Catalytic types

An exopeptidase that sequentially releases an amino from the C-terminus of a protein or peptide. Carbox-ypeptidases are classified in Enzyme Nomenclature according to catalytic type and are included in subsubclasses 3.4.16-3.4.18. 

The order and nature of the active site residues and metal ligands is conserved between homologous peptidases. All the members of a family will have the same catalytic type. 

Peptidases have been classified by the MEROPS system since 1993 [2], which has been available viatheMEROPS database since 1996 [3]. The classification is based on sequence and structural similarities. Because peptidases are often multidomain proteins, only the domain directly involved in catalysis, and which beais the active site residues, is used in comparisons. This domain is known as the peptidase unit. Peptidases with statistically significant peptidase unit sequence similarities are included in the same family. To date 186 families of peptidase have been detected. Examples from 86 of these families are known in humans. A family is named from a letter representing the catalytic type ( A for aspartic, G for glutamic, M for metallo, C for cysteine, S for serine and T for threonine) plus a number. Examples of family names are shown in Table 1. There are 53 families of metallopeptidases (24 in human), 14 of aspartic peptidases (three of which are found in human), 62 of cysteine peptidases (19 in human), 42 of serine peptidases (17 in human), four of threonine peptidases (three in human), one of ghitamicpeptidases and nine families for which the catalytic type is unknown (one in human). It should be noted that within a family not all of the members will be peptidases. Usually non-peptidase homologues are a minority and can be easily detected because not all of the active site residues are conserved. 

All peptidases within a family will have a similar tertiary structure, and it is not uncommon for peptidases in one family to have a similar structure to peptidases in another family, even though there is no significant sequence similarity. Families of peptidases with similar structures and the same order of active site residues are included in the same clan. A clan name consists of two letters, the first representing the catalytic type as before, but with the extra letter P , and the second assigned sequentially. Unlike families, a clan may contain peptidases of more than one catalytic type. So far this has only been seen for peptidases with protein nucleophiles, and these clans are named with an initial P . Only three such clans are known. Clan PA includes peptidases with a chymotrypsin-like fold, which besides serine peptidases such as chymotrypsin... 

It is recommended that a well-characterized peptidase should have a trivial name. Although not rigidly adhered to, there is a different suffix for each catalytic type, metallopeptidases names end with lysin , aspartic peptidases with pepsin , cysteine pqrtidase with ain and serine peptidases with in . 

The action of a peptidase can be neutralized by an inhibitor. Some inhibitors are very broad in their action and are capable of inhibiting many different peptidases, including peptidases of different catalytic types. Some inhibitors are assumed to be specific for a particular catalytic type, but can inhibit peptidases of different types. Leupeptin, for example, is widely used as an inhibitor of serine peptidases from family SI, but it is also known to inhibit cysteine peptidases from family Cl. Cysteine pqrtidase inhibitors such as iodoacetic acid interact with the thiol of the catalytic cysteine. However, this reduction can occur on any thiol group and can affect other, predominantly intracellular, peptidases with a thiol dependency. One example is thimet oligopepti-dase. Metal chelators such as EDTA can inhibit meta-llopeptidases, but can also affect peptidases that have a requirement for metal ions that is indq>endent of their catalytic activity, such as the calcium-dependent cysteine endopqrtidase calpain 1. 

Inhibitors which interact only with peptidases of one catalytic type include pepstatin (aspartic peptidases) E64 (cysteine peptidases from clan CA) diisopropyl fluorophosphates (DFP) and phenylmethane sulfonyl-fluoride (PMSF) (serine peptidases). Bestatin is a useful inhibitor of aminopeptidases. 

The role of bulk diffusion in controlling reaction rates is expected to be significant during surface (catalytic-type) processes for which transportation of the bulk participant is slow (see reactions of sulphides below) or for which the boundary and desorption steps are fast. Diffusion may, for example, control the rate of Ni3C hydrogenation which is much more rapid than the vacuum decomposition of this solid. 

Afterburners may be of the flame, thermal, or catalytic type. In each case the object is to cause a chemical reaction which will result in an acceptable product, such as water and carbon dioxide. This is not possible, hence this is an undesirable method, if heavy metals, sulfides, halogens, or phosphates are present. The costs associated with this method are given in reference 22. 

The peptidases were separated into catalytic types according to the chemical nature of the group responsible for catalysis. The major catalytic types are, thus, Serine (and the related Threonine), Cysteine, Aspartic, Metallo, and As-Yet-Unclassified. An in-depth presentation of catalytic sites and mechanisms, based on this classification, is the subject of Chapt. 3. 

