8 research outputs found
Effects of C5-substituent group on the hydrogen peroxide-mediated tautomerisation of protonated cytosine: a theoretical perspective
<p>The direct tautomerism (path A) and H<sub>2</sub>O<sub>2</sub> as a catalyst (path B) have been studied in conversion of Cyt2t<sup>+</sup> into CytN3<sup>+</sup> isomer. The protonated 5-carboxycytosine (5-caCyt) is represented and has been further explored in the presence of H<sub>2</sub>O<sub>2</sub> (path C). In going from a four-membered-ring transition state in the case of the direct tautomerism to the six-membered ring for H<sub>2</sub>O<sub>2</sub>, the H<sub>2</sub>O<sub>2</sub> significantly contributes to decreasing the free energy barrier of tautomerisation. Although the carboxylic substituent of 5-carboxycytosine has certain affected on the electron distribution of the pyrimidine ring, the six-membered-ring transition state has not changed. This result illustrates that the C5-carboxylation has no significant effect on the H<sub>2</sub>O<sub>2</sub>-mediated isomerisation of Cyt2t<sup>+</sup> to CytN3<sup>+</sup> isomer. Meanwhile, these paths A–C have been further explored in the presence of two water molecules. Use of implicit solvent models (PCM) does not significantly alter the energetics of water-mediated paths A–C compared to those in gas phase. Furthermore, the rate constant with Wigner tunnelling correction of path A is obviously smaller than those of paths B and C. Finally, the lifetime τ<sub>99.9%</sub> of paths B and C is 10<sup>−5</sup> s, which is implemented by the mechanism of the concerted synchronous double proton transfer.</p
Homology modeling and identified substrate tunnel.
<p><b>A.</b> The residues involved in coordinating dinuclear iron. These residues were labeled in cyan, and the dinuclear iron sites were shown in sphere; <b>B.</b> Tunnel identified in the homology modeling of PHN component from <i>Arthrobacter</i> sp. W1 using CAVER. The white sticks represent five formed residues, i.e. Thr-201, Asn-202, Phe-205, Glu-231 and Met-235. The tunnel is labeled as yellow surface and the residues formed entrance are in purple.</p
Interactions between PHN<sub>W1</sub> component and indole derivatives.
<p>Orientations of docked indoles in the active site of PHN<b><sub>W1</sub></b> component: <b>A.</b> Indole; <b>B.</b> 4-Methylindole; <b>C.</b> 5-Methylindole; <b>D.</b> 7-Methylindole; <b>E.</b> 4-Chloroindole; <b>F.</b> 7-Chloroindole; <b>G.</b> 5-Methyoxyindole; <b>H.</b> 3-Methylindole. Atom designation: carbon atom, blue; hydrogen atom, white; chlorine atom, green; oxygen atom, red. Orange spheres represent for diiron, of which located above is designated as Fe1; green represent for tunnel entrance residues Asn-202 and Phe-205; other important residues are shown in grey.</p
Identification of transformation products by TLC.
<p>The transformation samples were extracted with equal volume of ethyl acetate and concentrated by N<sub>2</sub>. 200 µL of the extracts were applied to the TLC plates (silica gel 60 F254), and then the TLC plates were resolved with a solvent mixture of dichloromethane-methanol (50∶1, v/v). The samples were designated as following: <b>1.</b> Indigo (standard); <b>2.</b> Products of indole transformation; <b>3.</b> Products of 4-methylindole transformation; <b>4.</b> Products of 5-methylindole transformation; <b>5.</b> Products of 7-methylindole transformation; <b>6.</b> Products of 5-methoxyindole transformation; <b>7.</b> Products of 4-chloroindole transformation; <b>8.</b> Products of 7-chloroindole transformation. The products with different <i>R<sub>f</sub></i> values were indicated in three regions by the arrows.</p
Comparisons of active sites in various oxygenases.
*<p>PH: phenol hydroxylase; TMO: toluene 4-monooxygenase; MMO: methane monooxygenase;</p><p>NDO: naphthalene 1,2-dioxygenase.</p>**<p>The distance of Val-260 CG1 and His-295 NE2.</p>***<p>Calculated by CASTp server.</p
Residues involved in binding different indoles.
<p>Residues involved in binding different indoles.</p
Bacterial strains and plasmids used in this study.
<p>Bacterial strains and plasmids used in this study.</p
Characteristics of indigoids produced by whole cells of strain PH_<sub>IND</sub>.
*<p>Transformation yield (%) was calculated as the reduced indoles concentration to the initial indoles concentration in the reaction systems.</p