Abstract
A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI.
Highlights
As computer simulations of biomolecules advance, efforts are underway to mimic the behavior of many macromolecules at the same time
We have investigated anomalous diffusion (AD), which has been observed in some experiments [40,41,42,43,44,45], using Fractional Brownian Motion (FBM) analysis
green fluorescent protein (GFP) was modeled as a collection of spheres as done for other proteins and only one GFP was used in our simulation
Summary
As computer simulations of biomolecules advance, efforts are underway to mimic the behavior of many macromolecules at the same time. The group of Martin Field, in their pioneering work, modeled a collection of proteins, t-RNAs and ribosomes with spheres [6] They included both short-ranged Lennard-Jones and long-ranged electrostatic interactions in their model. We consider the most abundant proteins of E. coli in our cytoplasm model, describing each protein as a flexible unit consisting of a collection of spheres Another major departure from the previous models is that we accounted for hydrodynamic effects with a simple mean field approximation [35,36,37,38,39] based on a dynamic scaling of D of the spheres by their local volume fraction. The underlying physical reasons for the AD in our model were identified by running a series of control simulations in which the different interactions used to describe the cytoplasm were modulated
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