Theoretical study on keto–enol tautomerisation of glutarimide for exploration of the isomerisation reaction pathway of glutamic acid in proteins using density functional theory

<p>In order to elucidate the reason why glutamic acid residues have lesser racemisation reactivity than asparaginic acid, we investigated the racemisation energy barrier of piperidinedione, which is the presumed intermediate of the isomerisation reaction of L-Glu to D-Glu, by density functional theory calculations. In two-water-molecule-assisted racemisation, the activation barrier for keto–enol isomerisation was 28.1 kcal/mol. The result showed that the activation barrier for the racemisation of glutamic acid residues was not different from that for the racemisation of aspartic acid residues. Thus, glutamic acid residues can possibly cause the racemisation reaction if the cyclic intermediate stably exists.</p

Triazine-Based Cationic Leaving Group: Synergistic Driving Forces for Rapid Formation of Carbocation Species

A new triazine-based cationic leaving group has been developed for the acid-catalyzed alkylation of <i>O</i>- and <i>C</i>-nucleophiles. There are two synergistic driving forces, namely, stable CO bond formation and charge–charge repulsive effects, involved in the rapid generation of the carbocation species in the presence of trifluoromethanesulfonic acid (∼200 mol %). Considerable rate acceleration of benzylation, allylation, and <i>p</i>-nitrobenzylation was observed as compared to the reactions with less than 100 mol % of the acid catalyst. The triazine-based leaving group showed superior <i>p</i>-nitrobenzylation yield and stability in comparison to common leaving groups, trichloroacetimidate and bromide. A plausible reaction mechanism (the cationic leaving group pathway) was proposed on the basis of mechanistic and kinetic studies, NMR experiments, and calculations

Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62

<div><p>Many natural mutants of the drug metabolizing enzyme cytochrome P450 (CYP) 2D6 have been reported. Because the enzymatic activities of many mutants are different from that of the wild type, the genetic polymorphism of CYP2D6 plays an important role in drug metabolism. In this study, the molecular dynamics simulations of the wild type and mutants of CYP2D6, CYP2D6.1, 2, 10, 14A, 51, and 62 were performed, and the predictions of static and dynamic structures within them were conducted. In the mutant CYP2D6.10, 14A, and 61, dynamic properties of the F-G loop, which is one of the components of the active site access channel of CYP2D6, were different from that of the wild type. The F-G loop acted as the “hatch” of the channel, which was closed in those mutants. The structure of CYP2D6.51 was not converged by the simulation, which indicated that the three-dimensional structure of CYP2D6.51 was largely different from that of the wild type. In addition, the intramolecular interaction network of CYP2D6.10, 14A, and 61 was different from that of the wild type, and it is considered that these structural changes are the reason for the decrease or loss of enzymatic activities. On the other hand, the static and dynamic properties of CYP2D6.2, whose activity was normal, were not considerably different from those of the wild type.</p></div

Occurrence rates of hydrogen bonds including the heme in CYP2D6.62.

<p>Occurrence rates of hydrogen bonds including the heme in CYP2D6.62.</p

Occurrence rates of hydrogen bonds found proximate Glu216 in CYP2D6.14A.

<p>Occurrence rates of hydrogen bonds found proximate Glu216 in CYP2D6.14A.</p

Root mean square fluctuations (RMSFs) for the wild type and mutants of CYP2D6.

<p><b>(A) CYP2D6.1, (B) CYP2D6.2, (C) CYP2D6.10, (D) CYP2D6.14A, (E) CYP2D6.62.</b> The simulation of CYP2D6.51 did not converge. For the mutant CYP2D6, RMSF values (red) were compared with those of the wild type (gray).</p

Results of MD simulation for CYP2D6.1 using ff14SB force field.

<p>(A) RMSD, (B) RMSF, (C) distance between B-C and F-G loops, and (D) entrance residues used for the distance calculation.</p

Mutation and activity of the wild-type and mutants of CYP2D6.

<p>Mutation and activity of the wild-type and mutants of CYP2D6.</p

3D structures of the N-terminal region (red-orange) and the F-G loop region (yellow-yellow green).

<p>(A) CYP2D6.1, (B) CYP2D6.10. The 34th residues are shown in space fill model, and the hydrophobic residues located in the interdomain regions are illustrated in ball-and-stick model.</p

Root mean square deviations (RMSDs) for the wild type and mutants of CYP2D6.

<p><b>(A) CYP2D6.1, (B) CYP2D6.2, (C) CYP2D6.10, (D) CYP2D6.14A, (E) CYP2D6.51, (F) CYP2D6.62.</b> The reference structures of RMSD calculations were the initial structures of molecular dynamics simulations. Thus, the reference structure for CYP2D6.1 was the minimized crystal structure. For the mutants, initial structures constructed from three-dimensional structures of CYP2D6.1 were used as the reference.</p