How proteins squeeze through polymer networks: a Cartesian lattice study

TL;DR

This study models protein diffusion through polymer networks in cell nuclei using a lattice approach, revealing how network dynamics influence particle transport and trapping effects.

Contribution

It introduces a lattice-based model for particle diffusion in dynamic polymer networks, demonstrating the impact of network motion on large particle transport.

Findings

Dynamical networks facilitate large particle diffusion.

Subdiffusive behavior results from trapping in crowded environments.

Protein diffusion coefficient in chromatin network is quantified.

Abstract

In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense networks are created by a combined version of the bond fluctuation method and a Metropolis Monte Carlo algorithm. Semidilute behaviour of the dense chain networks is shown. By comparing diffusion of particles in a static and a dynamical chain network, we demonstrate that chain diffusion does not alter the diffusion process of small particles. However, we prove that a dynamical network facilitates the transport of large particles. By weighting the mean square displacement trajectories of particles in the static chain network data from the dynamical network can be reconstructed. Additionally, it is shown that subdiffusive behaviour of particles on short time scales results from trapping processes in the crowded environment of the chain network. In the presented model a protein with 30 nm diameter has an effective diffusion coefficient of 1.24E-11 m^2/s in a chromatin fiber network.