In a dense and crowded environment such as the cell, an individual protein feels the presence of surrounding proteins. It is thus expected that direct and hydrodynamic interactions strongly affect the diffusion of proteins. Examples are suspensions of eye lens proteins, where a dramatic slow down of the local short time diffusion of γB-crystallin and a dynamical arrest is observed experimentally under crowded conditions. It has recently been shown that an application of colloid models, together with appropriate theoretical and simulation tools that allow to incorporate direct and hydrodynamic interactions, provides detailed insight into the dynamics of protein solutions.
In a previous project SNIC-2017/1-55, we have studied the effect of nonspherical particle shape on the dynamics in crowded solutions using mesoscale simulations. The hybrid simulation approach combines the multiparticle collision dynamics (MPC) method for the fluid with molecular dynamics simulations (MD) for the globular proteins. We show that small deviations from a spherical shape decrease the particle mobility determined by hydrodynamics, and loosen the cage configurations governed by excluded volume. The resulting short-time cage diffusion shows a non-monotonic effect fundamentally different from spherical systems.
In this project, we will further investigate the effect of anisotropic interactions as well as hydrodynamic interactions between colloids on the dynamics in crowded solutions. In particular, we will focus on the effect of weak attractive patchy attractions known to exist between many globular proteins on the short time diffusion. This study is of great interest in applications such as formulations as well as for the fundamental understanding of soft matter in general and crowding effects in living cells in particular.