| 1. |
- Hersleth, Hans-Petter, et al.
(författare)
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The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection
- 2008
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Ingår i: Biochemical Journal. - 0264-6021. ; 412, s. 257-264
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Tidskriftsartikel (refereegranskat)abstract
- Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallograpic data collection. We have generated and solved the 1.30 angstrom (1 angstrom= 0.1 nin) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe-O distance of 1.8 angstrom and O-O bond of 1.3 angstrom in accordance with a Fe-II-O-O- (or Fe-III-O-O2-) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metal loproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O-O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.
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| 2. |
- Hersleth, Hans-Petter, et al.
(författare)
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The Influence of X-Rays on the Structural Studies of Peroxide-Derived Myoglobin Intermediates
- 2008
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Ingår i: Chemistry and Biodiversity. - 1612-1872. ; 5:10, s. 2067-2089
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Forskningsöversikt (refereegranskat)abstract
- In recent years, the awareness of potential radiation damage of metal centers in protein crystals during crystallographic data collection has received increasing attention. The radiation damage can lead to radiation-induced changes and reduction of the metal sites. One of the research fields where these concerns have been comprehensively addressed is the study of the reaction intermediates of the heme peroxidase and oxygenase reaction cycles. For both the resting states and the high-valent intermediates, the X-rays used in the structure determination have given undesired side effects through radiation-induced changes to the trapped intermediates. However, X-rays have been used to generate and trap the peroxy/hydroperoxy state in crystals. In this review, the structural work and the influence of X-rays on these intermediates in myoglobin are summarized and viewed in light of analogous studies on similar intermediates in peroxidases and oxygenases.
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| 3. |
- Hsiao, Ya-Wen, et al.
(författare)
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EXAFS structure refinement supplemented by computational chemistry
- 2006
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Ingår i: Physical Review B (Condensed Matter and Materials Physics). - 1098-0121. ; 74:21
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Tidskriftsartikel (refereegranskat)abstract
- We present a method that combines structure determination using extended x-ray absorption fine structure (EXAFS) measurements and computational chemistry (CC) calculations, EXAFS/CC. Using such an approach, it is possible to obtain a full structure of model complexes or protein metal active sites, although the EXAFS data primarily give radial distance information about the metal ion's nearest neighbors. In essence, CC provides a formalism within which chemical knowledge can be introduced to EXAFS modeling. In this sense, the method is analogous to the use of molecular mechanics in standard crystallographic or NMR structure refinement. In addition, the method provides structures that are a compromise between EXAFS data and the CC calculations. Therefore, they can be used directly to obtain energies or study reaction mechanisms. The method is implemented for both density functional theory and molecular mechanics calculations. It is applied to five Ni(II) (both low- and high-spin) and Cu(I/II) complexes with known crystal structures and it is shown to perform well. We also show that the method can be successfully combined with the calculation of ab initio Debye-Waller factors for all paths using the equation-of-motion method and force constants obtained from the CC calculations.
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| 4. |
- Hsiao, Ya-Wen, et al.
(författare)
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Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods
- 2006
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Ingår i: Inorganica Chimica Acta. - : Elsevier BV. - 0020-1693. ; 359:4, s. 1081-1092
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Tidskriftsartikel (refereegranskat)abstract
- The metallation of tetrapyrroles is believed to proceed via a sitting-atop (SAT) complex, in which some of the pyrrole nitrogen atoms are protonated and the metal ion resides above the ring plane. No crystal structure of such a complex has been presented, but NMR and EXAFS (extended X-ray absorption fine structure) data has been reported for Cu2+ in acetonitrile, which have been interpreted as the observation of a SAT complex. However, this interpretation has been challenged and other investigations have shown that there are many possible SAT structures. We have recently developed a method to combine quantum mechanical (QM) calculations and EXAFS fits (EXAFS/QM), which in principle is a standard EXAFS fit that employs all multiple-scattering information in an optimum and self-consistent way and uses the QM calculations to ensure that the obtained structures are chemically reasonable. By this approach, we show that out of the 15 putative SAT complexes, structures with the copper ion coordinating to two cis pyrrolenine nitrogen atoms and two or three acetonitrile molecules fit the experimental EXAFS spectrum best. However, an equally good fit can be obtained also by a mixture of the reactant and product complexes. (c) 2005 Elsevier B.V. All rights reserved.
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| 5. |
- Hsiao, Ya-Wen, et al.
(författare)
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NMR structure determination of proteins supplemented by quantum chemical calculations: Detailed structure of the Ca2+ sites in the EGF34 fragment of protein S
- 2005
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Ingår i: Journal of Biomolecular NMR. - : Springer Science and Business Media LLC. - 1573-5001 .- 0925-2738. ; 31:2, s. 97-114
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Tidskriftsartikel (refereegranskat)abstract
- We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular dynamics simulations restrained to experimental NMR data. In the first, we replace the molecular mechanics force field ( employed in standard refinement to supplement experimental data) for a site of interest by quantum chemical calculations. This way, we obtain an accurate description of the site, even if a molecular mechanics force field does not exist for this site, or if there is little experimental information about the site. Moreover, the site may change its bonding during the refinement, which often is the case for metal sites. The second method is to extract a molecular mechanics potential for the site of interest from a quantum chemical geometry optimisation and frequency calculation. We apply both methods to the two Ca2+ sites in the epidermal growth factor-like domains 3 and 4 in the vitamin K-dependent protein S and compare them to various methods to treat these sites in standard refinement. We show that both methods perform well and have their advantages and disadvantages. We also show that the glutamate Ca2+ ligand is unlikely to bind in a bidentate mode, in contrast to the crystal structure of an EGF domain of factor IX.
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| 6. |
- 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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