Influence of shape and interaction anisotropy on short-time protein diffusion

Dnr:

SNIC 2017/1-55

Type:

SNAC Medium

Principal Investigator:

Anna Stradner

Affiliation:

Lunds universitet

Start Date:

2017-02-15

End Date:

2018-03-01

Primary Classification:

10402: Fysikalisk kemi

Secondary Classification:

10603: Biofysik

Webpage:

http://www.physchem.lu.se/people/seniors/anna-stradner/

Allocation

Abstract

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 gammaB-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 incorporating direct and hydrodynamic interactions, provides detailed insight into the dynamics of protein solutions. In this project, we will study the short time diffusion of different model proteins using mesoscale simulations and compare them with experimental short time diffusion coefficients from Neutron Spin Echo measurements. The hybrid simulation approach combines the multiparticle collision dynamics (MPC) method for the fluid with molecular dynamics simulations (MD) for the globular proteins. The effect of shape anisotropy, hydrodynamic interactions as well as anisotropic interactions between proteins will be investigated. In particular, we will focus on the effect of weak attractive interactions known to exist between many globular proteins on the short time diffusion under crowded conditions.