Dispelling the effects of a sorceress in enzyme catalysis

Mulholland, Adrian J.

doi:10.1073/pnas.1601276113

Cited by 6 publications

(4 citation statements)

References 14 publications

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“…The constraints that are imposed in the model introduce small imaginary frequencies in the calculations, all of them under 50 i cm −1 . Although it has been demonstrated that entropy only has a small effect on the energies of the chemical step of enzyme reactions (Senn et al, 2005 , 2009 ; Hu and Zhang, 2006 ; Lonsdale et al, 2012 ; Kazemi et al, 2016 ; Mulholland, 2016 ), its contribution must be considered in the case of a release of a gas molecule, which is relevant for the CO 2 release considered in the current study. In line with previous studies (Blomberg and Siegbahn, 2012 ; Lind and Himo, 2014 ; Sheng et al, 2015 , 2017 ), the entropy gain can be estimated as the translational entropy for the gas molecule (calculated to 11.3 kcal/mol), which is added at all steps after the transition state of CO 2 formation.…”

Section: Computational Detailsmentioning

confidence: 94%

A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism

et al. 2018

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Density functional theory calculations are used to investigate the detailed reaction mechanism of benzoylformate decarboxylase, a thiamin diphosphate (ThDP)-dependent enzyme that catalyzes the nonoxidative decarboxylation of benzoylformate yielding benzaldehyde and carbon dioxide. A large model of the active site is constructed on the basis of the X-ray structure, and it is used to characterize the involved intermediates and transition states and evaluate their energies. There is generally good agreement between the calculations and available experimental data. The roles of the various active site residues are discussed and the results are compared to mutagenesis experiments. Importantly, the calculations identify off-cycle intermediate species of the ThDP cofactor that can have implications on the kinetics of the reaction.

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Section: Computational Detailsmentioning

confidence: 94%

A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism

et al. 2018

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“…That said, vibrational entropy changes in enzymatic reactions are often found to be quite small, − provided that the reaction does not induce a large-scale conformation change in the protein, so entropic effects are frequently ignored in the QM-only approach. This is justified by the observation that many enzymatic reactions proceed via an induced-fit or “lock and key” mechanism, for which it may be reasonable to assume that the vibrational entropy is approximately constant along the reaction path and therefore Δ H alone dictates the fate of the reaction .…”

Section: Introductionmentioning

confidence: 99%

Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites

Dasgupta

Herbert

2020

J. Phys. Chem. B

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Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.

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“…Although the value of activation entropy, Δ ‡ S˚, increases in both cases, comments on this variation must be careful, even in a general base catalysis, as occurred in the enzyme deacylation. This reaction has a transitional state with a lot of spatial freedom, although the variation of entropy in the activated state depends not only on factors intrinsic to the reaction, but also the environment in which this occurs [32]. .…”

Section: Discussionmentioning

confidence: 99%

Microcalorimetric Study of Acetylcholine and Acetylthiocholine Hydrolysis by Acetylcholinesterase

Neves¹,

Silva²,

Beirão³

2017

AER

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Acetylcholinesterase (AChE) is an important enzyme responsible for the cleavage of acetylcholine. Studies of the activity of this enzyme use an artificial substrate, acetylthiocholine, because a product of its catalysis, thiocholine, readily generates a light absorbing product upon reaction with Elman's reagent 5,5'-dithiobis-(2-nitrobenzoic acid (DTNB). The hydrolysis of acetylcholine cannot be assayed with this method. The isothermal titration calorimetry can assay the hydrolysis of both substrates, without requiring additional reagents other than the enzyme and the substrate. To compare kinetic values obtained in the hydrolysis of acetylcholine (ACh) and acetylthiocholine (ATCh), with carbaryl acting as inhibitor, a calorimetric technique was used to evaluate kinetic properties of the two reactions. This method can show the hydrolysis of both substrates by the heat exchange that occurs during catalysis. In addition, it allowed the assessment of the AChE inhibition by carbaryl, a common insecticide. The results show a similarity between values obtained with both substrates, which are slightly higher for acetylcholine, the enzyme natural substrate. Enzymatic parameters values from ATCh and ACh were similar to each other and inhibitory constants using carbaryl were also similar, displaying that any approach to ACh is feasible using ATCh. The results obtained from ITC show the precision achieved by the calorimetric method.

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Dispelling the effects of a sorceress in enzyme catalysis

Cited by 6 publications

References 14 publications

A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism

A Theoretical Study of the Benzoylformate Decarboxylase Reaction Mechanism

Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites

Microcalorimetric Study of Acetylcholine and Acetylthiocholine Hydrolysis by Acetylcholinesterase

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