New Ideas about Enzyme Reactions

Dewar, Michael J. S.

doi:10.1159/000469274

Cited by 60 publications

(26 citation statements)

References 16 publications

(29 reference statements)

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“…According to the desolvation hypothesis (10)(11)(12), an enzyme catalyzes its reaction by creating an environment around the reactants that is similar to the gas phase. This hypothesis stems from the fact that gas-phase calculations (10)(11)(12)(18)(19)(20)(21) as well as analysis of experimental data (15) indicate that the nucleophilic attack in the gas phase (starting from a state with the negative R-O-ion present while Aand BH' are kept at infinite distance) involves a small activation barrier (or no barrier at all), whereas the solution reaction is associated with a significant barrier (15).…”

Section: And 2)mentioning

confidence: 99%

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Enzymes work by solvation substitution rather than by desolvation.

Warshel

Åqvist

Creighton

1989

Proc. Natl. Acad. Sci. U.S.A.

139

102

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Considerable attention has recently been drawn to the hypothesis that enzymes catalyze their reactions by displacing solvent and creating an environment similar to the gas phase for the reacting substrates. This "desolvation hypothesis" is reexamined in this paper by defining a common reference energy for reactions in various environments. It is argued that consistent attempts to describe the actual energetics of enzymatic reactions, taking either gas phase or solution as a reference, would contradict the above hypothesis. That is, the enzyme does remove water molecules from its substrate, but substitutes these molecules for another polar environment (namely, its active site). By taking amide hydrolysis as an example, we use experimentally estimated salvation energies and analyze the reaction profile in the gas phase, in solution, and in enzyme active sites. We show that the gas-phase reaction is characterized by an enormous activation barrier (associated with forming the charged nucleophile from neutral fragments), although the nucleophilic attack is essentially barrierless. On the other hand, the enzyme and solution reactions are found to have similar reaction proffles, with a lower activation barrier for the enzymatic reaction. Presumably, the fact that previous analyses of this problem did not involve the construction of the relevant thermodynamic cycles (and quantitative estimates of the corresponding salvation energies) led to the desolvation hypothesis. Our conclusion is that enzyme active sites provide specific polar environments that do not resemble the gas phase but that are designed for electrostatic stabilization of ionic transition states and that "solvate" these states more than water does.The search for the origin of enzyme catalysis has led to several major hypotheses concerning the basic principles by which enzymes are able to accelerate chemical reactions (1-10). Although it is evident that an enzyme must reduce the activation barrier for the catalyzed reaction (3, 4), it is not entirely clear how this is accomplished. A considerable amount of attention has recently been drawn to the proposal that enzymes catalyze reactions by removing water molecules from the reactants, thereby creating an environment similar to the gas phase for the reacting subtrates (the desolvation hypothesis) (refs. 8-12; see also refs. 20, 29, and 30 for a related discussion). Since many reactions in the gas phase (e.g., SN2) have small activation barriers compared to the corresponding solution reactions, it might appear reasonable that enzymes could work by creating gas-phase-like conditions for the reactants. This hypothesis contrasts with the proposal that enzymes work by providing a specific solvation of the transition state of the relevant reactions, in terms of favorable electrostatic interactions between the protein and the ionic transition state (6, 7). In this paper, we examine the desolvation hypothesis and point out that it overlooks important thermodynamic elements associated with the formation of cha...

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Section: And 2)mentioning

confidence: 99%

“…A considerable amount of attention has recently been drawn to the proposal that enzymes catalyze reactions by removing water molecules from the reactants, thereby creating an environment similar to the gas phase for the reacting subtrates (the desolvation hypothesis) (refs. [8][9][10][11][12]; see also refs. 20, 29, and 30 for a related discussion).…”

mentioning

confidence: 99%

Enzymes work by solvation substitution rather than by desolvation.

Warshel

Åqvist

Creighton

1989

Proc. Natl. Acad. Sci. U.S.A.

139

102

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“…Beyond simple localization, these binding interactions can correctly position the reactive portion of a substrate relative to active site functional groups and relative to other substrates (7,(20)(21)(22)(23)(24)(25). Concomitant with substrate binding solvent is displaced and excluded from the active site and solvent exclusion may be important in shaping the electrostatic environment within the active site (26,27). Indeed, solvent exclusion by substrate binding has been suggested to be important for catalysis in numerous enzymes (e.g., refs.…”

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confidence: 99%

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

Schwans

Kraut

Herschlag

2009

Proc. Natl. Acad. Sci. U.S.A.

