Dj. Bicout et Mj. Field, STOCHASTIC DYNAMICS SIMULATIONS OF MACROMOLECULAR DIFFUSION IN A MODEL OF THE CYTOPLASM OF ESCHERICHIA-COLI, Journal of physical chemistry, 100(7), 1996, pp. 2489-2497
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.