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1.
Inorg Chem ; 62(36): 14715-14726, 2023 Sep 11.
Artículo en Inglés | MEDLINE | ID: mdl-37650683

RESUMEN

Nitrogenase is a fascinating enzyme in biology that reduces dinitrogen from air to ammonia through stepwise reduction and protonation. Despite it being studied in detail by experimental and computational groups, there are still many unknown factors in the catalytic cycle of nitrogenase, especially related to the addition of protons and electrons and their order. A recent biomimetic study characterized a potential dinitrogen-bridged diiron cluster as a synthetic model of nitrogenase. Using strong acid and reductants, the dinitrogen was converted into ammonia molecules, but details of the mechanism remains unknown. In particular, it was unclear from the experimental studies whether the proton and electron transfer steps are sequential or alternating. Moreover, the work failed to establish what the function of the diiron core is and whether it split into mononuclear iron fragments during the reaction. To understand the structure and reactivity of the biomimetic dinitrogen-bridged diiron complex [(P2P'PhFeH)2(µ-N2)] with triphenylphosphine ligands, we performed a density functional theory study. Our computational methods were validated against experimental crystal structure coordinates, Mössbauer parameters, and vibrational frequencies and show excellent agreement. Subsequently, we investigated the alternating and consecutive addition of electrons and protons to the system. The calculations identify a number of possible reaction channels, namely, same-site protonation, alternating protonation, and complex dissociation into mononuclear iron centers. The calculations show that the overall mechanism is not a pure sequential set of electron and proton transfers but a mixture of alternating and consecutive steps. In particular, the first reaction steps will start with double proton transfer followed by an electron transfer, while thereafter, there is another proton transfer and a second electron transfer to give a complex whereby ammonia can split off with a low energetic barrier. The second channel starts with alternating protonation of the two nitrogen atoms, whereafter the initial double proton transfer, electrons and protons are added sequentially to form a hydrazine-bound complex. The latter split off ammonia spontaneously after further protonation. The various reaction channels are analyzed with valence bond and orbital diagrams. We anticipate the nitrogenase enzyme to operate with mixed alternating and consecutive protonation and electron transfer steps.


Asunto(s)
Amoníaco , Protones , Hierro , Nitrógeno , Nitrogenasa
2.
Inorg Chem ; 62(40): 16401-16411, 2023 Oct 09.
Artículo en Inglés | MEDLINE | ID: mdl-37756478

RESUMEN

[MFe3S4] cubanes have for some time been of interest for their ability to mimic the electronic and geometric structure of the active site of nitrogenase, the enzyme responsible for fixing N2 to NH3. Nitrogenase naturally occurs in three forms, with the major difference being that the metal ion present in the cofactor active site is either molybdenum (FeMoco), vanadium (FeVco), or iron. The molybdenum and vanadium versions of these cofactors are more closely studied, owing to their larger abundance and rate of catalysis. In this study, we compare free energy profiles and electronic properties of the Mo/V cubanes at various stages during the reduction of N2H4 to NH3. Our findings highlight the differences in how the complexes facilitate the reaction, in particular, vanadium's comparatively weaker ability to interact with the Fe/S network and stabilize reducing electrons prior to N-N bond cleavage, which may have implications when considering the lower efficiency of the vanadium-dependent nitrogenase.

3.
J Am Chem Soc ; 142(23): 10240-10243, 2020 06 10.
Artículo en Inglés | MEDLINE | ID: mdl-32431144

RESUMEN

The identity of a key intermediate in the S2 to S3 transition of nature's water-oxidizing complex (WOC) in Photosystem 2 is presented. Broken-symmetry density functional theory (BS-DFT) calculations and Heisenberg-Dirac-van Vleck (HDvV) spin ladder calculations show that an S2 state open cubane model of the WOC containing a µ-hydroxo O4 changes from an S = 5/2 form to an S = 7/2, form upon deprotonation of W1. Combined with X-band electron paramagnetic resonance (EPR) spectral analysis, this indicates that the g = 4.1 EPR signal corresponds to an S = 5/2 form of the WOC with W1 present as a water ligand to Mn4, while the g = 4.8/4.9 form observed at high pH values corresponds to an S = 7/2 form, with W1 as a hydroxo ligand. The latter is also likely to represent the form needed to progress to S3 in the functioning enzyme.

