| Abstract
| - Molecular dynamics simulations have been performed to gain insights into the catalytic mechanismof the hydrolysis of epoxides to vicinal diols by soluble epoxide hydrolase (sEH). The binding of a substrate,1S,2S-trans-methylstyrene oxide, was studied in two conformations in the active site of the enzyme. It wasfound that only one is likely to be found in the active enzyme. In the preferred conformation the phenylgroup of the substrate is π-sandwiched between two aromatic residues, Tyr381 and His523, whereas theother conformation is π-stacked with only one aromatic residue, Trp334. Two simulations were carried outto 1 ns for each conformation to evaluate the protonation state of active site residue His523. It was foundthat a protonated histidine is essential for keeping the active site from being disrupted. Long time scale, 4ns, molecular dynamics simulation was done for the structure with the most likely combination of bindingconformation and protonation state of His523. Near Attack Conformers (NACs) are present 5.3% of thetime and nucleophilic attack on either epoxide carbon atom, ∼75% on C1 and ∼25% on C2, is found. Amaximum of one hydrogen bond between the epoxide oxygen and either of the active site tyrosines, Tyr465and Tyr381, is present, in agreement with experimental mutagenesis results that reveal a slight loss inactivity if one tyrosine is mutated and essential loss of all activity upon double mutation of the two tyrosinesin question. It was found that a hydrogen bond from Tyr465 to the substrate oxygen is essential for controllingthe regioselectivity of the reaction. Furthermore, a relationship between the presence of this hydrogenbond and the separation of reactants was found. Two groups of amino acid segments were identified eachas moving collectively. Furthermore, an overall anti-correlation was found between the movements of thesetwo individually collectively moving groups, made up by parts of the cap-region, including the two tyrosines,and the site of the catalytic triad, respectively. This overall anti-correlated collective domain motion is,perhaps, involved in the conversion of E·NAC to E·TS.
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