ABSTRACT
In this work, we have performed molecular dynamics simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) scheme to study the mechanism of l-lactate oxidation by flavocytochrome b2 (Fcb2). Our results obtained at the QM(AM1)/MM level have been improved by single-point corrections using density functional theory (DFT) methods. Free energy surfaces have been calculated in the framework of the hydride transfer hypothesis. This mechanism involves the transfer of the lactate hydroxyl proton to H373 while the substrate αH atom is transferred as a hydride to the flavin mononucleotide (FMN) prosthetic group anchored in the active site. Four different systems have been modeled: wild-type enzyme considering R289 in a distal or a proximal conformation observed in crystal structures and the D282N and Y254L variants (with R289 in a distal position). Simulation results highlight the influence of the environment on the catalytic mechanism by describing a step-wise process in the WT enzyme with R289 in a distal position and a concerted mechanism for the other systems. In the step-wise mechanism, the hydride transfer to flavin can occur only after a proton transfer from substrate to H373. Modifications of the electrostatic field around l-lactate or H373 disfavor the highly charged complex resulting from this proton transfer. Simulations of the Y254L variant also reveal some effect of steric changes.
ABSTRACT
We report a joint experimental and molecular simulation study of water condensation in silicalite-1 zeolite. A sample was synthesized using the fluoride route and was found to contain essentially no defects. A second sample synthesized using the hydroxide route was found to contain a small amount of silanol groups. The thermodynamics of water condensation was studied in these two samples, as well as in a commercial sample, in order to understand the effect of local defects on water adsorption. The molecular simulation study enabled us to qualitatively reproduce the experimentally observed condensation thermodynamics features. A shift and a rounding of the condensation transition was observed with an increasing hydrophilicity of the local defect, but the condensation transition was still observed above the water saturation vapor pressure P0. Both experiments and simulations agree on the fact that a small water uptake can be observed at very low pressure, but that the bulk liquid does not form from the gas phase below P0. The picture that emerges from the observed water condensation mechanism is the existence of a heterogeneous internal surface that is overall hydrophobic, despite the existence of hydrophilic "patches". This heterogeneous surface configuration is thermodynamically stable in a wide range of reduced pressures (from P/P0 = 0.2 to a few thousands), until the condensation transition takes place.
