Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase; comparisons with methane monooxygenase

Lovell, Timothy; Li, Jian; Noodleman, Louis

doi:10.1007/s00775-002-0358-y

Cited by 16 publications

(23 citation statements)

References 47 publications

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“…b E. coli 1RIB structure from PDB from ref a. c Reduced model from ref . d E. coli 1XIK structure from the PDB from ref b.…”

Section: Resultsmentioning

confidence: 99%

“…After verification that a linear relationship exists between experimental isomer shifts and the calculated nuclear densities and that there is a close correspondence between calculated and observed quadrupole splittings as well for the synthetic systems of the training set, the reliability of our predictive methodology as applied to proteins is gauged. Calculated isomer shifts and quadrupole splitting parameters for the structurally characterized oxidized and reduced protein active sites of MMO and RNR are compared and contrasted with those values experimentally determined. In doing so, the accuracy of existing X-ray data for oxidized and reduced MMO and RNR is assessed in a qualitative manner by comparison both with DFT geometry optimized structures and spectroscopic indicators of active site structure.…”

Section: Introductionmentioning

confidence: 99%

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DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron−Oxo Complexes: Applications to Methane Monooxygenase and Ribonucleotide Reductase

et al. 2003

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To predict isomer shifts and quadrupole splitting parameters of Fe atoms in the protein active sites of methane monooxygenase and ribonucleotide reductase, a correlation between experimental isomer shifts ranging 0.1-1.5 mm s(-)(1) for Fe atoms in a training set with the corresponding density functional theory (DFT) calculated electron densities at the Fe nuclei in those complexes is established. The geometries of the species in the training set, consisting of synthetic polar monomeric and dimeric iron complexes, are taken from the Cambridge structural database. A comparison of calculated Mössbauer parameters for Fe atoms from complexes in the training set with their corresponding experimental values shows very good agreement (standard deviation of 0.11 mm/s, correlation coefficient of -0.94). However, for the Fe atoms in the active sites of the structurally characterized proteins of methane monooxygenase and ribonucleotide reductase, the calculated Mössbauer parameters deviate more from their experimentally measured values. The high correlation that exists between calculated and observed quadrupole splitting and isomer shift parameters for the synthetic complexes leads us to conclude that the main source of the error arising for the protein active sites is due to the differing degrees of atomic-level resolution for the protein structural data, compared to the synthetic complexes in the training set. Much lower X-ray resolutions associated with the former introduce uncertainty in the accuracy of several bond lengths. This is ultimately reflected in the calculated isomer shifts and quadrupole splitting parameters of the Fe sites in the proteins. For the proteins, the closest correspondence between predicted and observed Mössbauer isomer shifts follows the order MMOH(red), RNR(red), MMOH(ox), and RNR(ox), with average deviations from experiment of 0.17, 0.17, 0.17-0.20, and 0.32 mm/s, but this requires DFT geometry optimization of the iron-oxo dimer complexes.

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“…b E. coli 1RIB structure from PDB from ref a. c Reduced model from ref . d E. coli 1XIK structure from the PDB from ref b.…”

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron−Oxo Complexes: Applications to Methane Monooxygenase and Ribonucleotide Reductase

et al. 2003

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“…The similarities in coordinating residues in RR, MMO, and ∆9D do not extend to the second coordination sphere, with the hydrogen-bonding residues that orient the coordinating residues in specific geometries differing between these three proteins. 8,11,12 Thus, while the general structural motif of the diiron active site is preserved, the relative energetics of different oxygen intermediate structures may vary between these enzymes.…”

Section: Introductionmentioning

confidence: 99%

Nature of the Peroxo Intermediate of the W48F/D84E Ribonucleotide Reductase Variant: Implications for O₂ Activation by Binuclear Non-Heme Iron Enzymes

et al. 2004

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Analysis of the spectroscopic signatures of the R2-W48F/D84E biferric peroxo intermediate identifies a cis mu-1,2 peroxo coordination geometry. DFT geometry optimizations on both R2-W48F/D84E and R2-wild-type peroxo intermediate models including constraints imposed by the protein also identify the cis mu-1,2 peroxo geometry as the most stable peroxo intermediate structure. This study provides significant insight into the electronic structure and reactivity of the R2-W48F/D84E peroxo intermediate, structurally related cis mu-1,2 peroxo model complexes, and other enzymatic biferric peroxo intermediates.

