Substrate-assisted stabilization

A structural anomaly in subtilisin has functional consequences Transition-state stabilization in subtilisin is dissected by protein engineering Catalysis occurs without a catalytic triad Substrate molecules provide catalytic groups in substrate-assisted catalysis Conclusion Selected readings... 

Scheme 4.17 Active site of Candida antarctica lipase B (a) transition-state stabilization in wild type and (b) substrate-assisted transition-state stabilization in Thr-nVal mutant.

In view of the overall increased reactivity of furan compared with thiophene it would be anticipated that furan would be less regioselective in its reactions with electrophiles than thiophene. Possible reasons for the high regioselectivity of furan in electrophilic substitution reactions include complex formation between substrates and reagents and the ability of heteroatoms to assist in the stabilization of cationic intermediates (80CHE1195). 

The intron group I ribozymes feature common secondary structure and reaction pathways. Active sites capable of catalyzing consecutive phosphodi-ester reactions produce properly spliced and circular RNAs. Ribozymes fold into a globular conformation and have solvent-inaccessible cores as quantified by Fe(II)-EDTA-induced free-radical cleavage experiments. The Tetrahy-mem group I intron ribozyme catalyzes phosphoryl transfer between guanosine and a substrate RNA strand—the exon. This ribozyme also has been proposed to use metal ions to assist in proper folding, to activate the nucleophile, and to stabilize the transition state. ... 

Efforts should be made to stabilize an enzyme s activity. Certain agents (such as glycerol, ammonium ions, boric acid, polyethylene glycol, and even talcum powder or bentonite clay) have proven widely to be effective enzyme stabilizers. For multisubstrate enzymes, inclusion of one particular substrate with the enzyme (in the absence of other substrates or cofactors) often stabilizes an enzyme s catalytic activity. Such a substrate may also assist in unlocking the enzyme from a particularly inactive conformational form. In addition to substrates, other ligands and effectors (including reaction products. 

Fig. 31. Mechanistic proposal for peptide hydrolysis catalyzed by carboxypeptidase A (Christianson and Lipscomb, 1989). (a) The precatalytic Michaelis complex with substrate carbonyl hydrogen bonded to Arg-127 allows for nucleophilic attack by a water molecule promoted by zinc and assisted by Glu-270 (an outer-sphere C==O Zn interaction is not precluded), (b) Tbe stabilized tetrahedral intermediate collapses, with required proton donation by Glu-270 (Monzingo and Matthews, 1984) Glu-270 may play a bifunctional catalytic role (Schepartz and Breslow, 1987), which results in the product complex (c). [Reprinted with permission from Christianson, D. W., Lipscomb, W. N. (1989) Acc. Chem. Res. 22,62-69. Copyright 1989 American Chemical Society.]...

For example, acetolysis of r/n /-6-tosyloxytricyclo[5.2.0.02 5]nona-3.8-diene proceeded smoothly at 35 C with stereospeeific rearrangement to c.Y0..mj-9-acetoxylricyclo[4.2.1,02 5]nona-3,7-diene (l).30 Interestingly, the rate of acetolysis of the substrate was considerably enhanced kre[25 C = 6.8 x 104) as compared with that of its bicyclic counterpart 2.30 An important conclusion from these studies is that the anchinteric assistances by cyclobutene in the form of homoallylic participation is effective in the stabilization of the carbocation intermediate. It was found in another study that cyclobutene is better than cyclobutane in terms of anchimeric assistance.31... 

In listing the ways in which metal ions may promote organic reactions, the requirement that the metal ion be suitably positioned within the substrate molecule was emphasized. Specific complexation or chelation of the metal ion with the substrate appears to be an absolute requirement of metal ion catalysis. In many cases chelation appears to be the rule, which usually means that the substrate must contain a donor atom in addition to the reactive center of the molecule with which the metal ion also complexes, or must contain two donor atoms in addition to the reactive center. Many attempts have been made to correlate the effectiveness of catalysis by a series of metal ions with the relative formation constants of the complexes. Such correlations have been successful in a number of reactions, but unsuccessful in others. In the successful correlations the complex chosen for the correlation closely approximates the transition state of the reaction. This indicates that the metal ion complex must stabilize the transition state of the reaction in order to assist the reaction effectively, and that metal ion complex formation in the ground state can have an effect exactly opposite to that of catalysis, since in such a case the ground state becomes stabilized. 

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