| 1. |
- Chalupsky, Jakub, et al.
(författare)
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Multireference ab initio calculations on reaction intermediates of the multicopper oxidases
- 2006
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 45:26, s. 11051-11059
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Tidskriftsartikel (refereegranskat)abstract
- The multicopper oxidases (MCOs) couple the four-electron reduction of dioxygen to water with four one-electron oxidations of various substrates. Extensive spectroscopic studies have identified several intermediates in the MCO catalytic cycle, but they have not been able to settle the structures of three of the intermediates, viz. the native intermediate (NI), the peroxy intermediate (PI), and the peroxy adduct (PA). The suggested structures have been further refined and characterized by quantum mechanical/molecular mechanical (QM/MM) calculations. In this paper, we try to establish a direct link between theory and experiment, by calculating spectroscopic parameters for these intermediates using multireference wave functions from the multistate CASPT2 and MRDDCI2 methods. Thereby, we have been able to reproduce low-spin ground states (S = 0 or S = 1/2) for all the MCO intermediates, as well as a low-lying (similar to 150 cm(-1)) doublet state and a doublet-quartet energy gap of similar to 780 cm(-1) for the NI. Moreover, we reproduce the zero-field splitting (similar to 70 cm(-1)) of the ground E-2 state in a D-3 symmetric hydroxy-bridged trinuclear Cu(II) model of the NI and obtain a quantitatively correct quartet-doublet splitting (164 cm(-1)) for a mu 3-oxo-bridged trinuclear Cu( II) cluster. All results support the suggestion that the NI has an O-2-atom in the center of the trinuclear cluster, whereas both the PI and PA have an O-2(2-) ion in the center of the cluster, in agreement with the QM/MM results and spectroscopic measurements.
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| 2. |
- Falk, Magnus, et al.
(författare)
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Mechanism of Bilirubin Oxidase : Fabrication and Characterization of Efficient Biocathode
- 2010
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Ingår i: Meeting abstracts (Electrochemical Society). - : ECS. - 1091-8213 .- 2151-2043. ; MA2010-02:1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- To elucidate the mechanism of bilirubin oxidase (BOx)function in order to design efficient and stablebiocathodes working at different conditions, the enzymewas studied thoroughly. BOx is a copper-containing redoxenzyme that catalyzes the oxidation of a variety ofdifferent organic and inorganic compounds withconcomitant reduction of O2 directly to H2O.
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| 3. |
- Heimdal, Jimmy, et al.
(författare)
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Reduction Potentials and Acidity Constants of Mn Superoxide Dismutase Calculated by QM/MM Free-Energy Methods.
- 2011
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Ingår i: ChemPhysChem. - : Wiley. - 1439-7641 .- 1439-4235. ; 12:Online: 29 SEP 2011, s. 3337-3347
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Tidskriftsartikel (refereegranskat)abstract
- We used two theoretical methods to estimate reduction potentials and acidity constants in Mn superoxide dismutase (MnSOD), namely combined quantum mechanical and molecular mechanics (QM/MM) thermodynamic cycle perturbation (QTCP) and the QM/MM-PBSA approach. In the latter, QM/MM energies are combined with continuum solvation energies calculated by solving the Poisson-Boltzmann equation (PB) or by the generalised Born approach (GB) and non-polar solvation energies calculated from the solvent-exposed surface area. We show that using the QTCP method, we can obtain accurate and precise estimates of the proton-coupled reduction potential for MnSOD, 0.30±0.01 V, which compares favourably with experimental estimates of 0.26-0.40 V. However, the calculated potentials depend strongly on the DFT functional used: The B3LYP functional gives 0.6 V more positive potentials than the PBE functional. The QM/MM-PBSA approach leads to somewhat too high reduction potentials for the coupled reaction and the results depend on the solvation model used. For reactions involving a change in the net charge of the metal site, the corresponding results differ by up to 1.3 V or 24 pK(a) units, rendering the QM/MM-PBSA method useless to determine absolute potentials. However, it may still be useful to estimate relative shifts, although the QTCP method is expected to be more accurate.
