Substrate-assisted

Substrate molecules provide catalytic groups in substrate-assisted catalysis... 

Figure 11.16 Substrate-assisted catalysis. Schematic diagram from model building of a substrate, NHa-Phe-Ala-His-Tyr-Gly-COOH (red), bound to the subtilisin mutant His 64-Ala. The diagram illustrates that the His residue of the substrate can occupy roughly the same position in this mutant as His 64 in wild-type subtilisin (see Figure 11.14) and thereby partly restore the catalytic triad.

Carter, P., Wells, J.A. Engineering enzyme specificity by "substrate-assisted catalysis." Science 237 394-399, 1987. 

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... 

Thompson, Damien Plateau, Pierre Simonson, Thomas, Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase., ChemBioChem Feb 2006, 7, 337-344. 

Acid and base catalysis of a chemical reaction involves the assistance by acid or base of a particular proton-transfer step in the reaction. Many enzyme catalysed reactions involve proton transfer from an oxygen or nitrogen centre at some stage in the mechanism, and often the role of the enzyme is to facilitate a proton transfer by acid or base catalysis. Proton transfer at one site in the substrate assists formation and/or rupture of chemical bonds at another site in the substrate. To understand these complex processes, it is necessary to understand the individual proton-transfer steps. The fundamental theory of simple proton transfers between oxygen and nitrogen acids and... 

In this conformation, the N-acetyl carbonyl oxygen is foimd only 3.0 A from the anomeric carbon, in a position favorable for nucleophiUc attack on Cl and formation of an oxazolinum ion, which is the first step in the substrate-assisted catalytic mechanism of family 18 enzymes. 

SUBSTRATE-ASSISTED CATALYSIS SUBSTRATE CHANNELING Substrate contaminated with the enzyme, BASAL RATE Substrate cycling,... 

Carter, P., Abrahmsen, L. and Wells, J.A. (1991) Probing the mechanism and improving the rate of substrate-assisted catalysis in subtihsin BPN. Biochemistry, 30, 6142-6148. Carter, P. and Wells, J.A. (1988) Dissecting the catalytic triad of a serine protease. 

Schweins,T., Geyer,M., Scheffzek.K., Warshel,A.,mm Kalbitzer.H.R. and Wittinghofer,A. Substrate assisted catalysis as a mechanism for GTP hydrolysis of p2P and other GTP-binding proteins (1995) Struct.Biol. 2, 36-44... 

Pasqualato, S., and Cherfils, J. (2005). Crystallographic evidence for substrate-assisted GTP hydrolysis by a small GTP binding protein. Structure 13, 533-540. 

Further, for antibody catalysis the methyl ester is too small to be an effective epitope but the participation could be induced if an antibody were able to recruit cocaine from the chair conformation to the less stable boat form (see Fig. 4 for the structure) and reorient the syn-protonated amine and benzoyl ester into proximity. Antibodies can provide significant binding energy and in principle antibody binding could effect conformer selection and promotion of substrate-assisted catalysis. To examine this idea, a detailed computational analysis [89] of the energetics of this reaction was also performed for design of novel TSA structures for the alkaline hydrolysis of boat cocaine in comparison with the hydrolysis of chair cocaine. 

Macauley MS, Whitworth GE, Debowski AW, Chin D, Vocadlo DJ. 0-GlcNAcase uses substrate-assisted catalysis kinetic analysis and development of highly selective mechanism-inspired inhibitors. J. Biol. Chem. 2005 280 25313-25322. 

Substrate Positioning and Substrate Assisted Catalysis in the Peptidyl Transferase Center of the Ribosome... 

Figure 3. Substrate-assisted mechanism for ENGase-cataiyzed reactions... 

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