STOCHASTIC DYNAMICS SIMULATIONS OF MACROMOLECULAR DIFFUSION IN A MODEL OF THE CYTOPLASM OF ESCHERICHIA-COLI

Stochastic dynamics simulations have been performed to investigate mac romolecular diffusion in the cytoplasm of the bacterium Escherichia co li. The cytoplasm was modeled as a polydisperse mixture of three diffe rent types of spherical particles representing ribosomes, proteins, an d tRNA molecules at their physiological concentrations, The interactio ns between the particles consisted of short-range Lennard-Jones and lo ng-range electrostatic terms, A number of properties, including the pa ir distributions functions, the static structure factor, and the long- time self-diffusion coefficients, were obtained for various model syst ems differing from each other by the size of the charges on the partic les. The effect of macromolecular crowding on these properties is exam ined, and their implication for the dynamics of macromolecules within living cells is discussed.