Influence of hydrogen bond geometry on quadrupole coupling parameters: A theoretical study of imidazole–water and imidazole–semiquinone complexes

Fritscher, Jörg

doi:10.1039/b408764j

Cited by 30 publications

(46 citation statements)

References 47 publications

(58 reference statements)

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“…Based on the measurement of its nuclear quadrupole parameters by S-band HYSCORE spectroscopy ( ϭ 0.49, ϭ 0.50), this nucleus was assigned to the N ␦ imidazole nitrogen from the heme b D axial ligand His-66 (13). In addition, this model is consistent with the relatively small value found for this imidazole nitrogen that is close to that predicted by density functional theory calculations on imidazoles forming a strong in-plane hydrogen bond to one of the benzosemiquinone oxygen atoms (45). Finally, the presence of the positive charges on the nearby heme Fe 2ϩ ion may also contribute to the observed asymmetrical spin distribution in MSQ D .…”

Section: Single Exchangeable Proton Coupling With Peculiar Hyperfinesupporting

confidence: 81%

Determination of the Proton Environment of High Stability Menasemiquinone Intermediate in Escherichia coli Nitrate Reductase A by Pulsed EPR

Grimaldi¹,

Arias-Cartin²,

Lanciano³

et al. 2012

Journal of Biological Chemistry

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Background: Escherichia coli nitrate reductase A highly stabilizes a semiquinone catalytic intermediate. Results:Three proton hyperfine couplings to this radical with atypical characteristics are characterized. Conclusion: Semiquinone binding is strongly asymmetric and occurs via a single short in-plane H-bond. Significance: Learning how the protein environment tunes the semiquinone properties is crucial for understanding the quinol utilization mechanism by energy-transducing enzymes.

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Section: Single Exchangeable Proton Coupling With Peculiar Hyperfinesupporting

confidence: 81%

Determination of the Proton Environment of High Stability Menasemiquinone Intermediate in Escherichia coli Nitrate Reductase A by Pulsed EPR

Grimaldi¹,

Arias-Cartin²,

Lanciano³

et al. 2012

Journal of Biological Chemistry

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“…in bacterial reaction centers (30,35,36) or in photosystem II (25,28). Interestingly, the quadrupole characteristics determined here for the 14 N nucleus interacting with MSQ D in NarGHI are very close to the values calculated by Fritscher for an imidazole making a strong in-plane hydrogen bond with a water molecule (r O-N ϳ2.7 Å) (46). Moreover, DFT calculations carried out on more realistic models of methylimidazole-benzosemiquinone complexes predict values of (, ) ϭ (0.48, 0.61) for short (i.e.…”

Section: Characteristics Of the Interaction And Assignment Of The Intsupporting

confidence: 66%

Direct Evidence for Nitrogen Ligation to the High Stability Semiquinone Intermediate in Escherichia coli Nitrate Reductase A

Grimaldi

Arias-Cartin

Lanciano

et al. 2010

Journal of Biological Chemistry

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In the absence of oxygen and in the presence of nitrate, Escherichia coli induces the production of two energy-converting enzymes: formate dehydrogenase-N (FdnGHI) and dissimilatory nitrate reductase A (NarGHI).3 These two complexes cooperate in generating a proton motive force through the redox loop mechanism as originally envisaged by Peter Mitchell in his chemiosmotic hypothesis (1). The separation of positive and negative charges across the cytoplasmic membrane is achieved through electron transfer from the formate oxidation site in the periplasm to the nitrate reduction site located on the cytoplasmic space with mena-or ubiquinone/quinol cycling between them (2, 3). The heterotrimeric NarGHI complex is composed of (i) a nitrate-reducing subunit NarG containing a Mo-bis-MGD cofactor (Moco) and a [4Fe-4S] cluster FeS0 with unusual His coordination (4, 5), (ii) an electron transfer subunit NarH carrying four FeS clusters (6), and (iii) a membrane anchor subunit NarI containing two b-type hemes termed b D and b P to indicate their distal and proximal positions with respect to the nitratereducing site (7-9). These prosthetic groups define an electron transfer pathway from a periplasmically oriented quinol oxidation site (Q D ) to a cytoplasmically oriented nitrate reduction site.Although considerable research has been devoted to nitrate reductase functioning, only partial information has been gained about the number, the structure, and the specificity of quinol binding sites within NarGHI. For instance, some studies have reported on mena-and ubiquinol analogue binding (10 -20), whereas the molecular details of the interaction between natural quinols and NarGHI remain to be established.Despite the absence of bound quinones in the available high resolution structures of NarGHI (7,20), the crystal structure of the enzyme in complex with pentachlorophenol (PCP), an inhibitor of the quinol oxidase activity, has been determined (20). Based on mutagenesis data, biochemical analyses, and molecular modeling, a model of the Q D quinol binding site has been proposed (20). In this working model, a quinone carbonyl group interacts with the protein via a hydrogen bond to a histidine residue (His-66), which is one of the axial ligands of heme b D . Molecular modeling of a menaquinone in the PCP binding site suggested that the opposite carbonyl group could form a hydrogen bond to . Additionally, an elongated