The evolutionary classification has a rational basis, since, to date, the catalytic mechanisms for most peptidases have been established, and the elucidation of their amino acid sequences is progressing rapidly. This classification has the major advantage of fitting well with the catalytic types, but allows no prediction about the types of reaction being catalyzed. For example, some families contain endo- and exopeptidases, e.g., SB-S8, SC-S9 and CA-Cl. Other families exhibit a single type of specificity, e.g., all families in clan MB are endopeptidases, family MC-M14 is almost exclusively composed of carboxypeptidases, and family MF-M17 is composed of aminopeptidases. Furthermore, the same enzyme specificity can sometimes be found in more than one family, e.g., D-Ala-D-Ala carboxypeptidases are found in four different families (SE-S11, SE-S12, SE-S13, and MD-M15). 

Exercise 11-8 Consider that it is necessary to synthesize pure samples of d.l-hexane-3,4-D2 and meso-hexane-3,4-D2. Show how this might be done both with diimide and catalytic-type reductions, assuming that any necessary deuterium-iabeled reagents and six-carbon organic compounds are available. 

Further examination of "reductive oxidation" ECL using polyaromatic compounds in non-aqueous media has revealed three signific ant features of the luminescence mechanism (10). First, the cyclic voltammograms fojj the reduction of the polyaromatic compounds in the presence of S2O8 were of a highly catalytic type. Second, the efficiency of ECL was qualitatively dependent on the stability of the aromatic radical cation rather than of the aromatic radical anion. Third, the importance of the aromatic radical cation ion in the mechanism for the formation of excited states was illustrated using a tertiary reactant system. The results of these studies are summarized below. 

As indicated in Chapter 1, principally, the reactions may be conjugated, when one of them slows another one down, and somewhat inhibits it. The mechanism of slowing down the secondary reaction may have different origins (e.g. if the target reaction is of the catalytic type, and intermediate products (IP) poisoning the catalyst are formed in the primary reaction). Another possible case is realized when IP of both reactions recombine or disproportionate (active sites are eliminated). Such negative effects of chemical reactions allow us to... 

Figure 4.7 shows that after reaching the maximum yield the consumption rate of vinylethylbenzenes decreases only slightly. This indicates deficient H202 concentration at the stage of divinylbenzene synthesis. The S-shape of the kinetic curves obtained testifies to the auto-catalytic type of the process with the autoacceleration period from the beginning of these curves to inflection points. 

Another important application of the iminium catalysis concept has been the development of enantioselective Type I [15, 30] and Type II [15] intramolecular Diels-Alder reactions (IMDA). (For experimental details see Chapter 14.18.3). For these transformations, both catalysts 1 and 3 proved to be highly efficient, as demonstrated by both the short and effective preparation of the marine methabo-lite solanapyrone D via Type I IMDA (Scheme 3.4, top) and the development of an early example of an enantioselective, catalytic Type II IMDA reaction (Scheme 3.4, bottom) [35]. Importantly, cycloadducts incorporating ether and quaternary carbon functionalities could be efficiently produced. 

In the above equations the symbols A, B, C, D designate phenol, hydrogen, cyclohexanone and cyclohexanol. Table 5.7 presents the model parameters at 423 K and 1 atm. The model takes into account the effect of the products on the reaction rate in the region of higher conversion. This feature is particularly useful for describing the product distribution in consecutive catalytic-type reactions. Note that the adsorption coefficients are different in the two reactions. Following the authors, this assumption, physically unlikely, was considered only to increase the accuracy of modeling. 

Recently, however, the implementation of several forms of modern, high resolution spectroscopy has made it possible to characterize, in relatively detailed fashion, the evolving chemistry of heterogeneous catalytic-type systems. In some cases, in fact, it has been possible to map the behavior of actual commercial catalysts, even following use. For example, much of our present understanding of the functionality of hydrodesulfurization catalysis has been a direct result of investigations of commercial systems with modern surface spectroscopies, as is also the case in the development of the basis reference for metals-support interactions (1). 

Based on matenal considerations, membrane reactors can be classified into (1) organic-membrane reactors, and (2) inorgamc-membrane reactors, with the latter class subdivided into dense (metals) membrane reactors and porous-membrane reactors Based on membrane type and mode of operation, Tsotsis et al. [15] classified membrane reactors as shown in Table 3. A CMR is a reactor whose permselective membrane is the catalytic type or has a catalyst deposited in or on it. A CNMR contains a catalytic membrane that reactants penetrate from both sides. PBMR and FBMR contain a permselective membrane that is not catalytic the catalyst is present in the form of a packed or a fluidized bed PBCMR and FBCMR differ from the foregoing reactors in that membranes are catalytic. 

In addition to the many investigations of the bulk properties of crystalline oxides, there has also been considerable interest in the surface chemistry of these compounds. Mechanistic studies in this field often include discussion of heterogeneous catalytic-type processes and intermediates, similar to or identical with, those postulated above as occurring during oxide dissociation. Some reference is made below to relevant aspects of the surface chemistry of oxides. 

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