Modeling protein association from homogeneous to mixed environments: A reaction-diffusion dynamics approach

• Published in: Journal of molecular graphics & modelling 2021-09, Vol.107, p.107936-107936, Article 107936
• Main Authors: Sahu, Suraj Kumar, Biswas, Mithun
• Format: Article
• Language: English
• Subjects: Mixed macromolecular crowding; Protein association; Soft interaction
• ISSN: 1093-3263; 1873-4243
• DOI: 10.1016/j.jmgm.2021.107936

Protein-protein association in vivo occur in a crowded and complex environment. Theoretical models based on hard-core repulsion predict stabilization of the product under crowded conditions. Soft interactions, on the contrary, can either stabilize or destabilize the product formation. Here we modeled protein association in presence of crowders of varying size, shape, interaction potential and used different mixing parameters for constituent crowders to study the influence on the association reaction. It was found that size is a more dominant factor in crowder-induced stabilization than the shape. Furthermore, in a mixture of crowders having different sizes but identical interaction potential, the change of free energy is additive of the free energy changes produced by individual crowders. However, the free energy change is not additive if two crowders of same size interact via different interaction potentials. These findings provide a systematic understanding of crowding influences in heterogeneous medium. [Display omitted] •Crowding influence on reaction equilibrium depends on the nature of inter-particle interaction.•Size is a more dominant factor than shape in crowder induced stabilization.•Mixed crowder solution can have additive or non-additive effect depending on how it is prepared.