Substrate destabilization

Nowotny, M. and Yang, W. (2006) Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release, EMBO J., 25, 1924-1933. 

Strain and stress in enzymes arise from several different causes. We have seen in this chapter, and we shall see further in Chapters 15 and 16, that stress and strain may be divided into two processes, substrate destabilization and transition state stabilization. Substrate destabilization may consist of steric strain, where there are unfavorable interactions between the enzyme and the substrate (e.g., with proline racemase, lysozyme) desolvation of the enzyme (e.g., by displacement of two bound water molecules from the carboxylate of Asp-52 of lysozyme) and desolvation of the substrate (e.g., by displacement of any bound water molecules from a peptide28). Transition state stabilization may consist of the presence of transition state binding modes that are not available for the... 

Makinen, M.W. (1998) Electron nuclear double resonace determined structure of enzyme reaction intermediates structural evidence for substrate destabilization, Spectrochimica Acta Part A 54, 2269-2281. 

This article will describe the different chemical strategies used by enzymes to achieve rate acceleration in the reactions that they catalyze. The concept of transition state stabilization applies to all types of catalysts. Because enzyme-catalyzed reactions are contained within an active site of a protein, proximity effects caused by the high effective concentrations of reactive groups are important for enzyme-catalyzed reactions, and, depending on how solvent-exposed the active site is, substrate desolvation may be important also. Examples of acid-base catalysis and covalent (nucleophilic) catalysis will be illustrated as well as examples of "strain" or substrate destabilization, which is a type of catalysis observed rarely in chemical catalysis. Some more advanced topics then will be mentioned briefly the stabilization of reactive intermediates in enzyme active sites and the possible involvement of protein dynamics and hydrogen tunneling in enzyme catalysis. 

In conclusion, enzymes use a variety of strategies to achieve high rates of catalysis. Transition state stabilization seems to be the dominant factor in catalysis, but in some enzymes, the more sophisticated strategies such as substrate destabilization and protein dynamics seem to play an important role. 

The calculated barrier to reaction in chorismate mutase was 17.8 kcal/mol, compared to 42 kcal/mol in the gas phase. Factors other than substrate distortion also play an important part in reducing the barrier to reaction in the enzyme important interactions were identified by a simple decomposition analysis (as described in sections 6.1 and 6.2 above). It was found that Glu78 and Arg90 specifically stabilize the transition state, relative to the bound substrate [8]. Overall, therefore, catalysis in chorismate mutase can be rationalized in terms of a combination of substrate strain and transition state stabilization. While it is possible to analyse all these catalytic effects as arising from maximal binding in the enzyme being achieved at the transition state, it appears useful to separate the different types of contribution. The possible role of substrate destabilization/distortion or strain in lowering the barrier to reaction in enzyme reactions, as put forward by Haldane [219], and invoked in... 

Mock, W.L. Irra. T.A. Wepsiec. J.P. Adhya, M. Catalysis by cucurbituril. The significance of bound-substrate destabilization for induced triazole formation. J. Org. Chem. 1989. 54 (22), 5302-5308. 

It is not necessary that entropy loss and substrate destabilization mechanisms, such as strain, are actually manifested directly in the enzyme-substrate complex it is only necessary that they exist so that the substrate cannot bind strongly. The requirements for optimal binding may be so stringent that parts of the substrate do... 

The importance of substrate destabilization is illustrated by the antibody-catalyzed decarboxylation of 3-carboxybenzisoxazoles (5) to give salicylo-nitriles (7) [34]. This reaction is extraordinarily sensitive to its solvent microenvironment, with rate enhancements up to 10 -fold observed upon transfer of the reactant from aqueous buffCT to aprotic dipolar solvents [35]. De solvation of the negatively charged carboxylate group greatly destabilizes the substrate, while the charge delocalized transition state (6) may be stabilized by dispersion interactions with solvent. Similar factors are believed... 

Following the biosynthetic mechanism, initial ionization of GDP to the cation followed by the subsequent addition of the IDP unit forms the FDP cation in a reaction that is catalyzed by FPPS prenyltransferase (Scheme 7.1) [2]. The mechanism is based on the findings that the enzyme, which normally catalyzes the addition of GDP to IDP, is also able to catalyze the hydrolysis of GDP [3]. Deuterium experiments of this hydrolysis process either with D O or with (1S)-[1- H] GDP indicated that C—O bond was broken and the chirality of the C-1 carbon of GDP was inverted in this process. In addition, when trifluoromethyl group was present at the C-3 position or fluoro atom at the C-2 position of the allylic substrate, destabilization of the cation has been witnessed as observed on the retard of enzyme reaction [4]. In the elimination step (Scheme 7.1) hydrogen is removed from C-2 of IDP part with simultaneous formation of a double bond. The formation of a trans or cis double bond during the FPPS reaction depends on the spatial orientation of IDP relative to the elongating FDP. In the tranx-prenyltransferases, the GDP... 

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