Why and how does cellular crowding affect enzymatic activity?

Enzymatic activities are usually investigated in dilute solutions even though these reactions occur in crowded cellular environments. We describe how crowding affects the activity, internal dynamics and diffusion of the hepatitis C virus (HCV) protease — NS3/4A. This enzyme is crucial for viral replication and is used as the therapeutic target. The aim of this project is to perform atomistic molecular dynamics simulations with two types of crowders that are typically used in experiments: the polyethylene glycol (PEG) and polysaccharide (Ficoll) and explain why these crowders exert different effects on the dynamics and activity of the NS3/4A enzyme. The aim includes determination of the force field parameters for Ficoll that can be used in molecular dynamics simulations.