Free-Energy Landscape of Enzyme Catalysis

Benkovic, Stephen J.; Hammes, Gordon G.; Hammes‐Schiffer, Sharon

doi:10.1021/bi800049z

Cited by 269 publications

(254 citation statements)

References 40 publications

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“…If this were the case, the single-ring substrate could then react from a variety of conformers (see ref. 53). In this scenario, mutation of the oxyanion hole hydrogen bonding groups is predicted to have smaller effects on k cat for reaction with S mini than for reaction with S full .…”

Section: Effect Of Ksi Oxyanion Hole Mutations On Reaction Of the Sinmentioning

confidence: 89%

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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Section: Effect Of Ksi Oxyanion Hole Mutations On Reaction Of the Sinmentioning

confidence: 89%

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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“…Finally, we mention that recently there has been increasing discussion of the fact that reactions that in the past had been described in terms of a one-dimensional FES [e.g., enzymatic reactions (34) or the analysis of single-molecule experiments (35)] in fact require more than one dimension for a valid description. Although we have illustrated the present methodology by applying it to protein folding, we note that the approach is perfectly general.…”

Section: Concluding Discussionmentioning

confidence: 99%

Diffusive reaction dynamics on invariant free energy profiles

Krivov

Karplus

2008

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

119

192

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A fundamental problem in the analysis of protein folding and other complex reactions in which the entropy plays an important role is the determination of the activation free energy from experimental measurements or computer simulations. This article shows how to combine minimum-cut-based free energy profiles (F C), obtained from equilibrium molecular dynamics simulations, with conventional histogram-based free energy profiles (F H) to extract the coordinatedependent diffusion coefficient on the F C (i.e., the method determines free energies and a diffusive preexponential factor along an appropriate reaction coordinate). The F C, in contrast to the FH, is shown to be invariant with respect to arbitrary transformations of the reaction coordinate, which makes possible partition of configuration space into basins in an invariant way. A ''natural coordinate,'' for which F H and FC differ by a multiplicative constant (constant diffusion coefficient), is introduced. The approach is illustrated by a model onedimensional system, the alanine dipeptide, and the folding reaction of a double ␤-hairpin miniprotein. It is shown how the results can be used to test whether the putative reaction coordinate is a good reaction coordinate.diffusion ͉ protein folding ͉ one-dimensional free energy surfaces ͉ variable diffusion coefficient F ree energy surface (FES) projected on a few progress variables (usually one or two) is often used to describe the equilibrium and kinetic properties of complex systems with a very large number (100 to 1,000 or more) of degrees of freedom. Studies of protein folding are an important example where this type of projected surface has been introduced and progress variables such as the number of native contacts and radius of gyration have been used (1-3). Most experimental analyses of protein folding have used a related approach; for example, if the distribution of folding times is exponential, it is assumed that there is a single free energy barrier along a generally unknown one-dimensional reaction coordinate. For a few systems that show more complex kinetics, the results have been interpreted in terms of projected FESs in two dimensions (4), although, again, the actual progress variables are not known. However, even when a one-dimensional single-barrier free energy projection seems adequate to describe the kinetics, there is a fundamental difficulty in determining the barrier height, because the measurements provide only one parameter (e.g., in protein folding, the rate constant of the corresponding unimolecular reaction is obtained). In such a standard ''one-dimensional'' analysis, the rate constant, k, is written as k ϭ k 0 e Ϫ⌬F/kT , where k 0 is the preexponential factor and ⌬F is the free energy of activation. Thus, there are two unknowns, k 0 and ⌬F, to be determined from one measurement. For many small-molecule reactions, the entropic contribution to the barrier is negligible (⌬F Ϸ ⌬E, the activation energy), so that a measurement of the temperature dependence of the reaction rate can be used t...

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“…The nature and magnitude of these forces remains an active area of research. [10][11][12][13][14][15] Enzymes have evolved to create elaborate active sites containing precise arrangements of hydrogen-bonding networks, electrostatic interactions, and functional group availability specifically aimed at increasing the reactivity of bound substrates. While the development of synthetic host-guest systems has not reached the level of enzyme specificity, the characteristics of each synthetic assembly, such as the size, shape, charge, and functional group availability, greatly influence the guest-binding characteristics and have led to remarkable and often unexpected reactivity.…”

Section: Introductionmentioning

confidence: 99%

Spin Equilibria in Monomeric Manganocenes: Solid-State Magnetic and EXAFS Studies

et al. 2009

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A water-soluble self-assembled supramolecular host molecule catalyzes the hydrolysis of orthoformates in basic solution. Comparison of the rate constants of the catalyzed and uncatalyzed reactions for hydrolysis displays rate accelerations of up to 3900 for tri-n-propyl orthoformate. Kinetic analysis shows that the mechanism of hydrolysis with the supramolecular host obeys the Michaelis-Menten model.Mechanistic studies, including 13 C-labeling experiments, revealed that the resting state of the catalytic system is the neutral substrate encapsulated in the host. Activation parameters for the k cat step of the reaction revealed that upon encapsulation in the assembly, the entropy of activation becomes more negative in contrast to the uncatalyzed reaction. Furthermore, solvent isotope effects reveal a normal k(H 2 O)/k(D 2 O) = 1.6, confirming that proton transfer is occurring in the transition state and is rate limiting in the catalyzed reaction. In comparison to the uncatalyzed reaction, which operates by an A-1 mechanism in which the decomposition of the protonated substrate is rate limiting, the encapsulated reaction proceeds through an A-S E 2 mechanism in which proton transfer from protonated water to the substrate is rate limiting.

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Free-Energy Landscape of Enzyme Catalysis

Cited by 269 publications

References 40 publications

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

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

Diffusive reaction dynamics on invariant free energy profiles

Spin Equilibria in Monomeric Manganocenes: Solid-State Magnetic and EXAFS Studies

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