed, there are stiU many questions to be answered in order to better mderstand the reaction and the catalyst (1-4). 

The Pt/Ru catalyst is the material of choice for the direct methanol fuel cell (DMFC) (and hydrogen reformate) fuel cell anodes, and its catalytic function needs to be completely understood. In the hrst approximation, as is now widely acknowledged, methanol decomposes on Pt sites of the Pt/Ru surface, producing chemisorbed CO that is transferred via surface motions to the active Pt/Ru sites to become oxidized to CO2... 

The understanding of the catalytic function of enzymes is a prime objective in biomolecular science. In the last decade, significant developments in computational approaches have made quantum chemistry a powerful tool for the study of enzymatic mechanisms. In all applications of quantum chemistry to proteins, a key concept is the active site, i.e. a local region where the chemical reactivity takes place. The concept of the active site makes it possible to scale down large enzymatic systems to models small enough to be handled by accurate quantum chemistry methods. 

Biomimetic chemistry of nickel was extensively reviewed.1847,1848 Elaborate complexes have been developed in order to model structural and spectroscopic properties as well as the catalytic function of the biological sites. Biomimetic systems for urease are described in Section 6.3.4.12.7, and model systems for [Ni,Fe]-hydrogenases are collected in Section 6.3.4.12.5. 

The cytoplasmic domain primarily consists of the catalytic domain and various autophosphorylation sites that regulate catalytic function and serve as docking sites for SH2 do main-containing proteins. The protein kinase catalytic domains of RPTKs are highly conserved and similar in structure to those of the NRPTK (see above). 

A single sentence describing some properties of the unknown protein is not regarded as optimal automatic annotation of TrEMBL. As with SWISS-PROT, as much information as possible is required about properties such as function (s) of the protein, domains and sites, catalytic activity, cofactors, regulation, induction, pathways, tissue specificity, developmental stages, and subcellular location. 

These three catalytic functionalities are similar in practically all hydrolytic enzymes, but the actual functional groups performing the reactions differ among hydrolases. Based on the structures of their catalytic sites, hydrolases can be divided into five classes, namely serine hydrolases, threonine hydrolases, cysteine hydrolases, aspartic hydrolases, and metallohydrolases, to which the similarly acting calcium-dependent hydrolases can be added. Hydrolases of yet unknown catalytic mechanism also exist. 

The functions of porous electrodes in fuel cells are 1) to provide a surface site where gas/liquid ionization or de-ionization reactions can take place, 2) to conduct ions away from or into the three-phase interface once they are formed (so an electrode must be made of materials that have good electrical conductance), and 3) to provide a physical barrier that separates the bulk gas phase and the electrolyte. A corollary of Item 1 is that, in order to increase the rates of reactions, the electrode material should be catalytic as well as conductive, porous rather than solid. The catalytic function of electrodes is more important in lower temperature fuel cells and less so in high-temperature fuel cells because ionization reaction rates increase with temperature. It is also a corollary that the porous electrodes must be permeable to both electrolyte and gases, but not such that the media can be easily "flooded" by the electrolyte or "dried" by the gases in a one-sided manner (see latter part of next section). 

For all these reasons, some chemical or genetical modifications have been applied into the binding sites of antibodies in order to improve their reactivity [22]. Antibodies can be modified by the incorporation of natural or synthetic catalysts into the antibody recognition site, as for instance transition metal complexes, cofactors, and bases or nucleophiles, to carry other catalytic functions, which open the way to... 

Following this reasoning, a rational route for proceeding calls for the deliberate and prudent exchange of functions or structural motifs or the addition of new ones in fully functional biopolymers and observe the consequences in terms of stability and catalytic activity. There is hope that a limited structural modification at one particular site will entail a locally limited response that can be dissected and analyzed. The results emerging in the context of the functional catalyst are expected to be more readily translated into measures to be taken for the improvement of catalytic function. 

Finally, there is a class of molecules—some large and many small— termed enzyme inhibitors. These molecules bind to enzymes, generally quite specifically, and prevent them from carrying out their catalytic function. These are keys that fit the lock but do not open it. This is another example of molecular recognition. In the simplest cases, the inhibitor of an enzyme is structurally related to the normal physiological substrate for the enzyme. The inhibitor looks enough like the normal substrate to bind to the enzyme at the site where the substrate normally binds but is sufficiently different so that no reaction subsequently occurs. The key fits in the lock but cannot open it. It follows that the enzyme is captured in the form of an enzyme-inhibitor complex, E 1, where 1 denotes the inhibitor. The point is that E 1 cannot make products. The enzyme has been rendered nonfunctional as long as 1 is bound to it. 

Of the five snRNAs, U2 and U6 interact with the reaction site (the 5 splice site and the branch point) in the first chemical step. These two snRNAs are known to anneal together to form a stable-based paired structure in the absence of proteins and in the presence of ions as shown in Fig. 13, with U2 acting as an inducer molecule that displaces the U4 (that is an antisense molecule that regulates the catalytic function of U6 RNA) from the initially formed U4-U6 duplex. The secondary (or higher ordered) structure of the U2-U6 complex consists of the active site of the spliceosome. Recent data suggests that these two snRNAs function as the catalytic domain of the spliceosome that catalyzes the first step of the splicing reaction [145]. 

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