4.
J Phys Chem A ; 124(47): 9771-9776, 2020 Nov 25.
Artículo en Inglés | MEDLINE | ID: mdl-33180494

RESUMEN

A localized bond orbital analysis of the bonding in dioxygen and related species provides a unique fundamental insight into its bonding characteristics. It reveals the coalescence of the molecular orbital and valence bond/Lewis approaches and clearly demonstrates that the often stated inability of valence bond theory to describe the bonding of O2 is a myth. The analysis indicates that the σ-bond strength of 3O2 is not weak as previously believed and accounts for much of its enhanced stability compared with hydroperoxyl. We attribute the stability and persistence of 3O2 to a combination of this attribute and favorable maximization of exchange coupling between the valence electrons.

5.
Biochemistry ; 55(40): 5714-5725, 2016 Oct 11.
Artículo en Inglés | MEDLINE | ID: mdl-27622672

RESUMEN

The respiratory cytochrome bo3 ubiquinol oxidase from Escherichia coli has a high-affinity ubiquinone binding site that stabilizes the one-electron reduced ubisemiquinone (SQH), which is a transient intermediate during the electron-mediated reduction of O2 to water. It is known that SQH is stabilized by two strong hydrogen bonds from R71 and D75 to ubiquinone carbonyl oxygen O1 and weak hydrogen bonds from H98 and Q101 to O4. In this work, SQH was investigated with orientation-selective Q-band (∼34 GHz) pulsed 1H electron-nuclear double resonance (ENDOR) spectroscopy on fully deuterated cytochrome (cyt) bo3 in a H2O solvent so that only exchangeable protons contribute to the observed ENDOR spectra. Simulations of the experimental ENDOR spectra provided the principal values and directions of the hyperfine (hfi) tensors for the two strongly coupled H-bond protons (H1 and H2). For H1, the largest principal component of the proton anisotropic hfi tensor Tz' = 11.8 MHz, whereas for H2, Tz' = 8.6 MHz. Remarkably, the data show that the direction of the H1 H-bond is nearly perpendicular to the quinone plane (∼70° out of plane). The orientation of the second strong hydrogen bond, H2, is out of plane by ∼25°. Equilibrium molecular dynamics simulations on a membrane-embedded model of the cyt bo3 QH site show that these H-bond orientations are plausible but do not distinguish which H-bond, from R71 or D75, is nearly perpendicular to the quinone ring. Density functional theory calculations support the idea that the distances and geometries of the H-bonds to the ubiquinone carbonyl oxygens, along with the measured proton anisotropic hfi couplings, are most compatible with an anionic (deprotonated) ubisemiquinone.


Asunto(s)
Citocromos/química , Proteínas de Escherichia coli/química , Escherichia coli/enzimología , Ubiquinona/análogos & derivados , Aniones , Grupo Citocromo b , Espectroscopía de Resonancia por Spin del Electrón , Electrones , Enlace de Hidrógeno , Simulación de Dinámica Molecular , Ubiquinona/química
6.
J Am Chem Soc ; 138(13): 4358-61, 2016 Apr 06.
Artículo en Inglés | MEDLINE | ID: mdl-27007277

RESUMEN

The oxidation state assignment of the manganese ions present in the superoxidized manganese (III/IV) catalase active site is determined by comparing experimental and broken symmetry density functional theory calculated (14)N, (17)O, and (1)H hyperfine couplings. Experimental results have been interpreted to indicate that the substrate water is coordinated to the Mn(III) ion. However, by calculating hyperfine couplings for both scenarios we show that water is coordinated to the Mn(IV) ion and that the assigned oxidation states of the two manganese ions present in the site are the opposite of that previously proposed based on experimental measurements alone.


Asunto(s)
Catalasa/metabolismo , Compuestos de Manganeso/química , Manganeso/química , Óxidos/química , Dominio Catalítico , Espectroscopía de Resonancia por Spin del Electrón , Nitrógeno/química , Oxidación-Reducción , Complejo de Proteína del Fotosistema II/química , Thermus thermophilus/metabolismo , Agua/química
7.
Biochemistry ; 54(32): 5030-44, 2015 Aug 18.
Artículo en Inglés | MEDLINE | ID: mdl-26196462

