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- Chen, Shilu, et al.
(författare)
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Peptide Hydrolysis by the Binuclear Zinc Enzyme Aminopeptidase from Aeromonas proteolytica : A Density Functional Theory Study
- 2008
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 112:8, s. 2494-2500
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Tidskriftsartikel (refereegranskat)abstract
- Aminopeptidase from Aeromonas proteolytica (AAP) is a binuclear zinc enzyme that catalyzes the cleavage of the N-terminal amino acid residue of peptides and proteins. In this study, we used density functional methods to investigate the reaction mechanism of this enzyme. A model of the active site was constructed on the basis of the X-ray crystal structure of the native enzyme, and a model dipeptide was used as a substrate. It was concluded that the hydroxide is capable of performing a nucleophilic attack at the peptide carbonyl from its bridging position without the need to first become terminal. The two zinc ions are shown to have quite different roles. Zn2 binds the amino group of the substrate, thereby orienting it toward the nucleophile, while Zn1 stabilizes the alkoxide ion of the tetrahedral intermediate, thereby lowering the barrier for the nucleophilic attack. The rate-limiting step is suggested to be the protonation of the nitrogen of the former peptide bond, which eventually leads to the cleavage of the C−N bond.
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- Spiegel, Maciej, et al.
(författare)
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Antioxidant and copper-chelating power of new molecules suggested as multiple target agents against Alzheimer's disease. A theoretical comparative study
- 2022
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 24:26, s. 16353-16359
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Tidskriftsartikel (refereegranskat)abstract
- In this study, the scavenging activity against OOH radicals and the copper-chelating ability of two new synthesized molecules (named L1 and L2) that can act as multiple target agents against Alzheimer's disease have been investigated at the density functional theory level. The pKa and molar fractions at physiological pH have been predicted. The main antioxidant reaction mechanisms in lipid-like and water environments have been considered and the relative rate constants determined. The copper-chelating ability of the two compounds has also been explored at different coordination sites and computing the complexation kinetic constants. Results show the L1 compound is a more effective radical scavenging and copper-chelating agent than L2.
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- Spiegel, Maciej, et al.
(författare)
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Primary and secondary antioxidant properties of scutellarin and scutellarein in water and lipid-like environments : A theoretical investigation
- 2022
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Ingår i: Journal of Molecular Liquids. - : Elsevier BV. - 0167-7322 .- 1873-3166. ; 366
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Tidskriftsartikel (refereegranskat)abstract
- The scavenging capability of scutellarin flavonoid against the OOH radical has been studied, at Density Functional level of theory, by considering different reaction mechanisms in both lipid-like and water media. In water phase, the neutral and charged species present in solution, identified from the computed pKa equilibria, have been determined. Furthermore, the complexation ability of Scutellarin and its metabolite scutellarein with respect to the Cu2+ and Fe3+ ions has been determined at the same level of theory. From the obtained rate constants results that scutellarin is a better Fe(III) ligand while scutellarein show a revers behavior. The glucuronidation process affect both the primar and secondary antiox-idant properties of the systems.
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