title: IMPORTANCE OF EXCLUDED VOLUME AND HYDRODYNAMIC INTERACTIONS ON MACROMOLECULAR DIFFUSIONIN VIVO.
abstract: The interiors of all living cells are highly crowded with macromolecules, which results in a considerable difference between the thermodynamics and kinetics of biological reactionsin vivofrom thatin vitro. To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing Brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromoleculesin vivofrom that at infinite dilution. In anE. colicytoplasm modelcomprised of 15 different macromolecule types at physiological concentrations, where macromolecules were represented by spheres with their Stokes radii, BD simulations were performed with and without hydrodynamic interactions (HI). Without HI, the calculated diffusion constant of green fluorescent protein (GFP) is much larger than experiment. On the other hand, when HI were considered, thein vivoexperimental GFP diffusion constant is almost reproduced without adjustable parameters. In addition, HI give rise to significant, size independent intermolecular dynamic correlations. These results suggest that HI play an important role on macromolecular dynamicsin vivo.
authors.affiliation: Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology 250 14th Street NW, Atlanta, GA 30318-5304, USA.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Ando
authors.affiliation: Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology 250 14th Street NW, Atlanta, GA 30318-5304, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Skolnick