| 1. |
- Källrot, Niklas, et al.
(författare)
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Theoretical study of structure of catalytic copper site in nitrite reductase
- 2005
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Ingår i: International Journal of Quantum Chemistry. - : Wiley. - 0020-7608. ; 102:5, s. 520-541
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Tidskriftsartikel (refereegranskat)abstract
- The catalytic copper site in nitrite reductase contains a Cu2+ ion bound to three histidine (His) ligands and a solvent molecule. Sites from various sources show a conspicuous variation in the structure. In some proteins, it is close to tetrahedral (even more so than are blue copper proteins), whereas in other proteins, it has a structure more similar to that expected for a type 2 copper site. We have studied this site with a number of theoretical methods, ranging from vacuum optimizations, combined quantum and molecular mechanics (QM/MM) optimization, quantum refinement (X-ray crystallography supplemented by quantum chemical calculations), and accurate energy calculations. We show that the difference in the structure arises from a movement of the solvent molecule and that this movement is determined by a compromise between its hydrogen bond interactions and the intrinsic preferences of the copper site. If the solvent molecule is deprotonated, the two structures have a similar energy, whereas if it is protonated, the more tetrahedral structure is energetically favorable. Neither of the structures involves a pi interaction as in the blue copper proteins; instead, both are strongly distorted tetragonal structures with sigma bonds to all four ligands. We have also examined the position of hydrogen atoms shared between second-sphere carboxylate groups and the first-sphere solvent molecule and one of the His ligands. In the oxidized state, the structure with the solvent deprotonate(d) but the His residue protonated seems to be most stable. (c) 2004 Wiley Periodicals, Inc.
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| 2. |
- Nilsson, Kristina, et al.
(författare)
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An automatic method to generate force-field parameters for hetero-compounds.
- 2003
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Ingår i: Acta Crystallographica. Section D: Biological Crystallography. - 1399-0047. ; 59:2, s. 274-289
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Tidskriftsartikel (refereegranskat)abstract
- A method has been developed that automatically constructs a crystallographic refinement force field (topology and parameter files) for any molecule from a theoretical frequency calculation. The approach has been tested on five proteins containing metal sites or non-standard inhibitors or coenzymes and it is shown that the structures are improved in various aspects.
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| 3. |
- Nilsson, Kristina, et al.
(författare)
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Protonation status of metal-bound ligands can be determined by quantum refinement
- 2004
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Ingår i: Journal of Inorganic Biochemistry. - : Elsevier BV. - 1873-3344 .- 0162-0134. ; 98:9, s. 1539-1546
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Tidskriftsartikel (refereegranskat)abstract
- The protonation status of key residues and bound ligands are often important for the function of a protein. Unfortunately, protons are not discerned in normal protein crystal structures, so their positions have to be determined by more indirect methods. We show that the recently developed quantum refinement method can be used to determine the position of protons in crystal structures. By replacing the molecular-mechanics potential, normally used in crystallographic refinement, by more accurate quantum chemical calculations, we get information about the ideal structure of a certain protonation state. By comparing the refined structures of different protonation states, the one that fits the crystallographic raw data best can be decided using four criteria: the R factors, electron density maps, strain energy, and divergence from the unrestrained quantum chemical structure. We test this method on alcohol dehydrogenase, for which the pK(a) of the zinc-bound solvent molecule is experimentally known. We show that we can predict the correct protonation state for both a deprotonated alcohol and a neutral water molecule. (C) 2004 Elsevier Inc. All rights reserved.
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| 4. |
- Nilsson, Kristina, et al.
