| 1. |
- Brânzanic, Adrian M.V., et al.
(författare)
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Why does sulfite reductase employ siroheme?
- 2019
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Ingår i: Chemical Communications. - : Royal Society of Chemistry (RSC). - 1359-7345 .- 1364-548X. ; 55:93, s. 14047-14049
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Tidskriftsartikel (refereegranskat)abstract
- Sulfite reductase (SiR) contains in the active site a unique assembly of siroheme and a [4Fe4S] cluster, linked by a cysteine residue. Siroheme is a doubly reduced variant of heme that is not used for a catalytic function in any other enzyme. We have used non-equilibrium Green's function methods coupled with density functional theory computations to explain why SiR employs siroheme rather than heme. The results show that direct, through vacuum, charge-transfer routes are inhibited when heme is replaced by siroheme. This ensures more efficient channelling of the electrons to the catalytic iron during the six-electron reduction of sulfite to sulfide, limiting potential side-reactions that could occur if the incoming electrons were delocalized onto the macrocyclic ring.
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| 2. |
- Li, Jilai, et al.
(författare)
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A Computational Comparison of Oxygen Atom Transfer Catalyzed by Dimethyl Sulfoxide Reductase with Mo and W
- 2015
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Ingår i: European Journal of Inorganic Chemistry. - : Wiley. - 1099-0682 .- 1434-1948. ; :21, s. 3580-3589
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Tidskriftsartikel (refereegranskat)abstract
- A thorough computational study has been performed to investigate oxygen atom transfer (OAT) reactions catalyzed by dimethyl sulfoxide reductase (DMSOR) with a catalytic molybdenum or tungsten ion. Thirteen different density functional theory (DFT) methods have been employed to obtain structural parameters along the reaction pathway, and single-point energies were computed with local correlation coupled-cluster methods [LCCSD(T0)]. For both Mo and W, most DFT methods indicate that the enzyme follows a twostep mechanism with a stable intermediate in which a DMSO molecule coordinates to the metal ion in the +IV oxidation state, and this is also confirmed by the LCCSD(T0) energies. The W-substituted models have a 26-30 kJ/mol lower activation barrier for the OAT reaction, and the reaction is 6370 kJ/mol more exothermic than that with Mo. Different DFT methods give widely different activation and reaction energies, which roughly depend on the amount of exact exchange in the method; these differences are also reflected in the structures, especially for the rate-limiting transition state. Consequently, there is quite a large variation in energies and various energy corrections (thermal, solvation, dispersion, and relativistic; up to 39 kJ/mol) depending on which DFT method is used to obtain the geometries. Therefore, a mechanism predicted by a single method should be viewed with caution.
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| 3. |
- Meelua, Wijitra, et al.
(författare)
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A computational study of the reaction mechanism and stereospecificity of dihydropyrimidinase
- 2023
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 25:12, s. 8767-8778
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Tidskriftsartikel (refereegranskat)abstract
- Dihydropyrimidinase (DHPase) is a key enzyme in the pyrimidine pathway, the catabolic route for synthesis of β-amino acids. It catalyses the reversible conversion of 5,6-dihydrouracil (DHU) or 5,6-dihydrothymine (DHT) to the corresponding N-carbamoyl-β-amino acids. This enzyme has the potential to be used as a tool in the production of β-amino acids. Here, the reaction mechanism and origin of stereospecificity of DHPases from Saccharomyces kluyveri and Sinorhizobium meliloti CECT4114 were investigated and compared using a quantum mechanical cluster approach based on density functional theory. Two models of the enzyme active site were designed from the X-ray crystal structure of the native enzyme: a small cluster to characterize the mechanism and the stationary points and a large model to probe the stereospecificity and the role of stereo-gate-loop (SGL) residues. It is shown that a hydroxide ion first performs a nucleophilic attack on the substrate, followed by the abstraction of a proton by Asp358, which occurs concertedly with protonation of the ring nitrogen by the same residue. For the DHT substrate, the enzyme displays a preference for the l-configuration, in good agreement with experimental observation. Comparison of the reaction energetics of the two models reveals the importance of SGL residues in the stereospecificity of catalysis. The role of the conserved Tyr172 residue in transition-state stabilization is confirmed as the Tyr172Phe mutation increases the activation barrier of the reaction by ∼8 kcal mol−1. A detailed understanding of the catalytic mechanism of the enzyme could offer insight for engineering in order to enhance its activity and substrate scope.
