| 1. |
- Pang, Yun-Jie, et al.
(författare)
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Theoretical Study of the Catalytic Mechanism of the Cu-Only Superoxide Dismutase
- 2023
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 127:21, s. 4800-4807
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Tidskriftsartikel (refereegranskat)abstract
- The catalytic mechanisms for the wild-type and the mutated Cu-only superoxide dismutase were studied using the hybrid density functional B3LYP and a quantum chemical cluster approach. Optimal protonation states of the active site were examined for each stage of the catalytic cycle. For both the reductive and the oxidative half-reactions, the arrival of the substrate O-2(center dot-) was found to be accompanied by a chargecompensating H+ with exergonicities of -15.4 kcal center dot mol and -4.7 kcal center dot mol, respectively. The second-sphere Glu-110 and first-sphere His-93 were suggested to be the transient protonation site for the reductive and the oxidative half-reactions, respectively, which collaborates with the hydrogen bonding water chain to position the substrate near the redox-active copper center. For the reductive half-reaction, the rate-limiting step was found to be the inner-sphere electron transfer from the partially coordinated O-2(center dot-) to Cu-II with a barrier of 8.1 kcal center dot mol. The formed O-2 is released from the active site with an exergonicity of -14.9 kcal center dot mol. For the oxidative half-reaction, the inner-sphere electron transfer from CuI to the partially coordinated O-2(center dot-) was found to be accompanied by the proton transfer from the protonated His-93 and barrierless. The rate-limiting step was found to be the second proton transfer from the protonated Glu-110 to HO2 with a barrier of 7.3 kcal center dot mol. The barriers are reasonably consistent with experimental activities, and a proton-transfer rate-limiting step in the oxidative half-reaction could explain the experimentally observed pH-dependence. For the E110Q CuSOD, Asp-113 was suggested to be likely to serve as the transient protonation site in the reductive half-reaction. The rate-limiting barriers were found to be 8.0 and 8.6 kcal center dot mol, respectively, which could explain the slightly lower performance of E110X mutants. The results were found to be stable, with respect to the percentage of exact exchange in B3LYP.
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| 2. |
- Siegbahn, Per E. M., 1945-
(författare)
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Computational Model Study of the Experimentally Suggested Mechanism for Nitrogenase
- 2024
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 128:4, s. 985-989
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism for N-2 activation in the E-4 state of nitrogenase was investigated by model calculations. In the experimentally suggested mechanism, the E-4 state is obtained after four reductions to the ground state. In a recent theoretical study, results for a different mechanism have been found in excellent agreement with available Electron Paramagnetic Resonance (EPR) experiments for E-4. The two hydrides in E-4 leave as H-2 concertedly with the binding of N-2. The mechanism suggested differs from the experimentally suggested one by a requirement for four activation steps prior to catalysis. In the present study, the experimentally suggested mechanism is studied using the same methods as those used in the previous study on the theoretical mechanism. The computed results make it very unlikely that a structure obtained after four reductions from the ground state has two hydrides, and the experimentally suggested mechanism does therefore not agree with the EPR experiments for E-4. Another structure with only one hydride is here suggested to be the one that has been observed to bind N-2 after only four reductions of the ground state.
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| 3. |
- Siegbahn, Per E. M., 1945-
(författare)
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Computational modeling of redox enzymes
- 2023
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Ingår i: FEBS Letters. - : Wiley. - 0014-5793 .- 1873-3468. ; 597:1, s. 38-44
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Forskningsöversikt (refereegranskat)abstract
- A computational methodology is briefly described, which appears to be able to accurately describe the mechanisms of redox active enzymes. The method is built on hybrid density functional theory where the inclusion of a fraction of exact exchange is critical. Two examples of where the methodology has been applied are described. The first example is the mechanism for water oxidation in photosystem II, and the second one is the mechanism for N2 activation by nitrogenase. The mechanism for PSII has obtained very strong support from subsequent experiments. For nitrogenase, the calculations suggest that there should be an activation process prior to catalysis, which is still strongly debated.