RESUMEN

Cytochrome aa3-600 is a terminal oxidase in the electron transport pathway that contributes to the electrochemical membrane potential by actively pumping protons. A notable feature of this enzyme complex is that it uses menaquinol as its electron donor instead of cytochrome c when it reduces dioxygen to water. The enzyme stabilizes a menasemiquinone radical (SQ) at a high affinity site that is important for catalysis. One of the residues that interacts with the semiquinone is Arg70. We have made the R70H mutant and have characterized the menasemiquinone radical by advanced X- and Q-band EPR. The bound SQ of the R70H mutant exhibits a strong isotropic hyperfine coupling (a(14)N ≈ 2.0 MHz) with a hydrogen bonded nitrogen. This nitrogen originates from a histidine side chain, based on its quadrupole coupling constant, e(2)qQ/h = 1.44 MHz, typical for protonated imidazole nitrogens. In the wild-type cyt aa3-600, the SQ is instead hydrogen bonded with Nε from the Arg70 side chain. Analysis of the (1)H 2D electron spin echo envelope modulation (ESEEM) spectra shows that the mutation also changes the number and strength of the hydrogen bonds between the SQ and the surrounding protein. Despite the alterations in the immediate environment of the SQ, the R70H mutant remains catalytically active. These findings are in contrast to the equivalent mutation in the close homologue, cytochrome bo3 ubiquinol oxidase from Escherichia coli, where the R71H mutation eliminates function.


Asunto(s)
Bacillus subtilis/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Complejo IV de Transporte de Electrones/química , Complejo IV de Transporte de Electrones/metabolismo , Vitamina K 2/metabolismo , Sustitución de Aminoácidos , Bacillus subtilis/genética , Proteínas Bacterianas/genética , Dominio Catalítico/genética , Grupo Citocromo b , Citocromos/química , Citocromos/genética , Citocromos/metabolismo , Espectroscopía de Resonancia por Spin del Electrón , Transporte de Electrón , Complejo IV de Transporte de Electrones/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Enlace de Hidrógeno , Cinética , Mutagénesis Sitio-Dirigida , Plastoquinona/análogos & derivados , Plastoquinona/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
8.
Biochemistry ; 53(38): 6022-31, 2014 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-25184535

RESUMEN

Specific isotopic labeling at the residue or substituent level extends the scope of different spectroscopic approaches to the atomistic level. Here we describe (13)C isotopic labeling of the methyl and methoxy ring substituents of ubiquinone, achieved through construction of a methionine auxotroph in Rhodobacter sphaeroides strain BC17 supplemented with l-methionine with the side chain methyl group (13)C-labeled. Two-dimensional electron spin echo envelope modulation (HYSCORE) was applied to study the (13)C methyl and methoxy hyperfine couplings in the semiquinone generated in situ at the Qi site of the bc1 complex in its membrane environment. The data were used to characterize the distribution of unpaired spin density and the conformations of the methoxy substituents based on density functional theory calculations of (13)C hyperfine tensors in the semiquinone of the geometry-optimized X-ray structure of the bc1 complex (Protein Data Bank entry 1PP9 ) with the highest available resolution. Comparison with other proteins indicates individual orientations of the methoxy groups in each particular case are always different from the methoxy conformations in the anion radical prepared in a frozen alcohol solution. The protocol used in the generation of the methionine auxotroph is more generally applicable and, because it introduces a gene deletion using a suicide plasmid, can be applied repeatedly.


Asunto(s)
Proteínas Bacterianas/metabolismo , Metionina/metabolismo , Rhodobacter sphaeroides/metabolismo , Análisis Espectral/métodos , Ubiquinona/química , Benzoquinonas , Isótopos de Carbono , Regulación Bacteriana de la Expresión Génica , Marcaje Isotópico , Metionina/química , Estructura Molecular , Conformación Proteica
9.
J Phys Chem Lett ; 15(22): 5883-5886, 2024 Jun 06.
Artículo en Inglés | MEDLINE | ID: mdl-38804862

RESUMEN

Density functional theory calculated 14N hyperfine couplings are obtained for the Mn1 ligated π-N of residue His332 of the photosystem 2 water oxidizing complex. An open cubane, O4H, model closely matches the experimental coupling obtained for the high spin S = 5/2 form of the S2 state, supporting an open cubane structure for this state. We also investigate the unusual geometric features for the S2 state obtained by X-ray free electron laser structure determinations and rationalize it as an equilibrium occurring at room temperature between W1/O4 deprotonated and protonated forms of the open cubane structure.

