Diffusional Channeling in the Sulfate Activating Complex: Combined Continuum Modeling and Coarse-grained Brownian Dynamics Studies
Yuhui Cheng
Chemistry Department, UCSD
Abstract:
Enzymes required for sulfur metabolism have been suggested to gain efficiencyby restricted diffusion ("channeling") of an intermediate APS2- between activesites. This article describes modeling of the whole channeling process by numericalsolution of the Smoluchowski diffusion equation, as well as by coarse-grainedBrownian dynamics. The results suggest that electrostatics plays an essential rolein the APS2- channeling. Furthermore, with coarse-grained Brownian dynamics,the substrate channeling process has been studied with reactions in multiple activesites. Our simulations provide a bridge for numerical modeling with Browniandynamics to simulate the complicated reaction and diffusion and raise importantquestions relating to the electrostatically mediated substrate channeling in vitro, insitu and in vivo.