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- 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. |
- Olsen, L, et al.
(författare)
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Binding of benzylpenicillin to metallo-beta-lactamase: A QM/MM study
- 2004
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 108:45, s. 17639-17648
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Tidskriftsartikel (refereegranskat)abstract
- Metallo-beta-lactamases are bacterial enzymes that may function with either one or two zinc ions bound in the active site. In this work, the binding of benzylpenicillin to mono-zinc metallo-beta-lactamase from Bacillus cereus has been investigated in a docking procedure applying a combined quantum mechanical/molecular mechanical method as the final step. It is demonstrated that the substrate can bind with the carbonyl oxygen of the lactam ring coordinating to the zinc ion, and with the zinc-bound hydroxide ion in position for a nucleophilic attack on the carbonyl carbon of the lactam ring. In some structures, both the histidine and the cysteine at the other (unoccupied) metal-binding site are in a proper position to function as proton shuttles in proton transfer from the previously zinc-bound hydroxide, to the nitrogen in the lactam ring. In addition, the hydrophobic region formed by Phe34, Val39, Trp59, and Ala89 interacts with the phenyl group of benzylpenicillin, whereas the carboxylate group may be stabilized by Lys171 and Asn180. Alternatively, the carboxylate can bind to the zinc ion, prohibiting the nucleophilic attack of the zinc-bound hydroxide on the lactam carbonyl carbon. However, such a structure is energetically disfavored compared to the other enzyme-substrate complexes.
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