A perspective on biological catalysis

Cannon, W. Roger; Singleton, Scott F.; Benkovic, Stephen J.

doi:10.1038/nsb1096-821

Cited by 158 publications

(140 citation statements)

References 59 publications

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“…Specific association rate constants at defined sites can be reduced significantly from the 108-109 M-' s-' expected for diffusion-controlled reactions by a variety of factors including restricted solid angle geometry (Solc & Stockmayer, 1973), conformational changes in which the substrate reacts with a minor conformer, association coupled with pre-organization or desolvation of the binding site (Julin & Kirsch, 1989;Cannon et al, 1996), or association with a minor prototropic form of the enzyme or ligand.…”

Section: Why Are Q Values So Small In Protein-protein Interactions?mentioning

confidence: 98%

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

1998

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Section: Why Are Q Values So Small In Protein-protein Interactions?mentioning

confidence: 98%

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

1998

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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).…”

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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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“…It has long been recognized that dynamic processes play an important role in the catalytic function of enzymes (1,2). Protein motion is implicated in events such as binding of substrate or cofactor, allosteric regulation, and product release, and the catalyzed reaction itself is inherently dynamic, with changes in atomic positions occurring along the reaction coordinate (3). Despite mounting experimental evidence that the active sites of enzymes are inherently flexible (4-6), a detailed understanding of the relationship between the dynamics and thermodynamics of protein fluctuations and the catalytic process is currently lacking.…”

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confidence: 99%

Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis

McElheny

Schnell²,

Lansing³

et al. 2005

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

151

229

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Dynamic processes are implicit in the catalytic function of all enzymes. To obtain insights into the relationship between the dynamics and thermodynamics of protein fluctuations and catalysis, we have measured millisecond time scale motions in the enzyme dihydrofolate reductase using NMR relaxation methods. Studies of a ternary complex formed from the substrate analog folate and oxidized NADP ؉ cofactor revealed conformational exchange between a ground state, in which the active site loops adopt a closed conformation, and a weakly populated (4.2% at 30°C) excited state with the loops in the occluded conformation. Fluctuations between these states, which involve motions of the nicotinamide ring of the cofactor into and out of the active site, occur on a time scale that is directly relevant to the structural transitions involved in progression through the catalytic cycle.enzyme catalysis ͉ hydride transfer ͉ NMR relaxation P roteins are dynamic molecular machines, and conformational fluctuations on a wide range of time scales are intimately associated with protein function. It has long been recognized that dynamic processes play an important role in the catalytic function of enzymes (1, 2). Protein motion is implicated in events such as binding of substrate or cofactor, allosteric regulation, and product release, and the catalyzed reaction itself is inherently dynamic, with changes in atomic positions occurring along the reaction coordinate (3). Despite mounting experimental evidence that the active sites of enzymes are inherently flexible (4-6), a detailed understanding of the relationship between the dynamics and thermodynamics of protein fluctuations and the catalytic process is currently lacking.A number of experimental and theoretical investigations have suggested that protein motions play an important role in catalysis by the enzyme dihydrofolate reductase (DHFR) (see refs. 7 and 8 for recent reviews). DHFR catalyzes the reduction of 7,8-dihydrofolate (DHF) through stereo-specific hydride transfer from reduced nicotinamide-adenine dinucleotide phosphate (NADPH) cofactor. The enzyme is essential for tetrahydrofolate (THF) biosynthesis, plays a central role in promoting cell growth and proliferation, and is the target of several anticancer and antibiotic drugs. Escherichia coli DHFR has been subjected to extensive kinetic and structural studies that have defined the complete kinetic mechanism (9) and the structural transitions involved in the catalytic cycle (10, 11). During the reaction cycle (Fig. 1), the enzyme progresses through conformations in which the active site loops are in a closed state, in the holoenzyme and the Michaelis complex, and a series of product complexes in which the loops adopt an occluded conformation. In the closed state, the Met-20 loop (residues 9-24) packs against the nicotinamide ring of the cofactor and seals the active site (10). In the occluded state, Met-16 and Glu-17 in the Met-20 loop project into the active site and sterically occlude the binding site for the nicotinamide-r...

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A perspective on biological catalysis

Cited by 158 publications

References 59 publications

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

Kinetic epitope mapping of the chicken lysozyme.HyHEL‐10 fab complex: Delineation of docking trajectories

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

Defining the role of active-site loop fluctuations in dihydrofolate reductase catalysis

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