Electric Fields and Fast Protein Dynamics in Enzymes

Zoi, Ioanna; Antoniou, Dimitri; Schwartz, Steven D.

doi:10.1021/acs.jpclett.7b02989

Cited by 44 publications

(58 citation statements)

References 25 publications

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“…In particular, for the enzymes lactate dehydrogenase (LDH) and purine nucleoside phosphorylase (PNP), for which it has been shown that fast dynamics is part of the reaction mechanism, the electric field reaches its most favorable value in the active center for the transition state. These results seem to reconcile two theories, apparently antagonistic, which attribute the origin of the catalysis to the electrostatic preorganization or to the fast protein dynamics …”

Section: Resultssupporting

confidence: 51%

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Kemp Elimination Reaction Catalyzed by Electric Fields

et al. 2020

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The Kemp elimination reaction is the most widely used in the de novo design of new enzymes. The effect of two different kinds of electric fields in the reactions of acetate as a base with benzisoxazole and 5‐nitrobenzisoxazole as substrates have been theoretically studied. The effect of the solvent reaction field has been calculated using the SMD continuum model for several solvents; we have shown that solvents inhibit both reactions, the decrease of the reaction rate being larger as far as the dielectric constant is increased. The diminution of the reaction rate is especially remarkable between aprotic organic solvents and protic solvents as water, the electrostatic term of the hydrogen bonds being the main factor for the large inhibitory effect of water. The presence of an external electric field oriented in the direction of the charge transfer (z axis) increases it and, so, the reaction rate. In the reaction of the nitro compound, if the electric field is oriented in an orthogonal direction (x axis) the charge transfer to the NO2 group is favored and there is a subsequent increase of the reaction rate. However, this increase is smaller than the one produced by the field in the z axis. It is worthwhile mentioning that one of the main effects of external electric fields of intermediate intensity is the reorientation of the reactants. Finally, the implications of our results in the de novo design of enzymes are discussed.

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Section: Resultssupporting

confidence: 51%

“…These results seem to reconcile two theories, apparently antagonistic, which attribute the origin of the catalysis to the electrostatic preorganization or to the fast protein dynamics. [60]…”

Section: Implications In the De Novo Design Of A Kemp Eliminasementioning

confidence: 99%

Kemp Elimination Reaction Catalyzed by Electric Fields

et al. 2020

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“…Below each structure, a label of n-m is given in blue; n denotes the group number (reflecting the type of VSE probe bond and m is the number of the molecule within this group. Vibrational probe labels with superscripts are taken from the literature (a [95], b [5,96], c [96], d [5,7,25,28], e [5,13,97], f [13], g [13,26], h [14,15,98]). The corresponding performance score as VSE probe is given in purple.…”

Section: Resultsmentioning

confidence: 99%

“…Given a simplified electrostatic description of non-covalent interactions between the vibrational probe and surrounding molecules, the strength of these intermolecular interactions can be assessed by the electric field a target chemical bond feels, as revealed by the VSE [5,13]. The VSE has been extensively applied to study the non-covalent interactions in different types of chemical systems and environments including proteins/enzymes [6][7][8]10,11,[14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33], nucleic acids [34,35], ionic liquids [36,37], biological membranes [38], electrochemical interfaces/surfaces [12,[39][40][41][42][43], and polymers [3,44,45]. Recently, the range of applications has been extended to the investigation of water clusters [46,47] and molecular solids [48].…”

Section: Introductionmentioning

confidence: 99%

A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

Verma

Tao

Zou

et al. 2020

Sensors

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Over the past two decades, the vibrational Stark effect has become an important tool to measure and analyze the in situ electric field strength in various chemical environments with infrared spectroscopy. The underlying assumption of this effect is that the normal stretching mode of a target bond such as CO or CN of a reporter molecule (termed vibrational Stark effect probe) is localized and free from mass-coupling from other internal coordinates, so that its frequency shift directly reflects the influence of the vicinal electric field. However, the validity of this essential assumption has never been assessed. Given the fact that normal modes are generally delocalized because of mass-coupling, this analysis was overdue. Therefore, we carried out a comprehensive evaluation of 68 vibrational Stark effect probes and candidates to quantify the degree to which their target normal vibration of probe bond stretching is decoupled from local vibrations driven by other internal coordinates. The unique tool we used is the local mode analysis originally introduced by Konkoli and Cremer, in particular the decomposition of normal modes into local mode contributions. Based on our results, we recommend 31 polyatomic molecules with localized target bonds as ideal vibrational Stark effect probe candidates.

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“…[42] It has also been shown that, in some reactions, the fast motions lead to a configuration which is electrostatically favourable for catalysis. [43] In this work the effect of the intensity and orientation of an external electric field have been analyzed. We have found that catalysis is very sensitive to the intensity of the field, but much less to its orientation.…”

Section: Implications In the De Novo Design Of A Kemp Eliminasementioning

confidence: 99%

Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

et al. 2020

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The effect of solvent reaction fields and oriented electric fields on the Kemp elimination reaction between methylamine or imidazole and 5-nitrobenzisoxazole has been theoretically studied. The Kemp reaction is the most widely used for the design of new enzymes. Our results, using the SMD continuous model for solvents, are in quite good agreement with the experimental fact that the rate of the analogous reaction with butylamine is one order of magnitude smaller in water than in acetonitrile. In the case of external electric fields, our results show that they can increase or decrease the energy barrier depending on the magnitude and orientation of the field. A duly oriented electric field may have a notable catalytic effect on the reaction. So, external electric fields and reaction fields due to the medium can contribute to the design of new enzymes. Several factors that must be taken into account to increase the catalytic effect are discussed.

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Electric Fields and Fast Protein Dynamics in Enzymes

Cited by 44 publications

References 25 publications

Kemp Elimination Reaction Catalyzed by Electric Fields

Kemp Elimination Reaction Catalyzed by Electric Fields

A Critical Evaluation of Vibrational Stark Effect (VSE) Probes with the Local Vibrational Mode Theory

Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

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