10.
J Phys Chem Lett ; 15(2): 499-506, 2024 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-38190694

RESUMEN

Using BS-DFT (broken-symmetry density functional theory), the electronic and magnetic properties of the S3YZ• state of photosystem II were investigated and compared to those of the S3 state. While the O5 oxo-O6 hydroxo species presents little difference between the two states, a previously identified [O5O6]3- exhibits reduced stabilization of the O5-O6 shared spin. This species is shown to have some coupling with the YZ• center through Mn1 and O6. Similarly, a peroxo species is found to exhibit significant exchange couplings between the YZ• center and the Mn cluster through Mn1. Mechanistic changes in O-O bond formation in S3YZ• are highlighted by analysis of IBOs (intrinsic bonding orbitals) showing deviation for Mn1 and O6 centered IBOs. This change in coupling interactions throughout the complex as a result of S3YZ• formation presents implications for the determination of the mechanism spanning the end of the S3 and the start of the S4 states, affecting both electron movement and oxygen bond formation.

11.
Biochemistry ; 52(27): 4648-55, 2013 Jul 09.
Artículo en Inglés | MEDLINE | ID: mdl-23745576

RESUMEN

Ubiquinone is an almost universal, membrane-associated redox mediator. Its ability to accept either one or two electrons allows it to function in critical roles in biological electron transport. The redox properties of ubiquinone in vivo are determined by its environment in the binding sites of proteins and by the dihedral angle of each methoxy group relative to the ring plane. This is an attribute unique to ubiquinone among natural quinones and could account for its widespread function with many different redox complexes. In this work, we use the photosynthetic reaction center as a model system for understanding the role of methoxy conformations in determining the redox potential of the ubiquinone/semiquinone couple. Despite the abundance of X-ray crystal structures for the reaction center, quinone site resolution has thus far been too low to provide a reliable measure of the methoxy dihedral angles of the primary and secondary quinones, QA and QB. We performed 2D ESEEM (HYSCORE) on isolated reaction centers with ubiquinones (13)C-labeled at the headgroup methyl and methoxy substituents, and have measured the (13)C isotropic and anisotropic components of the hyperfine tensors. Hyperfine couplings were compared to those derived by DFT calculations as a function of methoxy torsional angle allowing estimation of the methoxy dihedral angles for the semiquinones in the QA and QB sites. Based on this analysis, the orientation of the 2-methoxy groups are distinct in the two sites, with QB more out of plane by 20-25°. This corresponds to an ≈50 meV larger electron affinity for the QB quinone, indicating a substantial contribution to the experimental difference in redox potentials (60-75 mV) of the two quinones. The methods developed here can be readily extended to ubiquinone-binding sites in other protein complexes.


Asunto(s)
Proteínas del Complejo del Centro de Reacción Fotosintética/química , Rhodobacter sphaeroides/química , Ubiquinona/química , Cristalografía por Rayos X , Espectroscopía de Resonancia por Spin del Electrón , Oxidación-Reducción
12.
Biochemistry ; 52(41): 7164-6, 2013 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-24079813

RESUMEN

Only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from Rhodobacter sphaeroides. (13)C hyperfine sublevel correlation measurements of the 2-methoxy in the semiquinone states, SQA and SQB, were compared with quantum mechanics calculations of the (13)C couplings as a function of the dihedral angle. X-ray structures support dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of ~180 mV. This is consistent with the failure of a ubiquinone analogue lacking the 2-methoxy to function as QB in mutant reaction centers with a ΔEm of ≈160-195 mV.


Asunto(s)
Coenzimas/química , Quinonas/química , Rhodobacter sphaeroides/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Coenzimas/metabolismo , Transporte de Electrón , Cinética , Modelos Moleculares , Oxidación-Reducción , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Proteínas del Complejo del Centro de Reacción Fotosintética/genética , Proteínas del Complejo del Centro de Reacción Fotosintética/metabolismo , Quinonas/metabolismo , Rhodobacter sphaeroides/química , Rhodobacter sphaeroides/genética
13.
Biochemistry ; 51(45): 9086-93, 2012 Nov 13.
Artículo en Inglés | MEDLINE | ID: mdl-23016832

