Title: Effects of soft interactions and bound mobility on diffusion in crowded environments: a model of sticky and slippery obstacles,
Abstract: Crowded environments modify the diffusion of macromolecules, generally
slowing their movement and inducing transient anomalous subdiffusion. The
presence of obstacles also modifies the kinetics and equilibrium behavior of
tracers. While previous theoretical studies of particle diffusion have
typically assumed either impenetrable obstacles or binding interactions that
immobilize the particle, in many cellular contexts bound particles remain
mobile. Examples include membrane proteins or lipids with some entry and
diffusion within lipid domains and proteins that can enter into membraneless
organelles or compartments such as the nucleolus. Using a lattice model, we
studied the diffusive movement of tracer particles which bind to soft
obstacles, allowing tracers and obstacles to occupy the same lattice site. For
sticky obstacles, bound tracer particles are immobile, while for slippery
obstacles, bound tracers can hop without penalty to adjacent obstacles. In both
models, binding significantly alters tracer motion. The type and degree of
motion while bound is a key determinant of the tracer mobility: slippery
obstacles can allow nearly unhindered diffusion, even at high obstacle filling
fraction. To mimic compartmentalization in a cell, we examined how obstacle
size and a range of bound diffusion coefficients affect tracer dynamics. The
behavior of the model is similar in two and three spatial dimensions. Our work
has implications for protein movement and interactions within cells.