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Cascade Kinetics of an Artificial Metabolon by Molecular Dynamics and Kinetic Monte Carlo

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journal contribution
posted on 10.07.2018, 00:00 by Yuanchao Liu, Ivana Matanovic, David P. Hickey, Shelley D. Minteer, Plamen Atanassov, Scott Calabrese Barton
Natural enzyme cascades are able to employ electrostatic channeling as an efficient mechanism for shuttling charged intermediates between sequential active sites. Application of channeling mechanisms to artificial cascades has drawn increasing attention for its potential to improve cascade design. We report a quantitative model of a two-step artificial metabolon that accounts for molecular-level complexity. Conversion of glucose to phospho-6-gluconolactone by hexokinase and glucose-6-phosphate dehydrogenase, covalently conjugated by a cationic oligopeptide bridge, is simulated and validated by comparison to stopped-flow lag time analysis. Specifically, molecular dynamics (MD) simulations enable the calculation of energy-determined surface equilibrium constants and surface diffusivity, and a kinetic Monte Carlo (KMC) model integrated all rate constants from MD (e.g., surface diffusion and desorption rate) and experiments (e.g., turnover frequency), to estimate the product evolution on an experimental time scale, starting from presteady state. Simulations, conducted as a function of ionic strength, compare well to experiment and indicate that bridge-enzyme leakage is a major limitation accounting for significant lag time increase. Reducing the energy barrier between the channeling pathway and binding pocket could further improve channeling efficiency. Bridge length is also found to have a significant effect on overall kinetics.