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O ver the past decades, visualization of enzyme threedimensional structures has revealed that active sites are located in crevices or pockets. Within these active sites are found coenzymes, cofactors, metal ions, and side chains that participate in a rich array of chemical reactions. Based on this information and decades of enzymology and bioorganic chemistry, reasonable chemical mechanisms using these groups can be posited for most enzymatic reactions. Nevertheless, we still cannot quantitatively account for the enormous enzymatic rate enhancements and exquisite specificities observed by enzymes.Over the past century, Polanyi, Haldane, Pauling, and Jencks recognized a key distinguishing feature between chemical reactions taking place in an enzyme's active site and the corresponding reaction taking place in solution (1-4). Even if the enzymatic and solution reactions use the same cofactors, metal ions, and functional groups, an enzyme can use noncovalent interactions between the enzyme and substrate to accelerate the reaction. Indeed, binding interactions between enzymes and substrates, both directly at the site of chemical transformation and with nonreacting portions of the substrate have been shown to contribute to catalysis (e.g., refs. 5-19). The mechanisms by which these noncovalent interactions can assist catalysis have been widely discussed, as briefly described in the following two paragraphs.In the simplest scenario an enzyme can use binding interactions to localize the substrate to the active site. Beyond simple localization, these binding interactions can correctly position the reactive portion of a substrate relative to active site functional groups and relative to other substrates (7, 20-25). Concomitant with substrate binding solvent is displaced and excluded from the active site and solvent exclusion may be important in shaping the electrostatic environment within the active site (26,27). Indeed, solvent exclusion by substrate binding has been suggested to be important for catalysis in numerous enzymes (e.g., refs. 26-32).Jencks and others realized that remote binding interactions can do more than provide for tight binding between substrate and enzyme. Reactions of bound substrates can be facilitated by use of so-called ''intrinsic binding energy'', which can pay for substrate desolvation, distortion, electrostatic destabilization, and entropy loss (3,7,33,34). The term intrinsic binding energy is not a molecular explanation for catalysis, but rather provides a conceptual framework for analyzing the energetics of enzymatic catalysis. In this scenario the maximum binding energy is not realized in the ground state, because aspects of the bound state, such as restricted positioning of substrates, are energetically unfavorable relative to the interactions and freedom of motion in aqueous solution. However, changes associated with achievement of the transition state, such as charge and geometric rearrangements and the formation of partial covalent bonds between positioned substrates, allow the binding ...

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“…They reported a water activity of 0.004 in their reaction medium, similar to that observed in this study. Other studies have also reported enhancement in enzyme activity by addition of molecular sieves (Dewar, 1986, Dewar et al, 1988Oosterom et al, 1996;Wu and Akoh, 1996). Water also contributes to the hydrolysis of the esters, both substrate (VA) and product (MGA), leading to a net decrease in reaction eciency.…”

Section: Effect Of Watermentioning

confidence: 95%

Scale‐up of pseudo solid‐phase enzymatic synthesis of α‐methyl glucoside acrylate

Rethwisch²

2002

Biotech & Bioengineering

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The successful scale-up of the enzymatic synthesis of alpha-methyl glucoside acrylate from laboratory-scale (milliliter) to pilot-scale (liter) was examined. Specifically, Candida antarctica lipase B (Novozym 435) was used as a biocatalyst to produce alpha-methyl glucoside acrylate via the transesterification of alpha-methyl glucoside (MG) with vinyl acrylate (VA) using acetone as a solvent. This is a pseudo-solid-phase synthesis; only a fraction of the alpha-methyl glucoside and the product are soluble in acetone. Molecular sieves were used to remove traces of water in the reaction medium and to increase enzyme stability by removing the acetaldehyde by-product. A general method was also developed to purify and recover the monoacrylate product from unreacted sugar and undesired diester by a simple crystallization and precipitation process.

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New Ideas about Enzyme Reactions

Cited by 60 publications

References 16 publications

Enzymes work by solvation substitution rather than by desolvation.

Enzymes work by solvation substitution rather than by desolvation.

Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase

Scale‐up of pseudo solid‐phase enzymatic synthesis of α‐methyl glucoside acrylate

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