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“…This tendency was already reported by Fritscherand co-workers. [58] One can notice that the out-of-plane angle has also as ignificant effect on the 14 Nh yperfine coupling constant (comparem odels 1a nd 4). Similarc onclusions can be drawn for the 1 …”

Section: à4mentioning

confidence: 99%

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective ²H and ¹⁵N Labeling, HYSCORE Spectroscopy, and DFT Modeling

et al. 2017

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In vivo specific isotope labeling at the residue or substituent level is used to probe menasemiquinone (MSK) binding to the quinol oxidation site of respiratory nitrate reductase A (NarGHI) from E. coli. 15N selective labeling of His15Nδ or Lys15Nζ in combination with hyperfine sublevel correlation (HYSCORE) spectroscopy unambiguously identified His15Nδ as the direct hydrogen‐bond donor to the radical. In contrast, an essentially anisotropic coupling to Lys15Nζ consistent with a through‐space magnetic interaction was resolved. This suggests that MSK does not form a hydrogen bond with the side chain of the nearby Lys86 residue. In addition, selective 2H labeling of the menaquinone methyl ring substituent allows unambiguous characterization of the 2H—and hence of the 1H—methyl isotropic hyperfine coupling by 2H HYSCORE. DFT calculations show that a simple molecular model consisting of an imidazole Nδ atom in a hydrogen‐bond interaction with a MSK radical anion satisfactorily accounts for the available spectroscopic data. These results support our previously proposed one‐sided binding model for MSK to NarGHI through a single short hydrogen bond to the Nδ of His66, one of the distal heme axial ligands. This work establishes the basis for future investigations aimed at determining the functional relevance of this peculiar binding mode.

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Influence of hydrogen bond geometry on quadrupole coupling parameters: A theoretical study of imidazole–water and imidazole–semiquinone complexes

Cited by 30 publications

References 47 publications

Determination of the Proton Environment of High Stability Menasemiquinone Intermediate in Escherichia coli Nitrate Reductase A by Pulsed EPR

Determination of the Proton Environment of High Stability Menasemiquinone Intermediate in Escherichia coli Nitrate Reductase A by Pulsed EPR

Direct Evidence for Nitrogen Ligation to the High Stability Semiquinone Intermediate in Escherichia coli Nitrate Reductase A

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective ²H and ¹⁵N Labeling, HYSCORE Spectroscopy, and DFT Modeling

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Influence of hydrogen bond geometry on quadrupole coupling parameters: A theoretical study of imidazole–water and imidazole–semiquinone complexes

Cited by 30 publications

References 47 publications

Determination of the Proton Environment of High Stability Menasemiquinone Intermediate in Escherichia coli Nitrate Reductase A by Pulsed EPR

Determination of the Proton Environment of High Stability Menasemiquinone Intermediate in Escherichia coli Nitrate Reductase A by Pulsed EPR

Direct Evidence for Nitrogen Ligation to the High Stability Semiquinone Intermediate in Escherichia coli Nitrate Reductase A

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective 2H and 15N Labeling, HYSCORE Spectroscopy, and DFT Modeling

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Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective ²H and ¹⁵N Labeling, HYSCORE Spectroscopy, and DFT Modeling