A 21st century revisionist's view at a turning point in enzymology

Nagel, Zachary D.; Klinman, Judith P.

doi:10.1038/nchembio.204

Cited by 280 publications

(426 citation statements)

References 64 publications

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“…In many cases it is clearly suggested that improving such effects will be crucial for optimal enzyme design (e.g., ref. 30). However, it seems to us that by far the main factor that actually contributes to catalysis is the preorganization effect and thus we feel that there is no rational way for improving dynamics and related effects as these factors do not contribute to catalysis (29).…”

Section: Discussionmentioning

confidence: 99%

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Frushicheva

Cao

Chu

et al. 2010

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

113

181

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One of the fundamental challenges in biotechnology and in biochemistry is the ability to design effective enzymes. Doing so would be a convincing manifestation of a full understanding of the origin of enzyme catalysis. Despite an impressive progress, most of the advances on this front have been made by placing the reacting fragments in the proper places, rather than by optimizing the environment preorganization, which is the key factor in enzyme catalysis. Rational improvement of the preorganization would require approaches capable of evaluating reliably the actual catalytic effect. This work takes apreviously designed kemp eliminases as a benchmark for a computer aided enzyme design, using the empirical valence bond as the main screening tool. The observed absolute catalytic effect and the effect of directed evolution are reproduced and analyzed (assuming that the substrate is in the designed site). It is found that, in the case of kemp eliminases, the transition state charge distribution makes it hard to exploit the active site polarity, even with the ability to quantify the effect of different mutations. Unexpectedly, it is found that the directed evolution mutants lead to the reduction of solvation of the reactant state by water molecules rather that to the more common mode of transition state stabilization used by naturally evolved enzymes. Finally it is pointed out that our difficulties in improving Kemp eliminase are not due to overlooking exotic effect, but to the challenge in designing a preorganized environment that would exploit the small change it charge distribution during the formation of the transition state.computer aided enzyme design | empirical valence bond | directed evolution R ational enzyme design is expected to have a great potential in industrial application and eventually in medicine (1). Furthermore, the ability to design efficient enzymes might be considered as the best manifestation of a true understanding of enzyme catalysis. However, at present there has been a limited success in most attempts of rational enzyme design, and the resulting constructs have been much less effective than the corresponding natural enzymes (1). Furthermore, despite the progress in directed evolution (e.g., ref.2), we do not have unique rationales for the resulting rate enhancements.Most attempts to identify the problems with the current rational design approaches (for review, see ref. 1) have not been based on actual simulations of the given effect. In fact, it has been argued (3,4), that the problems are due to the incomplete modeling of the transition state (TS) and to the limited awareness to the key role of the reorganization energy. Even a recent attempt to use a molecular orbital-combined quantum mechanical /molecular mechanics (MO-QM/MM) approach (5) has not provided a reasonable estimate of the observed catalytic effect or the trend of the mutational effects in an artificially design enzyme. Thus, reproducing the effect of directed evolution and eventually obtaining better performance in enzyme de...

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Section: Discussionmentioning

confidence: 99%

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Frushicheva

Cao

Chu

et al. 2010

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

113

181

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“…Some examples of this include Ref. 158, that not only renamed the preorganization concept to describe something fundamentally different, but even more dangerously, incorrectly used the terminology of the original preorganization concept in doing this (see discussion in Ref. 2).…”

Section: Preorganization Is the Key Factor In Enzyme Catalysismentioning

confidence: 99%

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

Warshel

Bora

2016

The Journal of Chemical Physics

186

168

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Enzymes control chemical reactions that are key to life processes, and allow them to take place on the time scale needed for synchronization between the relevant reaction cycles. In addition to general interest in their biological roles, these proteins present a fundamental scientific puzzle, since the origin of their tremendous catalytic power is still unclear. While many different hypotheses have been put forward to rationalize this, one of the proposals that has become particularly popular in recent years is the idea that dynamical effects contribute to catalysis. Here, we present a critical review of the dynamical idea, considering all reasonable definitions of what does and does not qualify as a dynamical effect. We demonstrate that no dynamical effect (according to these definitions) has ever been experimentally shown to contribute to catalysis. Furthermore, the existence of non-negligible dynamical contributions to catalysis is not supported by consistent theoretical studies. Our review is aimed, in part, at readers with a background in chemical physics and biophysics, and illustrates that despite a substantial body of experimental effort, there has not yet been any study that consistently established a connection between an enzyme’s conformational dynamics and a significant increase in the catalytic contribution of the chemical step. We also make the point that the dynamical proposal is not a semantic issue but a well-defined scientific hypothesis with well-defined conclusions.

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confidence: 99%

“…It has been suggested that "promoting protein motions", i.e., specific fluctuations that might reduce the barrier height or promote tunneling by reducing donor-acceptor distances, can drive enzymatic reactions (1,2). Such models include promoting vibrations (3), environmentally coupled tunneling (1), and vibrationally enhanced ground-state tunneling (4). Several of these proposals suggest that the anomalous temperature and pressure dependences of experimentally observed reaction rates and kinetic isotope effects are the consequence of protein motions on the pico-to femtosecond timescale that reduce the width and/ or height of the potential energy barrier along the chemical reaction coordinate.…”

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confidence: 99%

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

Luk

Ruiz‐Pernía

Dawson

et al. 2013

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

127

262

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Protein dynamics have controversially been proposed to be at the heart of enzyme catalysis, but identification and analysis of dynamical effects in enzyme-catalyzed reactions have proved very challenging. Here, we tackle this question by comparing an enzyme with its heavy ( 15 N, 13 C, 2 H substituted) counterpart, providing a subtle probe of dynamics. The crucial hydride transfer step of the reaction (the chemical step) occurs more slowly in the heavy enzyme. A combination of experimental results, quantum mechanics/molecular mechanics simulations, and theoretical analyses identify the origins of the observed differences in reactivity. The generally slightly slower reaction in the heavy enzyme reflects differences in environmental coupling to the hydride transfer step. Importantly, the barrier and contribution of quantum tunneling are not affected, indicating no significant role for "promoting motions" in driving tunneling or modulating the barrier. The chemical step is slower in the heavy enzyme because protein motions coupled to the reaction coordinate are slower. The fact that the heavy enzyme is only slightly less active than its light counterpart shows that protein dynamics have a small, but measurable, effect on the chemical reaction rate.kinetics | computational chemistry | biological chemistry | biophysics | quantum biology

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A 21st century revisionist's view at a turning point in enzymology

Cited by 280 publications

References 64 publications

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

Unraveling the role of protein dynamics in dihydrofolate reductase catalysis

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