Transition State in DNA Polymerase β Catalysis: Rate-Limiting Chemistry Altered by Base-Pair Configuration

Oertell, Keriann; Chamberlain, Brian T.; Wu, Yue; Ferri, Elena; Kashemirov, B. A.; Beard, William A.; Wilson, Samuel H.; McKenna, Charles E.; Goodman, Myron F.

doi:10.1021/bi500101z

Cited by 27 publications

(110 citation statements)

References 48 publications

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“…2−5 These compounds were shown to bind to pol β and to alter the reactant and TS properties for the nucleotide-transfer reaction.…”

Section: Resultsmentioning

confidence: 99%

“…5 The correlation coefficients are R = 0.93 and 0.87 for the doubly protonated (black circle, slope −0.00423) and unprotonated triphosphates (blue square, slope −0.00338), respectively. The green triangle is for the parent O compound in the dianion system that was not included in the linear fit line for unprotonated triphosphates.…”

Section: Resultsmentioning

confidence: 99%

“…Atoms bound to the chiral center (bridging C) are ordered with the lowest atomic number atom pointing away and the remaining atoms from P β to P γ to the remaining substitutent are ordered clockwise in the R -form. This means that when looking from P β to bridging C to P γ , the heavier substituent is on the left in the R -form.cReference (5). …”

Section: Resultsmentioning

confidence: 99%

“…2−5 These experiments initially showed that the rate constant of the enzymatic reaction is directly proportional to the equilibrium constant for the protonation of PP i or its bisphosphonate analogues and that the slope (β lg ) of this linear free energy relationship (LFER) differs between the right and wrong dNTP substrates. 2 Later, a structurally broader range of substituents showed a clearly separate LFER for the insertion of a wrong dNTP with mono- and dihalogenated β–γ bridging substituents.…”

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confidence: 99%

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Quantum Mechanical Analysis of Nonenzymatic Nucleotidyl Transfer Reactions: Kinetic and Thermodynamic Effects of β–γ Bridging Groups of dNTP Substrates

2014

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Rate (k) and equilibrium (K) constants for the reaction of tetrahydrofuranol with a series of Mg2+ complexes of methyl triphosphate analogues, CH3O-P(O2)-O-P(O2)-X-PO34–, X = O, CH2, CHCH3, C(CH3)2, CFCH3, CHF, CHCl, CHBr, CFCl, CF2, CCl2, and CBr2, forming phosphate diester and pyrophosphate or bisphosphonate in aqueous solution were evaluated by B3LYP/TZVP//HF/6-31G* quantum chemical calculations and Langevin dipoles and polarized continuum solvation models. The calculated log k and log K values were found to depend linearly on the experimental pKa4 of the conjugate acid of the corresponding pyrophosphate or bisphosphonate leaving group. The calculated slopes of these Brønsted linear free energy relationships were βlg = −0.89 and βeq = −0.93, respectively. The studied compounds also followed the linear relationship Δlog k = 0.8Δlog K, which became less steep, Δlog k = 0.6Δlog K, after the range of studied compounds was extended to include analogues that were doubly protonated on γ-phosphate, CH3O-P(O2)-O-P(O2)-X-PO3H22–. The scissile Pα–Olg bond length in studied methyl triphosphate analogues slightly increases with decreasing pKa of the leaving group; concomitantly, the CH3OPα(O2) moiety becomes more positive. These structural effects indicate that substituents with low pKa can facilitate both Pα–Olg bond breaking and the Pα–Onuc bond forming process, thus explaining the large negative βlg calculated for the transition state geometry that has significantly longer Pα–Onuc distance than the Pα–Olg distance.

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“…2−5 These compounds were shown to bind to pol β and to alter the reactant and TS properties for the nucleotide-transfer reaction.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Quantum Mechanical Analysis of Nonenzymatic Nucleotidyl Transfer Reactions: Kinetic and Thermodynamic Effects of β–γ Bridging Groups of dNTP Substrates

2014

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“…The more positive Pα with M g present would facilitate the attack of O3′ anion at Pα (dNTP). The additional negative charge at the bridging oxygen between Pα and Pβ promotes bond breakage and the subsequent protonation of PP i which is rate limiting [24]. The role of the M g binding site during catalysis with natural unmodified nucleotides is currently being investigated.…”

Section: Nucleotide Insertionmentioning

confidence: 99%

New structural snapshots provide molecular insights into the mechanism of high fidelity DNA synthesis

2015

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Time-lapse X-ray crystallography allows visualization of intermediate structures during the DNA polymerase catalytic cycle. Employing time-lapse crystallography with human DNA polymerase β has recently allowed us to capture and solve novel intermediate structures that are not stable enough to be analyzed by traditional crystallography. The structures of these intermediates reveal exciting surprises about active site metal ions and enzyme conformational changes as the reaction proceeds from the ground state to product release. In this perspective, we provide an overview of recent advances in understanding the DNA polymerase nucleotidyl transferase reaction and highlight both the significance and mysteries of enzyme efficiency and specificity that remain to be solved.

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Recent Advances in Synthesis of Difluoromethylene Phosphonates for Biological Applications

et al. 2021

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For almost 40 years, difluoromethylene phosphonates have proven to be versatile molecular tools in biochemical studies owing to their close resemblance to naturally occurring phosphates and phosphonates. As bioisosteric, non‐hydrolyzable analogs of these essential molecules, difluoromethylene phosphonates can target the critical parts of the cellular machinery and therefore exhibit a diverse spectrum of biological activity. In the past ten years, there have appeared many new methods for the synthesis of difluoromethylene phosphonates. Most notably, photoredox catalysis has firmly entered the field, while cross‐coupling and nucleophilic strategies have met considerable elaboration and refinement, entirely in accord with the current trends in synthetic organic chemistry. Herein, we introduce difluoromethylene phosphonates as a distinct, high‐tech subclass of synthetic phosphonates resulting from the research efforts on the cross‐section of organophosphorus, organofluorine, and bioorganic chemistry. We then proceed to the discussion of general methods for the preparation of difluoromethylene phosphonates, comprehensively reviewing reactions developed in the past 15 years while providing the context of earlier works where appropriate. Finally, we present selected examples of molecules with high biological activity, their biological targets, and the synthetic steps employed for their preparation.

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Transition State in DNA Polymerase β Catalysis: Rate-Limiting Chemistry Altered by Base-Pair Configuration

Cited by 27 publications

References 48 publications

Quantum Mechanical Analysis of Nonenzymatic Nucleotidyl Transfer Reactions: Kinetic and Thermodynamic Effects of β–γ Bridging Groups of dNTP Substrates

Quantum Mechanical Analysis of Nonenzymatic Nucleotidyl Transfer Reactions: Kinetic and Thermodynamic Effects of β–γ Bridging Groups of dNTP Substrates

New structural snapshots provide molecular insights into the mechanism of high fidelity DNA synthesis

Recent Advances in Synthesis of Difluoromethylene Phosphonates for Biological Applications

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