RESUMEN

In the Q(B) site of the Rhodobacter sphaeroides photosynthetic reaction center, the donation of a hydrogen bond from the hydroxyl group of Ser-L223 to the ubisemiquinone formed after the first flash is debatable. In this study, we use a combination of spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations to comprehensively explore this topic. We show that ENDOR, ESEEM, and HYSCORE spectroscopic differences between mutant L223SA and the wild-type sample (WT) are negligible, indicating only minor perturbations in the ubisemiquinone spin density for the mutant sample. Qualitatively, this suggests that a strong hydrogen bond does not exist in the WT between the Ser-L223 hydroxyl group and the semiquinone O(1) atom, as removal of this hydrogen bond in the mutant should cause a significant redistribution of spin density in the semiquinone. We show quantitatively, using QM/MM calculations, that a WT model in which the Ser-L223 hydroxyl group is rotated to prevent hydrogen bond formation with the O(1) atom of the semiquinone predicts negligible change for the L223SA mutant. This, together with the better agreement between key QM/MM calculated and experimental hyperfine couplings for the non-hydrogen-bonded model, leads us to conclude that no strong hydrogen bond is formed between the Ser-L223 hydroxyl group and the semiquinone O(1) atom after the first flash. The implications of this finding for quinone reduction in photosynthetic reaction centers are discussed.


Asunto(s)
Ubiquinona/análogos & derivados , Espectroscopía de Resonancia por Spin del Electrón , Enlace de Hidrógeno , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Proteínas del Complejo del Centro de Reacción Fotosintética/genética , Proteínas del Complejo del Centro de Reacción Fotosintética/metabolismo , Teoría Cuántica , Rhodobacter sphaeroides/química , Rhodobacter sphaeroides/metabolismo , Análisis Espectral , Ubiquinona/química , Ubiquinona/genética
14.
Biochemistry ; 51(18): 3827-38, 2012 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-22497216

RESUMEN

Selective (15)N isotope labeling of the cytochrome bo(3) ubiquinol oxidase from Escherichia coli with auxotrophs was used to characterize the hyperfine couplings with the side-chain nitrogens from residues R71, H98, and Q101 and peptide nitrogens from residues R71 and H98 around the semiquinone (SQ) at the high-affinity Q(H) site. The two-dimensional ESEEM (HYSCORE) data have directly identified N(ε) of R71 as an H-bond donor carrying the largest amount of unpaired spin density. In addition, weaker hyperfine couplings with the side-chain nitrogens from all residues around the SQ were determined. These hyperfine couplings reflect a distribution of the unpaired spin density over the protein in the SQ state of the Q(H) site and the strength of interaction with different residues. The approach was extended to the virtually inactive D75H mutant, where the intermediate SQ is also stabilized. We found that N(ε) of a histidine residue, presumably H75, carries most of the unpaired spin density instead of N(ε) of R71, as in wild-type bo(3). However, the detailed characterization of the weakly coupled (15)N atoms from selective labeling of R71 and Q101 in D75H was precluded by overlap of the (15)N lines with the much stronger ~1.6 MHz line from the quadrupole triplet of the strongly coupled (14)N(ε) atom of H75. Therefore, a reverse labeling approach, in which the enzyme was uniformly labeled except for selected amino acid types, was applied to probe the contribution of R71 and Q101 to the (15)N signals. Such labeling has shown only weak coupling with all nitrogens of R71 and Q101. We utilize density functional theory-based calculations to model the available information about (1)H, (15)N, and (13)C hyperfine couplings for the Q(H) site and to describe the protein-substrate interactions in both enzymes. In particular, we identify the factors responsible for the asymmetric distribution of the unpaired spin density and ponder the significance of this asymmetry to the quinone's electron transfer function.


Asunto(s)
Benzoquinonas/metabolismo , Grupo Citocromo b/metabolismo , Oxidorreductasas/metabolismo , Sitios de Unión , Espectroscopía de Resonancia por Spin del Electrón , Escherichia coli/enzimología , Escherichia coli/genética , Enlace de Hidrógeno , Isótopos de Nitrógeno , Oxidorreductasas/genética
15.
J Phys Chem B ; 126(41): 8214-8221, 2022 10 20.
Artículo en Inglés | MEDLINE | ID: mdl-36206029