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| 4. |
- Siegbahn, Per E. M., 1945-
(författare)
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Mechanisms for Methane and Ammonia Oxidation by Particulate Methane Monooxygenase
- 2024
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Ingår i: Journal of Physical Chemistry B. - 1520-6106 .- 1520-5207. ; 128:24, s. 5840-5845
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Tidskriftsartikel (refereegranskat)abstract
- Particulate MMO (pMMO) catalyzes the oxidation of methane to methanol and also ammonia to hydroxylamine. Experimental characterization of the active site has been very difficult partly because the enzyme is membrane-bound. However, recently, there has been major progress mainly through the use of cryogenic electron microscopy (cryoEM). Electron paramagnetic resonance (EPR) and X-ray spectroscopy have also been employed. Surprisingly, the active site has only one copper. There are two histidine ligands and one asparagine ligand, and the active site is surrounded by phenyl alanines but no charged amino acids in the close surrounding. The present study is the first quantum chemical study using a model of that active site (Cu-D). Low barrier mechanisms have been found, where an important part is that there are two initial proton-coupled electron transfer steps to a bound O-2 ligand before the substrate enters. Surprisingly, this leads to large radical character for the oxygens even though they are protonated. That result is very important for the ability to accept a proton from the substrates. Methods have been used which have been thoroughly tested for redox enzyme mechanisms.
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| 5. |
- Siegbahn, Per E. M., 1945-, et al.
(författare)
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The energetics of N2 reduction by vanadium containing nitrogenase
- 2024
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 26:3, s. 1684-1695
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Tidskriftsartikel (refereegranskat)abstract
- The main class of nitrogenases has a molybdenum in its cofactor. A mechanism for Mo-nitrogenase has recently been described. In the present study, another class of nitrogenases has been studied, the one with a vanadium instead of a molybdenum in its cofactor. It is generally believed that these classes use the same general mechanism to activate nitrogen. The same methodology has been used here as the one used for Mo-nitrogenase. N2 activation is known to occur after four reductions in the catalytic cycle, in the E4 state. The main features of the mechanism for Mo-nitrogenase found in the previous study are an activation process in four steps prior to catalysis, the release of a sulfide during the activation steps and the formation of H2 from two hydrides in E4, just before N2 is activated. The same features have been found here for V-nitrogenase. A difference is that five steps are needed in the activation process, which explains why the ground state of V-nitrogenase is a triplet (even number) and the one for Mo-nitrogenase is a quartet (odd number). The reason an additional step is needed for V-nitrogenase is that V3+ can be reduced to V2+, in contrast to the case for Mo3+ in Mo-nitrogenase. The fact that V3+ is Jahn–Teller active has important consequences. N2H2 is formed in E4 with reasonably small barriers.
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| 6. |
- Siegbahn, Per E. M., 1945-
(författare)
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The mechanism for N2 activation in the E4 – state of nitrogenase
- 2023
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - 1463-9076 .- 1463-9084. ; 25:35, s. 23602-23613
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Tidskriftsartikel (refereegranskat)abstract
- Nitrogenases take nitrogen from the air and reduce it to ammonia. It has long been known that N2 becomes activated after four reductions in the catalytic cycle, in the E4 state. Several mechanisms for the activation have been suggested. In the present study a previous mechanism has been revised based on recent experimental findings. In the present mechanism N2H2 is formed in E4. As in the previously suggested mechanism, there are four initial reductions before catalysis (the A-states), after which a sulfide is released and the first state in catalysis (E0) is formed. In E4, N2 becomes bound and protonated in the Fe1, Fe2, Fe4 region, in which the hydrides have left two electrons. The rate-limiting step is the formation of N2H by a hydrogen atom transfer from Cys275 to N2 bound to Fe4, concerted with an additional electron transfer from the cofactor. The mechanism fulfills all requirements set by experiments. The activation of N2 is preceded by a formation of H2 from two hydrides, the carbide is kinetically hindered from being protonated, the E4 state is reversible. An important aspect is the presence of a water molecule in the Fe2, Fe6 region. The non-allowed formations of H2 from a hydride and a proton have been investigated and found to have higher barriers than the allowed formation of H2 from two hydrides.
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