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| 4. |
- Pettersson, Gösta, et al.
(författare)
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A rapid‐equilibrium model for the control of the Calvin photosynthesis cycle by cytosolic orthophosphate
- 1987
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Ingår i: European Journal of Biochemistry. - : Wiley. - 0014-2956 .- 1432-1033. ; 169:2, s. 423-429
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Tidskriftsartikel (refereegranskat)abstract
- A simple model based on rapid‐equilibrium assumptions is derived which relates the steady‐state activity of the Calvin cycle for photosynthetic carbohydrate formation in C3 plants to the kinetic properties of a single cycle enzyme (fructose bisphosphatase) and of the phosphate translocator which accounts for the export of photosynthate from the chloroplast. Depending on the kinetic interplay of these two catalysts, the model system may exhibit a single or two distinct modes of steady‐state operation, or may be unable to reach a steady state. The predictions of the model are analysed with regard to the effect of external orthophosphate on the steady‐state rate of photosynthesis in isolated chloroplasts under conditions of saturating light and CO2. Due to the possible existence of two distinct steady states, the model may account for the stimulatory as well as the inhibitory effects of external phosphate observed in experiments with intact chloroplasts. Stability arguments indicate, however, that only the steady‐state case corresponding to phosphate inhibition of the rate of photosynthesis could be of physiological interest. It is concluded that chloroplasts under physiological conditions most likely operate in a high‐velocity steady state characterized by a negative Calvin cycle flux control coefficient for the phosphate translocator. This means that any factor enhancing the export capacity of the phosphate translocator can be anticipated to decrease the actual steady‐state rate of photosynthate export due to a decreased steady‐state rate of cyelic photosynthate production.
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| 5. |
- Pettersson, Gösta, et al.
(författare)
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Model studies of the regulation of the Calvin photosynthesis cycle by cytosolic metabolites
- 1990
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Ingår i: Biomedica Biochimica Acta. - 0232-766X. ; 49:8-9, s. 723-732
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Tidskriftsartikel (refereegranskat)abstract
- A kinetic model for photosynthetic carbohydrate formation in the chloroplast of C3 plants is presented which includes consideration of the interaction of the phosphate translocator of the chloroplast envelope with external reactants such as 3-phosphoglycerate, dihydroxyacetone phosphate, and glyceraldehyde 3-phosphate in addition to inorganic (ortho)phosphate. The model is shown to account satisfactorily for experimentally observed effects of such reactants on the rates of carbon dioxide fixation and starch production in isolated chloroplast. The predictions of the model with regard to the regulation of stromal processes of photosynthetic carbohydrate formation by cytosolic concentration variables have been examined. The results indicate that the cytosolic concentrations of metabolites that interact with the phosphate translocator represent important regulatory signals. Increasing levels of exported photosynthetic (phosphoglycerates and triose phosphates) in the cytosol do not suppress the rate of photosynthetic carbon dioxide fixation, but redirects reaction flux such that starch production within the chloroplast is favoured at the expense of a decreased rate of photosynthate export to the cytosol.
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| 6. |
- Rovaletti, Anna, et al.
(författare)
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A thiocarbonate sink on the enzymatic energy landscape of aerobic CO oxidation? Answers from DFT and QM/MM models of Mo–Cu CO-dehydrogenases
- 2019
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Ingår i: Journal of Catalysis. - : Elsevier BV. - 0021-9517. ; , s. 201-205
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Tidskriftsartikel (refereegranskat)abstract
- We present a theoretical investigation providing key insights on a long-standing controversial issue that dominated the debate on carbon monoxide oxidation by Mo–Cu CO-dehydrogenases. Previous investigations gravitate around the possible occurrence of a thiocarbonate intermediate, that was repeatedly reported to behave as a thermodynamic sink on the catalytic energy landscape. By using a hierarchy of quantum mechanical and hybrid quantum/classical models of the enzyme, we show that no such energy sink is present on the catalytic energy profile. Consequent perspectives for the definition of a novel mechanistic proposal for the enzyme-catalyzed CO-oxidation are discussed in light of the recent literature.
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