RESUMEN

In this paper, we combine broken symmetry density functional calculations and electron paramagnetic resonance analysis to obtain the electronic structure of the penultimate S3 state of nature's water-oxidizing complex and determine the electronic pathway of O-O bond formation. Analysis of the electronic structure changes along the reaction path shows that two spin crossovers, facilitated by the geometry and magnetism of the water-oxidizing complex, are used to provide a unique low-energy pathway. The pathway is facilitated via the formation and stabilization of the [O2]3- ion. This ion is formed between ligated deprotonated substrate waters, O5 and O6, and is stabilized by antiferromagnetic interaction with the Mn ions of the complex. Combining the computational, crystallographic, and spectroscopic data, we show that an equilibrium exists between the O5 oxo and O6 hydroxo forms with an S = 3 spin state and a deprotonated O6 form containing a two-center one-electron bond in [O5O6]3- which we identify as the form detected using crystallography. This form corresponds to an S = 6 spin state which we demonstrate gives rise to a low-intensity EPR spectrum compared with the accompanying S = 3 state, making its detection via EPR difficult and overshadowed by the S = 3 form. Simulations using 70% of the S = 6 component give rise to a superior fit to the experimental W-band EPR spectral envelope compared with an S = 3 only form. Analyses of the most recent X-ray emission spectroscopy first moment changes for solution and time-resolved crystal data are also shown to support the model. The computational, crystallographic, and spectroscopic data are shown to coalesce to the same picture of a predominant S = 6 species containing the first one-electron oxidation product of two water molecules, that is, [O5O6]3-. Progression of this form to the two-electron-oxidized peroxo and three-electron-oxidized superoxo forms, leading eventually to the evolution of triplet O2, is proposed to be the pathway nature adopts to oxidize water. The study reveals the key electronic, magnetic, and structural design features of nature's catalyst which facilitates water oxidation to O2 under ambient conditions.


Asunto(s)
Complejo de Proteína del Fotosistema II , Agua , Agua/química , Complejo de Proteína del Fotosistema II/química , Fotosíntesis , Oxidación-Reducción , Espectroscopía de Resonancia por Spin del Electrón/métodos , Iones , Electrónica , Oxígeno/química
16.
ACS Omega ; 7(45): 41783-41788, 2022 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-36406523

RESUMEN

ELDOR-detected nuclear magnetic resonance (EDNMR) spectral simulations combined with broken-symmetry density functional theory (BS-DFT) calculations are used to obtain and to assign the 55Mn hyperfine coupling constants (hfcs) for modified forms of the water oxidizing complex in the penultimate S3 state of the water oxidation cycle. The study shows that an open cubane form of the core Mn4CaO6 cluster explains the magnetic properties of the dominant S = 3 species in all cases studied experimentally with no need to invoke a closed cubane intermediate possessing a distorted pentacoordinate Mn4 ion as recently suggested. EDNMR simulations found that both the experimental bandwidth and multinuclear transitions may alter relative EDNMR peak intensities, potentially leading to incorrect assignment of hfcs. The implications of these findings for the water oxidation mechanism are discussed.

17.
Biochim Biophys Acta ; 1797(2): 250-4, 2010 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-19891954

RESUMEN

QM/MM calculations have been used to monitor the oxidation of the D2-Tyr160, Tyr(D), residue involved in redox reactions in Photosystem II. The results indicate that in the reduced form the residue is involved in hydrogen bond donation via its phenolic head group to the tau-nitrogen of the neighboring D2-His189 residue. Oxidation to form the radical is accompanied by spontaneous transfer of the phenolic hydrogen to the tau-nitrogen of D2-His189 leading to the formation of a tyrosyl-imidazolium ion complex. Deprotonation of the imidazolium ion leads to the formation of a tyrosyl-imidazole neutral hydrogen-bonded complex. Comparison of calculated and experimental hyperfine coupling tensors and g-tensors suggests that the neutral imidazole complex is formed at physiological temperatures while the imidazolium complex may be stabilized at cryogenic temperatures.


Asunto(s)
Complejo de Proteína del Fotosistema II/química , Teoría Cuántica , Tirosina/química , Espectroscopía de Resonancia por Spin del Electrón , Enlace de Hidrógeno , Modelos Químicos , Conformación Molecular , Oxidación-Reducción
18.
J Am Chem Soc ; 133(14): 5525-37, 2011 Apr 13.
Artículo en Inglés | MEDLINE | ID: mdl-21417328

