Active site chemical features

Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Bemi R (1996) Active site structural features for chemically modified forms of rhodanese. J Biol Chem 271(35) 21054-21061 Li S, Hall MB (2001) Modeling the active sites of metalloenzymes. 4. predictions of the unready states of [NiPe] desulfovibrio gigas hydrogenase from density functional theory. Inorg Chem 40(l) 18-24... 

Fig. 1.6 The increase in potency of a 1.3 mM p38 a protein kinase-binding fragment inhibitor identified by X-ray screening through the major changes made to the chemical series to exploit key binding features within the active site.

In summary, although subtle conformational differences between the various cycloamyloses and the effect of intramolecular hydrogen bonds on their solution conformations remain to be accurately resolved, overall structural features have been clearly defined. This is particularly advantageous and, in fact, a prerequisite if the cycloamyloses are to be profitably used as models for enzymatic or other catalytic processes. In subsequent sections of this article, various aspects of binding and catalysis will be explained on the basis of the chemical nature and geometrical dimensions of the cycloamylose cavity which is, in fact, their active site. 

Non-corrin cobalt has a number of interesting applications in the chemical industry, for example in the hydroformylation (OXO) reaction between CO, H2 and olefins. A number of non-corrin Co-containing enzymes have been described, including methionine aminopep-tidase, prolidase, nitrile hydratase and glucose isomerase. We describe the best characterized of these, namely the E. coli methionine aminopeptidase, a ubiquitous enzyme, which cleaves N-terminal methionine from newly translated polypeptide chains. The active site of the enzyme (Figure 15.13) contains two Co(II) ions that are coordinated by the side-chain atoms of five amino acid residues. The distance between the two Co2+ is similar to that between the two Zn2+ atoms in leucine aminopeptidase, and indeed the catalytic mechanism of methionine aminopeptidase shares many features with other metalloproteases, in particular leucine aminopeptidases. 

Unsaturated polyesters are low-molecular-weight fumarate esters containing various chemical structures designed for their specific cost and performance purposes. The two most important features of unsaturated polyesters are the fumarates, which provide the active sites for radical cross-linking with the diluent monomer and the random, low molecular weight, irregular nature of the rest of the molecule, which provide the necessary solubility in the diluent monomer. The preparation of the polyester thus requires the following considerations ... 

Structural models, which are synthesized to imitate features of the proposed structure of the active site. These may be used to demonstrate the chemical conditions, which allow such structures to exist, to investigate their chemical properties and to give a better understanding of the spectroscopic characteristics of the native proteins. Examples of these include the mixed carbonyl/cyano complexes of iron, used to verify the infrared spectra to the hydrogenases (Fig 7.4) (Lai et al. 1998) and the nickel-thiolate complexes which have low redox potentials like the hydrogenases (Franolic et al. 1992). 

In summary, the active site has control over the following features, which are difficult to replicate in a chemical catalyst ... 

Another possible explanation for the limitations of catalytic antibodies raised against TSA can be found in the different accessibility of the active site. In the case of natural enzymes, it is that their catalytic machinery and bound substrates are often buried. This feature isolates from the solvent the reactive functionalities that mediate chemical transformations. On the contrary, in antibody catalysis, the moieties of the bound haptens that mimic the TS are often positioned near the entrance of the antibody-combining site. This disparity in the overall architecture of natural enzymes and catalytic antibodies is undoubtedly a factor in the lower catalytic... 

Coenzymes facilitate chemical reactions through a range of different reaction mechanisms, some of which will be discussed in detail in this review. However, in all cases structural features of the coenzyme allow particular reactions to proceed along a mechanistic pathway in which reaction intermediates are more thermodynamically and kinetically accessible. When incorporated into apoen-zyme active sites, the coenzyme reactivity is influenced by a well-defined array of amino acid functional groups. For a given coenzyme, the particular array of amino acids presented by the different apoenzymes can drastically alter the degree of rate acceleration and product turnover and can specify the nature of the reaction catalyzed. 

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