Theoretical investigation of Q A −· -ligand interactions in bacterial reaction centers ofRhodobacter sphaeroides

Fritscher, Jörg; Prisner, Thomas F.; MacMillan, Fraser

doi:10.1007/bf03166200

Cited by 12 publications

(21 citation statements)

References 67 publications

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“…More recent DFT calculations of the Q A -site SQ in bacterial reaction centers report the hyperfine tensors (Table 2) for N δ of His-M219 and N p of Ala-M260 without any discussion of the values obtained or of the mechanism of spin density transfer 33. One can note, however, that the calculated isotropic and anisotropic components give high p / s ratios 3.13–3.55 for N δ of His-M219 and 6.61–7.92 for N p of Ala-M260.…”

Section: Discussionmentioning

confidence: 99%

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Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Q_B Site of Bacterial Reaction Centers

et al. 2010

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Photosynthetic reaction centers from Rhodobacter sphaeroides have identical ubiquinone-10 molecules functioning as primary (QA) and secondary (QB) electron acceptors. X-band 2D pulsed EPR spectroscopy, called HYSCORE, was applied to study the interaction of the QB site semiquinone with nitrogens from the local protein environment in natural and 15N uniformly labeled reactions centers. 14N and 15N HYSCORE spectra of the QB semiquinone show the interaction with two nitrogens carrying transferred unpaired spin density. Quadrupole coupling constants estimated from 14N HYSCORE spectra indicate them to be a protonated nitrogen of an imidazole residue and amide nitrogen of a peptide group. 15N HYSCORE spectra allowed estimation of the isotropic and anisotropic couplings with these nitrogens. From these data, we calculated the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen, and analyzed the contribution of different factors to the anisotropic hyperfine tensors. The hyperfine coupling of other protein nitrogens with the semiquinone is weak (<0.1 MHz). These results clearly indicate that the QB semiquinone forms hydrogen bonds with two nitrogens, and provide quantitative characteristics of the hyperfine couplings with these nitrogens, which can be used in theoretical modeling of the QB site. Based on the quadrupole coupling constant, one nitrogen can only be assigned to Nδ of His-L190, consistent with all existing structures. However, we cannot specify between two candidates the residue corresponding to the second nitrogen. Further work employing multifrequency spectroscopic approaches or selective isotope labeling would be desirable for unambiguous assignment of this nitrogen.

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Section: Discussionmentioning

confidence: 99%

“…al. 6 and values of 2.66 and 2.84 Å for N δ …O 4 and N p …O 1 distances in an optimized structure (in contrast to 2.91 and 2.83 Å read from the crystal structure) 33. Smaller values of 2.69 and 2.77–2.81 Å for N δ …O 4 and N p …O 1 distances were also used in other computational work 35.…”

Section: Discussionmentioning

confidence: 99%

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Q_B Site of Bacterial Reaction Centers

et al. 2010

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“…Hybrid density functional calculations for an imidazole H-bonded to a phenol radical suggest that spin polarization through the H-bonded proton transfers spin density to the interacting nitrogen nucleus from the spin density present on the O atom (58). The recent calculations report the isotropic hyperfine couplings 2.15 MHz (55) and ϳ2.5 MHz (56) for N ␦ of His M219 of the Q A Ϫ state but do not provide any discussion of the values or of the mechanism of spin density transfer. In addition, the results by Fritscher et al (56) have excluded possible assignment of the double-quantum peak in the three-pulse 14 N ESEEM spectra to N ␦ of His M219 (59).…”