RESUMEN

In the photosynthetic reaction center from Rhodobacter sphaeroides, the primary (Q(A)) and secondary (Q(B)) electron acceptors are both ubiquinone-10, but with very different properties and functions. To investigate the protein environment that imparts these functional differences, we have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)H(2)O solvent. The powder HYSCORE method is first validated against the orientation-selected Q-band ENDOR study of the Q(A) SQ by Flores et al. (Biophys. J.2007, 92, 671-682), with good agreement for two exchangeable protons with anisotropic hyperfine tensor components, T, both in the range 4.6-5.4 MHz. HYSCORE was then applied to the Q(B) SQ where we found proton lines corresponding to T ≈ 5.2, 3.7 MHz and T ≈ 1.9 MHz. Density functional-based quantum mechanics/molecular mechanics (QM/MM) calculations, employing a model of the Q(B) site, were used to assign the observed couplings to specific hydrogen bonding interactions with the Q(B) SQ. These calculations allow us to assign the T = 5.2 MHz proton to the His-L190 N(δ)H···O(4) (carbonyl) hydrogen bonding interaction. The T = 3.7 MHz spectral feature most likely results from hydrogen bonding interactions of O1 (carbonyl) with both Gly-L225 peptide NH and Ser-L223 hydroxyl OH, which possess calculated couplings very close to this value. The smaller 1.9 MHz coupling is assigned to a weakly bound peptide NH proton of Ile-L224. The calculations performed with this structural model of the Q(B) site show less asymmetric distribution of unpaired spin density over the SQ than seen for the Q(A) site, consistent with available experimental data for (13)C and (17)O carbonyl hyperfine couplings. The implications of these interactions for Q(B) function and comparisons with the Q(A) site are discussed.


Asunto(s)
Benzoquinonas/química , Proteínas del Complejo del Centro de Reacción Fotosintética/química , Rhodobacter sphaeroides , Benzoquinonas/metabolismo , Espectroscopía de Resonancia por Spin del Electrón , Enlace de Hidrógeno , Modelos Moleculares , Proteínas del Complejo del Centro de Reacción Fotosintética/metabolismo , Conformación Proteica , Protones , Teoría Cuántica
19.
J Phys Chem B ; 125(36): 10097-10107, 2021 09 16.
Artículo en Inglés | MEDLINE | ID: mdl-34463499

RESUMEN

Broken symmetry density functional theory (BS-DFT) calculations on large models of Nature's water oxidizing complex (WOC) are used to investigate the electronic structure and associated magnetic interactions of this key intermediate state. The electronic origins of the ferromagnetic and antiferromagnetic couplings between neighboring Mn ions are investigated and illustrated by using corresponding orbital transformations. Protonation of the O4 and/or O6 atoms leads to large variation in the distribution of spin around the complex with associated changes in its magnetic resonance properties. Models for Sr2+ exchange and methanol addition indicate minor perturbations reflected in slightly altered spin projection coefficients for the Mn1 and Mn2 ions. These are shown to account for the observed changes observed experimentally via electron paramagnetic resonance methods and suggest a reinterpretation of the experimental findings. By comparison with experimental determinations, we show that the spin projections and resulting calculated 55Mn hyperfine couplings support the open cubane form of an oxo (O5)-hydroxo (O6) cluster in all cases with no need to invoke a closed cubane intermediate. The implications of these findings for the water oxidation mechanism are discussed.


Asunto(s)
Complejo de Proteína del Fotosistema II , Agua , Espectroscopía de Resonancia por Spin del Electrón , Oxidación-Reducción , Oxígeno , Complejo de Proteína del Fotosistema II/metabolismo
20.
J Phys Chem B ; 125(26): 7147-7154, 2021 07 08.
Artículo en Inglés | MEDLINE | ID: mdl-34180671

RESUMEN

The nature of the bonding and magnetic exchange pathways of the water-oxidizing complex of photosystem 2 is explored using broken symmetry density functional theory. The electronic structure and superexchange pathways are illustrated and analyzed using corresponding orbitals and intrinsic bond orbitals. These demonstrate a dominating influence on the bonding and magnetic interactions by both the geometrical structure of the Mn4CaO5 core complex and the ionic interactions of the oxo bridges with the neighboring Ca2+ ion. The demonstrated ionic nature of the Ca2+ bonds is proposed to contribute to the stabilization of the oxygen atoms participating in O-O bond formation.


Asunto(s)
Complejo de Proteína del Fotosistema II , Agua , Fenómenos Magnéticos , Oxidación-Reducción , Oxígeno , Complejo de Proteína del Fotosistema II/metabolismo
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