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| 4. |
- Hu, LiHong, et al.
(författare)
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Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.
- 2011
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 115:Online September 28, 2011, s. 13111-13126
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Tidskriftsartikel (refereegranskat)abstract
- We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory.
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| 5. |
- Li, Jilai, et al.
(författare)
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Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods.
- 2015
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 119:26, s. 8268-8284
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Tidskriftsartikel (refereegranskat)abstract
- We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular, the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerization reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site.
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| 6. |
- Rulisek, Lubomir, et al.
(författare)
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A combined quantum and molecular mechanical study of the O-2 reductive cleavage in the catalytic cycle of multicopper oxidases
- 2005
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 1520-510X .- 0020-1669. ; 44:16, s. 5612-5628
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Tidskriftsartikel (refereegranskat)abstract
- The four-electron reduction of dioxygen to water in multicopper oxidases takes place in a trinuclear copper cluster, which is linked to a mononuclear blue copper site, where the substrates are oxidized. Recently, several intermediates in the catalytic cycle have been spectroscopically characterized, and two possible structural models have been suggested for both the peroxy and native intermediates, In this study, these spectroscopic results are complemented by hybrid quantum and molecular mechanical (QM/MM) calculations, taking advantage of recently available crystal structures with a full complement of copper ions. Thereby, we obtain optimized molecular structures for all of the Experimentally studied intermediates involved in the reductive cleavage of the O-2 molecule and energy profiles for individual reaction steps, This allows identification of the experimentally observed intermediates and further insight into the reaction mechanism that is probably relevant for the whole class of multicopper oxidases, We suggest that the peroxy intermediate contains an O-2(2-) ion, in which one oxygen atom bridges the type 2 copper ion and one of the type 3 copper ions, whereas the other one coordinates to the other type 3 copper ion, One-electron reduction of this intermediate triggers the cleavage of the O-O bond, which involves the uptake of a proton, The product of this cleavage is the observed native intermediate, which we suggest to contain a O-2 ion coordinated to all three of the copper ions in the center of the cluster.
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| 7. |
- Rulisek, Lubomir, et al.
(författare)
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Structure of reduced and oxidized manganese superoxide dismutase: A combined computational and experimental approach
- 2006
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 110:23, s. 11511-11518
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Tidskriftsartikel (refereegranskat)abstract
- Manganese superoxide dismutases catalyze the disproportionation of the superoxide radical anion to molecular oxygen and hydrogen peroxide. Recently, atomic-resolution crystal structures of the reduced and oxidized enzymes have been reported. They show an active site with the manganese ion bound to one aspartate, three histidine residues, and a solvent molecule. In this paper, we combine crystallographic refinement with quantum mechanical methods to show that the solvent ligand is undoubtedly a water molecule in the reduced state. However, the putative oxidized structure is to a large extent reduced during data collection, so that it contains a mixture of the Mn2+ and Mn3+ structure. The crystal structures show that the Mn-bound solvent molecule accepts a hydrogen bond from the side chain of the conserved Gln-146 residue. If the solvent ligand is water, then this could lead to a steric clash, but it is avoided by the plane of water molecule forming an angle of 72 degrees to the Mn-O bond. Such a conformation is also found outside the enzyme, giving a minimal destabilization of the reduced state. We show by molecular dynamics simulations that the suggested Mn2+-(HO)-O-2 and Mn3+OH- structures are stable. Moreover, we show that the superoxide substrate may bind both in the first coordination sphere of the Mn ion, opposite to the aspartate ligand, or in the second sphere, close to the conserved Tyr-34 and His-30 residues, similar to 5 angstrom from Mn. However, the second-sphere structures are not stable in long molecular dynamics simulations. We see no difference in the coordination between the reduced and the oxidized states of the enzyme.