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“…In contrast to the wealth of experimental studies, few theoretical studies have focused on the structure and spin states of the RNR active site. − One model of intermediate X has been examined in detail by Siegbahn, which contains (see Figure 6 in ref ) one μ-oxo bridge, one hydroxo bridge, and two bidentate carboxylates from Glu115 and Glu238. Following geometry optimization of this S total = 1/2 model using the B3LYP density functional theory (DFT) approach, an Fe−Fe distance of 2.61 Å was obtained.…”

Section: Introductionmentioning

confidence: 99%

A Density Functional Evaluation of an Fe(III)−Fe(IV) Model Diiron Cluster: Comparisons with Ribonucleotide Reductase Intermediate X

et al. 2003

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Using broken-symmetry density functional theory and spin-projection methods, we have examined the electronic structure and properties of a large mixed-valent Fe(III)-Fe(IV) diiron system that displays two bidentate carboxylates and a single mu-oxo moiety as bridging ligands. Two carboxylates and a single oxygen species have long been implicated as core elements of the elusive intermediate X in ribonucleotide reductase. Spectroscopic studies of X have also identified the presence of an additional terminal or bridging oxygen-based ligand. Introduction of a second oxygen and protonated variants thereof in the core of our structural model is favored as a bridging hydroxide based on the lowest energy structure. Mössbauer measurements indicate clearly that the two iron sites of X are distinct and that there is significant electron delocalization onto the oxygen-based ligands. For several examined spin states of our model cluster, Mössbauer parameters from density functional calculations are neither able to differentiate between the iron sites nor reproduce the strong spin delocalization onto the oxygen-based ligands observed experimentally. The combined comparison of the calculated geometries, spin states, spin densities, and Mössbauer properties for our model clusters with available experimental data for X implies that intermediate X is significantly different from the diiron structural models examined herein.

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Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase; comparisons with methane monooxygenase

Cited by 16 publications

References 47 publications

DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron−Oxo Complexes: Applications to Methane Monooxygenase and Ribonucleotide Reductase

DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron−Oxo Complexes: Applications to Methane Monooxygenase and Ribonucleotide Reductase

Nature of the Peroxo Intermediate of the W48F/D84E Ribonucleotide Reductase Variant: Implications for O₂ Activation by Binuclear Non-Heme Iron Enzymes

A Density Functional Evaluation of an Fe(III)−Fe(IV) Model Diiron Cluster: Comparisons with Ribonucleotide Reductase Intermediate X

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Density functional and electrostatics study of oxidized and reduced ribonucleotide reductase; comparisons with methane monooxygenase

Cited by 16 publications

References 47 publications

DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron−Oxo Complexes: Applications to Methane Monooxygenase and Ribonucleotide Reductase

DFT Calculations of Isomer Shifts and Quadrupole Splitting Parameters in Synthetic Iron−Oxo Complexes: Applications to Methane Monooxygenase and Ribonucleotide Reductase

Nature of the Peroxo Intermediate of the W48F/D84E Ribonucleotide Reductase Variant: Implications for O2 Activation by Binuclear Non-Heme Iron Enzymes

A Density Functional Evaluation of an Fe(III)−Fe(IV) Model Diiron Cluster: Comparisons with Ribonucleotide Reductase Intermediate X

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Nature of the Peroxo Intermediate of the W48F/D84E Ribonucleotide Reductase Variant: Implications for O₂ Activation by Binuclear Non-Heme Iron Enzymes