Enzymes structure-reactivity correlations

Klinman, J.P. (1976). Isotope effects and structure-reactivity correlations in the yeast alcohol dehydrogenase reaction. A study of the enzyme-catalyzed oxidation of aromatic alcohols. Biochemistry 15, 2018-2026... 

Site-directed mutagenesis is generally restricted to the 20 amino acids normally occurring in proteins. Thus, reliance on homologous series of compounds to establish structure-reactivity correlations, a hallmark of mechanistic studies with non-enzymic catalysts, has been lacking with enzymes. One manner in which this limitation can be partially overcome is provided by the demonstration that an enzyme, crippled because of an active-site substitution, can be rehabilitated... 

W.P. Jencks, Structure-Reactivity Correlations and General Acid-Base Catalysis in Enzymic Transacylation Reactions, Cold Spring Harbor Symp. Quant. Biol, 1971, 36, 1. 

In the case of enzymes working via a ternary complex mechanism, we have two extreme cases. The easiest to comprehend is the rapid equilibrium random mechanism (Scheme 5.4) this is the mechanism where the chemistry is most likely to be rate determining and kinetic isotope effects or structure-reactivity correlations are likely to be mechanistically informative. Enzymes acting on their physiological substrates at optimal pH are likely to show a degree of preference for one or the other substrate binding first, but they can often be induced to revert to a rapid equilibrium random mechanism by the use of non-optimal substrates or pH. 

Greenzaid, P. Jenks, W.P. (1971) Pig liver esterase. Reactions with alcohols, structure-reactivity correlations, and the acyl-enzyme intermediate. BiochemistrytO, 1210. 

In the case of enzymes reacting at measurable rates with a wide variety of substrates, structure-reactivity correlations are useful to establish mechanistic similarities with model reactions involving proton transfers [11]. As with most other methods applied to enzyme mechanisms, use of this criterion alone can be misleading. For a-chymotrypsin, for example, a limited series of substrates can be found which shows reactivities not inconsistent with the active-site imidazole acting as a nucleophile [12], whereas overwhelming evidence from all other methods shows that the imidazole acts as a general base [13,14]. 

Further structure-activity relationship (S AR) analyses of other cytoprotective enzyme inducers revealed the fact that all inducers can react with thiol/disulfide groups by alkylation, oxidoreduction, or thiol-disulfide interchange [Dinkova-Kostova and Talalay, 1999]. In fact, the capability of enzyme inducers to induce cytoprotective enzymes is well correlated with their reactivity with thiols. These results suggested a cellular sensor of inducers with highly reactive sulfhydryl groups, possibly reactive thiols in cysteine residues of a sensor protein. Nevertheless, the initial search for the sensor protein by using radioactively labeled inducers was not successful due to the abundance of thiol groups presented in many proteins in cells [Holtzclaw et al., 2004]. The molecular mechanism by which cytoprotective enzymes are induced remained to be elucidated. 

Once the protein interaction pattern is translated from Cartesian coordinates into distances from the reactive center of the enzyme and the structure of the ligand has been described with similar fingerprints, both sets of descriptors can be compared [25]. The hydrophobic complementarity, the complementarity of charges and H-bonds for the protein and the substrates are all computed using Carbo similarity indices [26]. The prediction of the site of metabolism (either in CYP or in UGT) is based on the hypothesis that the distance between the reactive center on the protein (iron atom in the heme group or the phosphorous atom in UDP) and the interaction points in the protein cavity (GRID-MIF) should correlate to the distance between the reactive center of the molecule (i.e. positions of hydrogen atoms and heteroatoms) and the position of the different atom types in the molecule [27]. 

Although a radical must be reactive in order to damage other components of a system, there is not necessarily a simple correlation between reactivity and the ability to cause irreversible damage to a complex structure. For example, the activity of certain enzymes is found to be inhibited more effectively by radicals of relatively low reactivity than by the reactive hydroxyl radical. This is because reactive radicals are not very selective in their reactions, having a tendency to react at many different sites in a molecule. Less reactive radicals are more selective and can be more effective at damaging a specific site. If this site happens to be essential for activity, then the less reactive radical will be more damaging. 

Most biological activities of STLs have been related to the presence of electrophilic structure elements, which undergo covalent reaction with functional biological macromolecules resulting in their deactivation [1-3]. In this respect, a,P-unsaturated carbonyl groups as well as epoxide and free aldehyde groups have to be considered reactive partial structures. The alkylation of free cysteine residues in enzymes and other functional proteins by STLs has in many instances been held responsible for STL bioactivity and there is a clear correlation between the presence of such residues in proteins and their susceptibility to inactivation by STLs [1-3], see section Alkylant Sesquiterpene Lactones . It was therefore of interest to investigate the distribution of such potential reactive sites (PRS) in the structures of the 4861 STLs (Table 1). 

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