Protein dynamics and enzyme catalysis: Insights from simulations

McGeagh, John D.; Ranaghan, Kara E.; Mulholland, Adrian J.

doi:10.1016/j.bbapap.2010.12.002

Cited by 88 publications

(81 citation statements)

References 217 publications

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“…4). The popularity of this idea persists, despite extensive evidence to render it controversial (4,18,23). However, a recent work is noteworthy (6) in its assumption that the reduction in the rate constant of the presented DHFR mutants is because of the elimination of the dynamical coupling to the occluded conformation.…”

Section: Discussionmentioning

confidence: 99%

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

Adamczyk

Cao

Kamerlin

et al. 2011

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

187

189

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The proposal that enzymatic catalysis is due to conformational fluctuations has been previously promoted by means of indirect considerations. However, recent works have focused on cases where the relevant motions have components toward distinct conformational regions, whose population could be manipulated by mutations. In particular, a recent work has claimed to provide direct experimental evidence for a dynamical contribution to catalysis in dihydrofolate reductase, where blocking a relevant conformational coordinate was related to the suppression of the motion toward the occluded conformation. The present work utilizes computer simulations to elucidate the true molecular basis for the experimentally observed effect. We start by reproducing the trend in the measured change in catalysis upon mutations (which was assumed to arise as a result of a "dynamical knockout" caused by the mutations). This analysis is performed by calculating the change in the corresponding activation barriers without the need to invoke dynamical effects. We then generate the catalytic landscape of the enzyme and demonstrate that motions in the conformational space do not help drive catalysis. We also discuss the role of flexibility and conformational dynamics in catalysis, once again demonstrating that their role is negligible and that the largest contribution to catalysis arises from electrostatic preorganization. Finally, we point out that the changes in the reaction potential surface modify the reorganization free energy (which includes entropic effects), and such changes in the surface also alter the corresponding motion. However, this motion is never the reason for catalysis, but rather simply a reflection of the shape of the reaction potential surface.T he enormous catalytic power of enzymes has been attempted to be rationalized by several proposals. Here, we would like to focus on a specific proposal that appears to be gaining significant support. Namely, there exists a long-standing assumption that enzyme dynamics and flexibility are important to the chemical step of catalysis (see, e.g., refs. 1-4 and references cited therein). This hypothesis has emerged in several forms, ranging from the assumption that enzymatic catalysis can be linked to lid closures upon binding (e.g., ref. 5) to more recent studies (6, 7) that considered the effect of modifying the accessibility of conformational states separated by relatively small structural differences. It was then argued that the observed changes in the rate of the chemical step upon mutations that appear to prevent the flexibility of the active-site residues could be interpreted as evidence for a dynamical coupling to catalysis. This proposal is particularly well defined in a recent study (6) that focused on dihydrofolate reductase (DHFR). That is, ref. 6 demonstrated that the N23PP, S148A, and N23PP/S148A mutants of DHFR have more limited conformational flexibility than the WT and cannot access the occluded (OC) conformation from the closed (CL) conformation, which is available to th...

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Section: Discussionmentioning

confidence: 99%

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

Adamczyk

Cao

Kamerlin

et al. 2011

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

187

189

View full text Add to dashboard Cite

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“…Some claim that protein dynamics are essential in understanding enzymatic processes, while others state that dynamics is not an important contribution to catalysis. However computer simulations demonstrate the importance of structural fluctuations and the need to include them in the modeling of certain enzyme reactions [8,9]. In some cases, e.g., in processes with significant changes in solvation it is even impossible to correctly predict activation energies if the dynamics of the protein and its active site is not considered in the calculation.…”

Section: Modelsmentioning

confidence: 99%

Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

2013

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Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods.

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“…Only few works have challenged validity of this proposal by presenting careful computational analysis of any possible aspects of this proposal [7,13,17,[23][24][25][26] (including at present the only valid study of the dynamical role of the coupling between conformation changes and dynamics in the long time accessible to experiment studies [13]). Other theoretical studies that gradually started to support the idea that dynamics does not play significant role in catalysis have only started to appear recently [27,28]. In parallel, one proponent of the dynamical proposal started to tune down and to modify their proposal (e.g.…”

Section: The Role Of Enzyme Dynamicsmentioning

confidence: 99%

Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

et al. 2012

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In the preceding article, ''Perspective: Prechemistry conformational changes in DNA polymerase mechanisms'' contributed by Schlick and coworkers as well as previous studies of these workers (Schlick et al. in Theor Chem Acc 131:1287 [5970][5971][5972][5973][5974][5975] 2004) have argued that the conformational changes preceding the chemical step contribute to DNA synthesis and to the fidelity of DNA polymerases. In one of our previous investigations (Ram Prasad and Warshel in Proteins 79:2900-2919, 2011), we argued and showed that as long as the free energy barriers associated with any of the prechemistry steps are not rate limiting, they could not contribute to the catalysis and then to the fidelity. Though all our arguments are based on exact and well-defined scientific logics, Schlick and coworkers seem to overlook some of the clear conditions in these arguments and in particular the requirement that the chemical step is rate limiting in their arguments that the prechemistry barriers contribute to the catalysis. In fact, as long as the prechemistry steps are not rate limiting, we have shown that the enzymes cannot carry the memory of the previous steps. We also address other potential misunderstandings about several key issues; First, we clarify that it is misleading to relate the prechemistry proposal to the clear fact that the substrate-induced conformational changes determine the final preorganization (the issue is the height of the barrier of the enzyme substrate system and not the trivial fact that the enzyme has to change its structure when the substrate binds). Second, we address the presumed role of dynamical effects in enzyme catalysis and the assumption that any observable should be explored in studies of biological function even if they are not relevant to the given effect. Third, we clarify that the fidelity cannot be explained or quantified by invoking the induced fit or conformational selection effects but by evaluating the free energy contributions to the rate-limiting steps from the structures of the corresponding systems (that of course can reflect the induce fit structural changes). Overall, we put a major emphasis on clarifying what is the prechemistry proposal and thus on trying to force the reader to focus on the only real controversy. We of course dismiss any implication that our studies cannot explore mutational effects as we actually pioneered such computational studies and we clarify that in studies of chemical rates, the focus Editor's Note: This paper and papers by Mulholland AJ, Roitberg AE, Tuñón I (doi:10.1007/s00214-012-1286 and Schlick T, Arora K, Beard WA, Wilson SH (doi:10.1007/s00214-012-1287-7) document and discuss contrasting outlooks on the questions of prechemistry and catalysis in DNA polymerase. All authors were initially provided with one another's manuscripts, at which point opportunities to make revisions were offered, and finally, Mulholland, Roitberg, and Tuñón were given the 'last word' on the revised manuscripts in their role as commentators. The e...

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Protein dynamics and enzyme catalysis: Insights from simulations

Cited by 88 publications

References 217 publications

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

Catalysis by dihydrofolate reductase and other enzymes arises from electrostatic preorganization, not conformational motions

Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions

Prechemistry barriers and checkpoints do not contribute to fidelity and catalysis as long as they are not rate limiting

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