The Effect of Electrostatic Shielding on H Tunneling in R67 Dihydrofolate Reductase

Yahashiri, Atsushi; Nimrod, Guy; Ben‐Tal, Nir; Howell, Elizabeth E.; Kohen, Amnon

doi:10.1002/cbic.200900451

Cited by 8 publications

(10 citation statements)

References 22 publications

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“…The quantum corrected ratios of phenomenological rates were computed, and using these ratios, H/D KIEs are plotted in Figure 1C. The temperaturedependent KIEs for R67 DHFR in this work are in good agreement with the experimentally obtained trend 87,88 although the values are slightly underestimated from the calculations (Figure 1D). As a comparison, we also compute the gas-phase KIEs within the standard harmonic approximation (no tunneling correction) for the hydride transfer between the reacting fragments CH 3 -H 2 nic and 6-CH 3 -H 3 pterin + .…”

Section: ■ Results and Discussionsupporting

confidence: 79%

“…Experimental studies on the primitive R67 DHFR revealed temperature-dependent KIEs. These studies suggested that the primitive enzyme is poorly preorganized and requires significant gating of its DAD prior to the reaction, resulting in significant temperature dependence. , The advantage of studying R67 DHFR is its simple kinetic scheme, with measured KIEs that are nearly free of kinetic complexity.…”

Section: Introductionmentioning

confidence: 99%

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Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations

Mhashal

Major

2021

J. Phys. Chem. B

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Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics–molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.

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Section: ■ Results and Discussionsupporting

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations

Mhashal

Major

2021

J. Phys. Chem. B

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“…In the earlier paper [24] reported is an enhancement in the rate of hydride transfer in a plasmid encoded dihydrofolate reductase R67 DHFR with increasing ionic strength. The findings are explained [25] in terms of effect of electrostatic shielding on hydrogen tunneling in the R67 dihydrofolate reductase where, at higher ionic strength, the donor and acceptor of the hydride were better oriented for hydrogen tunneling than the same system at lower ionic strength. To the best of our knowledge, there is no report on the issue related to solution chemistry.…”

mentioning

confidence: 83%

“…The question could be of relevance for other systems, among others the PCET systems in protein environment. There are only few reports on the matter related to an enzyme system [24] [25]. In the earlier paper [24] reported is an enhancement in the rate of hydride transfer in a plasmid encoded dihydrofolate reductase R67 DHFR with increasing ionic strength.…”

mentioning

confidence: 97%

Ions Can Move a Proton‐Coupled Electron‐Transfer Reaction into Tunneling Regime

Brala

Pilepić

Sajenko

et al. 2011

Helvetica Chimica Acta

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The effects of charged species on proton-coupled electron-transfer (PCET) reaction should be of significance for understanding/application of important chemical and biological PCET systems. Such species can be found in proximity of activated complex in a PCET reaction, although they are not involved in the charge transfer process. Reported here is the first study of the above-mentioned effects. Here, the effects of Na , 5.5 (0.9) (at 0.001m Ca 2þ ), and 7.9 (2.8) (at 0.001m Mg 2þ ) kJ mol À1 ; e) nonlinear proton inventory in reaction. In the H 2 O/dioxane 1 : 1, the observed KIE is 7.8 and 4.4 in the absence and in the presence of 0.1m K þ , respectively, and A H /A D ¼ 0.14 (0.03). The changes when cations are present in the reaction are explained in terms of termolecular encounter complex consisting of redox partners, and the cation where the cation can be found in a near proximity of the reaction-activated complex thus influencing the proton/electron double tunneling event in the PCET process. A molecule of H 2 O is involved in the transition state. The resulting configuration is more rigid and more appropriate for efficient tunneling with Na þ or K þ (extensive tunneling observed), i.e., there is more precise organized H transfer coordinate than in the case of Ca 2þ and Mg 2þ (moderate tunneling observed) in the reaction.Introduction. -Proton-coupled electron-transfer (PCET) reactions are of crucial importance in a wide range of biological, biochemical, and chemical systems [1 -16], including those related to artificial photosynthesis and solar fuels [4 -8], and nanostructures and interfaces [14] [15]. It is recognized now that many processes in biology would not be possible without the coupling of proton and electron motion [3] [5]. Within a unified theoretical framework, both sequential electron transfer, followed by proton transfer (ET/PT) or vice versa (PT/ET), and the concerted transfer of these particles with conspicuous quantum-mechanical character could be viewed as PCET reactions [16]. However, the concerted transfer of a proton and an electron should be of central importance in the issue; here, the single chemical reaction step and

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“…129 A primitive, bacterial plasmid encoded DHFR has been characterized 132 and shows temperature-dependent kinetic isotope effects, consistent with the idea that the temperature-independent kinetic isotope effects seen in native enzymes are characteristic of highly evolved enzymes. 133,134 …”

Section: Dihydrofolate Reductasesmentioning

confidence: 99%