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| 8. |
- Rulisek, Lubomir, et al.
(författare)
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The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations
- 2006
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 27:12, s. 1398-1414
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the detailed reaction mechanism of iron and manganese superoxide dismutase with density functional calculations on realistic active-site models, with large basis sets and including solvation, zero-point, and thermal effects. The results indicate that the conversion of O-2(-) to O-2 follows an associative mechanism, with O-2 directly binding to the metal, followed by the protonation of the metal-bound hydroxide ion, and the dissociation of O-3(2). All these reaction steps are exergonic. Likewise, we suggest that the conversion of O-2(-) to H2O2 follows an at least a partly second-sphere pathway. There are small differences in the preferred oxidation and spin states, as well as in the geometries, of Fe and Mn, but these differences have little influence on the energetics, and therefore on the reaction mechanism of the two types of superoxide dismutases. For example, the two metals have very similar reduction potentials in the active-site models, although they differ by 0.7 V in water solution. The reaction mechanisms and spin states seem to have been designed to avoid spin conversions or to facilitate them by employing nearly degenerate spin states. (c) 2006 Wiley Periodicals, Inc.
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| 9. |
- Rulisek, Lubomir, et al.
(författare)
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Theoretical Studies of the Active-Site Structure, Spectroscopic and Thermodynamic Properties, and Reaction Mechanism of Multicopper Oxidases
- 2013
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Ingår i: Coordination Chemistry Reviews. - : Elsevier BV. - 0010-8545. ; 257, s. 445-458
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Forskningsöversikt (refereegranskat)abstract
- In this article, we review recent theoretical work that has complemented the extensive experimental data available for multicopper oxidases (MCO) and led to the elucidation of the reaction mechanism of this class of enzymes. The MCOs couple four one-electron oxidations of substrates at the mononuclear type 1 copper (Cu-T1) site with the four-electron reduction of dioxygen at the trinuclear copper cluster (TNC). The TNC consists of three copper ions arranged in a unique triangular fashion. In its oxidised form and in some experimentally observed intermediates (the peroxy and native intermediates), this leads to a magnetic coupling of the unpaired electrons of the three copper ions, resulting in unusual spectroscopic features. By correlating experimental and theoretical data, an unambiguous mapping between the structural, energetic and spectroscopic properties of the various intermediates in the MCO reaction cycle can be established. In terms of theory, these studies involved quantum mechanics (QM; density-functional theory and multi-reference self-consistent field) calculations, combined QM and molecular mechanics (QM/MM) modelling, ranging from standard QM/MM optimisations to the combination of QM/MM optimisation with EXAFS spectroscopy and QM/MM free-energy perturbations to accurately address phenomena such as the Cu-T1 → TNC electron transfer, as well as the reduction potentials and acid constants of all the putative intermediates in the MCO reaction cycle. In summary, we try to demonstrate in this review that the MCOs are not only an attractive playground for theoretical methods, but the results of the calculations (when carefully correlated with and benchmarked against experimental data) can also be used to draw unambiguous conclusions about MCO structure and reactivity.
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| 10. |
- Ryde, Ulf, et al.
(författare)
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Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements
- 2007
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 129:4, s. 726-727
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Tidskriftsartikel (refereegranskat)abstract
- We have developed a computational method that combines extended X-ray absorption fine structure (EXAFS) refinements with the integrated quantum mechanical and molecular mechanics (QM/MM) method. This method allows us to obtain a structure of a metal site inside a protein that is compatible with both EXAFS data and QM calculations (i.e., that is chemically reasonable). Thereby, the QM/MM calculations play the same role as MM in nearly all NMR and crystallographic refinements-EXAFS ensures that the metal-ligand distances are accurate and QM/MM fills in all the other structural data. We have used this method to show that a structure with a peroxide ion in the center of the trinuclear cluster fits experimental EXAFS data better than a structure with the peroxide ion on the side of the cluster for the peroxide adduct of multicopper oxidases.
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