(författare)
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The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: Quantum refinement
- 2004
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Ingår i: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 87:5, s. 3437-3447
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Tidskriftsartikel (refereegranskat)abstract
- Treatment of met-myoglobin (Fe-III) with H2O2 gives rise to ferryl myoglobin, which is closely related to compound II in peroxidases. Experimental studies have given conflicting results for this species. In particular, crystallographic and extended x-ray absorption fine-structure data have shown either a short (similar to170 pm) or a longer (similar to190 pm) Fe-O bond, indicating either a double or a single bond. We here present a combined experimental and theoretical investigation of this species. In particular, we use quantum refinement to re-refine a crystal structure with a long bond, using 12 possible states of the active site. The states differ in the formal oxidation state of the iron ion and in the protonation of the oxygen ligand (O2-, OH-, or H2O) and the distal histidine residue (with a proton on N-delta1, N-epsilon2, or on both atoms). Quantum refinement is essentially standard crystallographic refinement, where the molecular-mechanics potential, normally used to supplement the experimental data, is replaced by a quantum chemical calculation. Thereby, we obtain an accurate description of the active site in all the different protonation and oxidation states, and we can determine which of the 12 structures fit the experimental data best by comparing the crystallographic R-factors, electron-density maps, strain energies, and deviation from the ideal structure. The results indicate that Fe-III OH- and Fe-IV OH- fit the experimental data almost equally well. These two states are appreciably better than the standard model of compound II, Fe-IV O2-. Combined with the available spectroscopic data, this indicates that compound II in myoglobin is protonated and is best described as Fe-IV OH-. It accepts a hydrogen bond from the distal His, which may be protonated at low pH.
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| 5. |
- Ryde, Ulf, et al.
(författare)
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Quantum chemical geometry optimizations in proteins using crystallographic raw data.
- 2002
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 1096-987X .- 0192-8651. ; 23:11, s. 1058-1070
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Tidskriftsartikel (refereegranskat)abstract
- A method is developed for the combination of quantum chemical geometry optimizations and crystallographic structure refinement. The method is implemented by integrating the quantum chemical software Turbomole with the crystallographic software Crystallography and NMR System (CNS), using three small procedures transferring information between the two programs. The program (COMQUM-X)is used to study the binding of the inhibitor N-methylmesoporphyrin to ferrochelatase, and we show that the method behaves properly and leads to an improvement of the structure of the inhibitor. It allows us to directly quantify in energy terms how much the protein distort the structure of the bound inhibitor compared to the optimum vacuum structure (4-6 kJ/mol). The approach improves the standard combined quantum chemical and molecular mechanics (QC/MM) approach by guaranteeing that the final structure is in accordance with experimental data (the reflections) and avoiding the risk of propagating errors in the crystal coordinates. The program can also be seen as an improvement of standard crystallographic refinement, providing an accurate empirical potential function for any group of interest. The results can be directly interpreted in standard crystallographic terms (e.g., R factors or electron density maps). The method can be used to interpret crystal structures (e.g., the protonation status of metal-bound water molecules) and even to locally improve them.
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| 6. |
- Ryde, Ulf, et al.
(författare)
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Quantum Chemistry Can Locally Improve Protein Crystal Structures
- 2003
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 1520-5126 .- 0002-7863. ; 125:47, s. 14232-14233
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Tidskriftsartikel (refereegranskat)abstract
- We have re-refined the X-ray structure of the heme site in cytochrome c553, supplementing the crystallographic data with quantum chemical geometry optimizations, instead of the molecular mechanics force field used in standard crystallographic refinement. By comparing the resulting structure, obtained using medium-resolution data (170 pm), with an atomic-resolution structure (95 pm) of the same protein, we show that the inclusion of quantum chemical information into the refinement procedure improves the structure significantly. Thus, errors in the Fe-ligand distances are reduced from 3 to 32 pm in the low-resolution structure to 0-5 pm in the re-refined structure, one side-chain atom changes its conformation (a movement by 214 pm toward its position in the high-resolution structure), and the R factors are improved by up to 0.018. Thus, quantum refinement may be a powerful method to obtain an accurate structure for interesting parts of a protein.
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| 7. |
- Ryde, Ulf, et al.
(författare)
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Quantum refinement - a combination of quantum chemistry and protein crystallography.
- 2003
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Ingår i: Journal of molecular structure. Theochem. - 0166-1280. ; 632:1-3, s. 259-275
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Forskningsöversikt (refereegranskat)abstract
- The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins. We here review our applications of QM/MM methods to alcohol dehydrogenase, blue copper proteins, iron–sulphur clusters, ferrochelatase, and myoglobin. We also describe our new quantum refinement method, which is a combination of quantum chemistry and protein crystallography. It has been shown to work properly and it can be used to improve the structure of protein metal centres in terms of the crystallographic Rfree factor and electron-density maps. It can be used to determine the protonation status of metal-bound solvent molecules in proteins by refining the various possible states and see which fits the crystallographic raw data best. Applications to ferrochelatase, cytochrome c553, alcohol dehydrogenase, myoglobin, and methylmalonyl coenzyme A mutase are described.
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