Effects of confinement on models of intracellular macromolecular dynamics

Abstract

The motions of particles in a viscous fluid confined within a spherical cell have been simulated using Brownian and Stokesian dynamics simulations. High volume fractions mimicking the crowded interior of biological cells were used. Importantly, although confinement yields an overall slowdown in motion, the qualitative effects of motion in the interior of the cell can be effectively modeled as if the system were an infinite periodic system. However, we observe layering of particles at the cell wall due to steric interactions in the confined space. Motions of nearby particles are also strongly correlated at the cell wall, and these correlations increase when hydrodynamic interactions are modeled. Further, particles near the cell wall have a tendency to remain near the cell wall. A consequence of these effects is that the mean contact time between particles is longer at the cell wall than in the interior of the cell. These findings identify a specific way that confinement affects the interactions between particles and points to a previously unidentified mechanism that may play a role in signal transduction and other processes near the membrane of biological cells.B rownian dynamics (BD) simulations have been used to help qualitatively understand the motions and interactions of proteins and other macromolecules inside biological cells (1-5). Quantitative accuracy for diffusion rates of different sized particles has also been obtained with Stokesian dynamics (SD) simulations (6). In all these studies, a small portion of the interior of the cell is simulated, generally using a periodic simulation box that effectively mimics the motion in an unconfined, infinite system. However, in actual cells, macromolecules diffuse in a confined space and also interact with the cell wall, even at long range. These features may play an important role in the motion of macromolecules within the cell.As a first step toward developing and understanding coarse grained models of entire biological cells, we performed BD simulations, with and without hydrodynamic interactions (HIs), of monodisperse particle suspensions in a confined space, mimicking a biological cell. We also performed SD simulations, which include short-range HIs, called lubrication forces. SD is considered to be more accurate for high volume fraction systems such as the crowded interiors of biological cells. Our goal is to understand the effect of confinement on macromolecular diffusion inside biological cells. Near the cell wall, we hypothesize increased correlated particle motions (1, 6). Away from the wall, we are interested in the extent to which models and simulation methods can neglect the cell wall and effects of confinement.Previous theoretical and experimental studies have shown that diffusion slows down near planar membranes and that this is due to HI (7). Most studies of diffusion in confined spaces have addressed simple geometries such as parallel walls, in part for their simplicity and in part for their application to microfluidic devices (8-10). Other methods...

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