Determination of enzyme mechanisms by molecular dynamics: Studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase

Abstract

Molecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted basecatalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1-hydroxyl of glucose, and hydride equivalent transfer from the substrate to the quinone carbonyl carbon C5 of PQQ. The products of methanol and glucose oxidation are formaldehyde and glucolactone, respectively. The immediate product of PQQ reduction, PQQH

Mechanism of methanol oxidation by quinoprotein methanol dehydrogenase

“…Computational findings based on the present QM/MM computations and MD simulations, as well as our previous MD simulations (6,7,9), lead to the conclusion that only Glu-171-CO 2 Ϫ could be the general base catalyst for the oxidation of CH 3 OH 3 CH 2 O.…”

“…3) of the PQQ methanol dehydrogenase (MDH⅐PQQ⅐MeOH⅐Wat1) complex in the water solvent was obtained from the final structure of 3-ns MD simulations (6,7,9). The ground state was obtained by QM/MM energy-minimizing the final structure from our previous MD simulation (6,7,9) for MDH⅐PQQ⅐MeOH⅐Wat1 complex by Adopted Basis Newton-Raphson (ABNR) method until the gradient was Ͻ0.01 kcal/(mol⅐Å). The similar procedure was used to obtain the QM/MM starting structure from the snapshot (1.2 ns) of 3-ns MD simulations for MDH⅐PQQ⅐MeOH model.…”

“…1-4). More recently, our attention has been directed to the employment of computational methods, particularly in the mechanism of the oxidation of methanol and glucose by the appropriate quinoprotein enzymes (5)(6)(7)(8)(9)(10)(11).…”

“…During 3-ns molecular dynamics (MD) simulations (6,7,9) with MeOH at the active site, it was found that MeOH became hydrogen bonded to Glu-171-CO 2 Ϫ , with the C-H of MeOH adjacent to the quinone C5 of PQQ and Wat1 hydrogen bonded to Asp-297-CO 2 Ϫ . This MD derived structure is not in accord with the following: (i) the suggestion that Asp-297-CO 2 Ϫ serves as the general-base catalyst (14)(15)(16)(17); and (ii) that the oxidation takes place, not by hydride transfer, but by an addition elimination reaction (18,19) (Scheme 1, in which the general base may be Glu-171-CO 2 Ϫ or Asp-297-CO 2 Ϫ ).…”

“…This MD derived structure is not in accord with the following: (i) the suggestion that Asp-297-CO 2 Ϫ serves as the general-base catalyst (14)(15)(16)(17); and (ii) that the oxidation takes place, not by hydride transfer, but by an addition elimination reaction (18,19) (Scheme 1, in which the general base may be Glu-171-CO 2 Ϫ or Asp-297-CO 2 Ϫ ). The MD studies (6,7,9) showed that Asp-297-CO 2 Ϫ is not in position to act as a generalbase catalyst for the oxidation of MeOH by MDH. The mechanism of Scheme 2 was proposed.…”