Enzyme action binding sites

Nature attempts to simplify its chemical environment and has selected L-amino acids as the natural form. This has the saving feature that only one set of enzymes with binding sites for L-amino acids must be produced. However, D-amino acids do arise in nature from spontaneous isomerization of L-amino acids (see above) or from a very few sites in nature (the action of penicillin involves a structure that contains D-alanine, see below). While the enzymes that act on L-amino acids will almost never interact with D-amino acids and vice versa, there are rare examples of enzymes that interact with both isomers. In the latter case, the enzyme binding site must be ambidextrous and have extra features that accommodate both isomers. In other words, enzymes naturally show stereoselectivity and avoidance of stereochemical selection is an exception. 

One form of biological poisoning mirrors the effect of lead on a catalytic converter. The activity of an enzyme is destroyed if an alien substrate attaches too strongly to the enzyme s active site, because then the site is blocked and made unavailable to the true substrate (Fig. 13.42). As a result, the chain of biochemical reactions in the cell stops, and the cell dies. The action of nerve gases is believed to stem from their ability to block the enzyme-controlled reactions that allow impulses to travel through nerves. Arsenic, that favorite of fictional poisoners, acts in a similar way. After ingestion as As(V) in the form of arsenate ions (As043 ), it is reduced to As(III), which binds to enzymes and inhibits their action. 

Site-directed mutagenesis, used to change residues suspected of being important in catalysis or substrate binding, provides insights into the mechanisms of enzyme action. 

There has been considerable discussion regarding the mode of action of the sea cucumber and starfish saponins. Both the triterpene and steroidal glycosides inhibit both Na/K ATPase and Ca/Mg ATPase 06) possibly as a result of their aglycone structures. However, their detergent properties cause membrane disruption which will influence the activity of membrane-bound enzymes such as the ATPases. In investigating the actions of saponins on multilamellar liposomes, it was found that cholesterol serves as the binding site for such saponins and that cholesterol-free lip-somes are not lysed by saponins 107). 

A similar interpretation of action patterns B and C (Scheme 1), and of the number of productive complexes, indicates that, in the corresponding enzymes, there is a binding site composed of three (B) or five (C) subsites having the catalytic groups situated between the first and second (B) and the second and third (C) subsites. Another indication of a binding site containing three subsites for enzymes of... 

Tyramide signal amplification (TSA PerkinElmer Life Sciences, Boston) and enzyme-labeled fluorescence (ELF Molecular Probes) are related detection technologies. In the tyramide amplification process, a tyramide-biotin complex is produced by the action of horseradish peroxidase. The complex precipitates near the binding site and accumulates. The complex is detected by the use of streptavidin-Cy3/Cy5. 

The topologically defined region(s) on an enzyme responsible for the binding of substrate(s), coenzymes, metal ions, and protons that directly participate in the chemical transformation catalyzed by an enzyme, ribo-zyme, or catalytic antibody. Active sites need not be part of the same protein subunit, and covalently bound intermediates may interact with several regions on different subunits of a multisubunit enzyme complex. See Lambda (A) Isomers of Metal Ion-Nucleotide Complexes Lock and Key Model of Enzyme Action Low-Barrier Hydrogen Bonds Role in Catalysis Yaga-Ozav /a Plot Yonetani-Theorell Plot Induced-Fit Model Allosteric Interaction... 

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