Section: The Characteristics Of H-bonded Imidazole Nitrogen-the Nqi Cmentioning

confidence: 99%

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Qi-site of the bc1 Complex

Dikanov

Holland

Endeward

et al. 2007

Journal of Biological Chemistry

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The ubisemiquinone stabilized at the Q i -site of the bc 1 complex of Rhodobacter sphaeroides forms a hydrogen bond with a nitrogen from the local protein environment, tentatively identified as ring N from His-217. The interactions of 14 N and 15 N have been studied by X-band (ϳ9.7 GHz) and S-band (3.4 GHz) pulsed EPR spectroscopy. The application of S-band spectroscopy has allowed us to determine the complete nuclear quadrupole tensor of the 14 N involved in H-bond formation and to assign it unambiguously to the N ⑀ of His-217. This tensor has distinct characteristics in comparison with H-bonds between semiquinones and N ␦ in other quinone-processing sites. The experiments with 15 N showed that the N ⑀ of His-217 was the only nitrogen carrying any considerable unpaired spin density in the ubiquinone environment, and allowed calculation of the isotropic and anisotropic couplings with the N ⑀ of His-217. From these data, we could estimate the unpaired spin density transferred onto 2s and 2p orbitals of nitrogen and the distance from the nitrogen to the carbonyl oxygen of 2.38 ؎ 0.13 Å . The hyperfine coupling of other protein nitrogens with semiquinone is <0.1 MHz. This did not exclude the nitrogen of the Asn-221 as a possible hydrogen bond donor to the methoxy oxygen of the semiquinone. A mechanistic role for this residue is supported by kinetic experiments with mutant strains N221T, N221H, N221I, N221S, N221P, and N221D, all of which showed some inhibition but retained partial turnover.The bc 1 complex (ubihydroquinone:cytochrome c oxidoreductase, or complex III of the mitochondrial respiratory chain) functions to oxidize ubihydroquinone (QH 2 , 4 quinol) in the membrane and reduce cytochrome c (or cytochrome c 2 in bacteria) in the aqueous phase, using the redox work to transport 2H ϩ per electron across the membrane (1-4). In the photosynthetic bacterium Rhodobacter sphaeroides, the bc 1 complex completes the photosynthetic chain containing the photochemical reaction center, which provides the substrates for the complex following photoactivation (5, 6). The Q-cycle mechanism is a well tested model to account for the function of the bc 1 complex (7-9), but several details are still controversial. The Q-cycle involves separate catalytic sites on opposite sides of the membrane for oxidation of QH 2 and reduction of ubiquinone (Q, quinone). The work function is provided by a bifurcation of electron transfer at the quinol-oxidizing site (the Q osite). The first electron is transferred to a high potential chain (the Rieske iron-sulfur protein, cytochrome c 1 , and cytochrome c), and the second to a low potential chain, consisting of heme b L and heme b H in cytochrome b, which delivers electrons to the quinone reduction site (Q i -site). Some of the work from the first electron transfer is stored in the strong reducing potential of an unstable semiquinone intermediate formed at the Q o -site. This provides the driving force for reduction of Q, or of ubisemiquinone (SQ), in the Q i -site, and for generation of the p...

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“…This may reflect a similar mechanism of spin density transfer onto these nuclei. In both systems, it is likely that the presence and the redox state of the nearby heme (b D in NarGHI, b H in the bc 1 complex) plays a significant role in this mechanism of spin density transfer, as the heme is coordinated by a histidine ligand that interacts with the semiquinone formed in the Q site (49 Further, systematical theoretical investigations of the influence of the hydrogen bond length r O-N and of an in-or out-ofplane distortion of the bond geometry on the semiquinonenitrogen hyperfine coupling constants would be useful to get a deeper insight into the mechanism of spin density transfer onto the histidine nitrogens coupled to Q i . and to MSQ D .…”

Section: Characteristics Of the Interaction And Assignment Of The Intmentioning

confidence: 99%

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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Theoretical investigation of Q A −· -ligand interactions in bacterial reaction centers ofRhodobacter sphaeroides

Cited by 12 publications

References 67 publications

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Q_B Site of Bacterial Reaction Centers

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Q_B Site of Bacterial Reaction Centers

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Qi-site of the bc1 Complex

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

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Theoretical investigation of Q A −· -ligand interactions in bacterial reaction centers ofRhodobacter sphaeroides

Cited by 12 publications

References 67 publications

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the QB Site of Bacterial Reaction Centers

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the QB Site of Bacterial Reaction Centers

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Qi-site of the bc1 Complex

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

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Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Q_B Site of Bacterial Reaction Centers

Hydrogen Bonds between Nitrogen Donors and the Semiquinone in the Q_B Site of Bacterial Reaction Centers