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The parameters for the OPLS-AA potential energy function have been extended to include some functional groups that are present in macrocyclic polyketides. Existing OPLS-AA torsional parameters for alkanes, alcohols, ethers, hemiacetals, esters, and ketoamides were improved based on MP2/aug-cc-pVTZ and MP2/aug-cc-pVDZ calculations. Nonbonded parameters for(More)
We report the identification and purification of a novel enzyme from soybean root nodules that catalyzes the hydrolysis of 5-hydroxyisourate, which is the true product of the urate oxidase reaction. The product of this reaction is 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline, and the new enzyme is designated 5-hydroxyisourate hydrolase. The enzyme was(More)
Conformational analysis of three small alcohols--ethanol, propanol, and isopropanol--was carried out by systematically improving the basis set and the level of electron correlation. Correlation energy contributions to conformational energies are strongly basis-set-dependent but accurate energy contributions can be obtained by extrapolation to the basis-set(More)
The kinetic mechanism of urate oxidase isolated from soybean root nodules has been determined by initial velocity kinetic studies monitoring oxygen uptake, in order to avoid potential artifacts in the spectrophotometric assay which arise from absorbance due to unidentified products of the enzymatic reaction. Urate and O2 bind to the enzyme sequentially;(More)
Delta(5)-3-Ketosteroid Isomerase (KSI) catalyzes the isomerization of 5,6-unsaturated ketosteroids to their 4,5-unsaturated isomers at a rate approaching the diffusion limit. The isomerization reaction follows a two-step general acid-base mechanism starting with Asp38-CO(2)(-) mediated proton abstraction from a sp(3)-hybridized carbon atom, alpha to(More)
It is well known that the convergence of harmonic frequencies with respect to the basis set size in traditional correlated calculations is slow. We now report that the convergence of cubic and quartic force constants in traditional CCSD(T) calculations on H(2)O with Dunning's cc-pVXZ family of basis sets is also frustratingly slow. As an alternative, we(More)
The S(N)2 displacement of Cl(-) from 1,2-dichloroethane by acetate (CH(3)CO(2)(-)) in water and by the carboxylate of the active site aspartate in the haloalkane dehalogenase of Xanthobacter autothropicus have been compared by using molecular dynamics simulations. In aqueous solution, six families of contact-pair structures (I-VI) were identified, and their(More)
Hybrid quantum mechanics/molecular mechanics calculations using Austin Model 1 system-specific parameters were performed to study the S(N)2 displacement reaction of chloride from 1,2-dichloroethane (DCE) by nucleophilic attack of the carboxylate of acetate in the gas phase and by Asp-124 in the active site of haloalkane dehalogenase from Xanthobacter(More)
The oxidation of urate catalyzed by soybean urate oxidase was studied under single-turnover conditions using stopped-flow absorbance and fluorescence spectrophotometry. Two discrete enzyme-bound intermediates were observed; the first intermediate to form had an absorbance maximum at 295 nm and was assigned to a urate dianion species; the second intermediate(More)
The mechanism of hydrolysis of the nitrile (N-acetyl-phenylalanyl-2-amino-propionitrile, I) catalyzed by Gln19Glu mutant of papain has been studied by nanosecond molecular dynamics (MD) simulations. MD simulations of the complex of mutant enzyme with I and of mutant enzyme covalently attached to both neutral (II) and protonated (III) thioimidate(More)