Investigating the Effects of Molecular Crowding on the Kinetics of Protein Aggregation

Abstract

The thermodynamics and kinetics of protein folding and protein aggregation in vivo are of great importance in numerous scientific areas including fundamental biophysics research, nanotechnology, and medicine. However, these processes remain poorly understood in both in vivo and in vitro systems. Here we extend an established model for protein aggregation that is based on the kinetic equations for the moments of the polymer size distribution by introducing macromolecular crowding particles into the model using scaledparticle and transition-state theories. The model predicts that the presence of crowders can either speed up, cause no change to, or slow down the progress of the aggregation compared to crowder-free solutions, in striking agreement with experimental results from nine different amyloid-forming proteins that utilized dextran as the crowder. These different dynamic effects of macromolecular crowding can be understood in terms of the change of excluded volume associated with each reaction step.

Review: Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein — R0/PR1

“…This is in excellent agreement with excluded volume theory that predicts that assembled species are favored when the volume is reduced (Minton, 2005b;Ellis and Minton, 2006). Also more elaborate modelling (including both scaled-particle and transition-state theories) predicts this for systems where the size of the monomer is smaller when in the amyloid fiber than when in the free form (Schreck et al, 2020). Notably, 200 mg ml À1 Ficoll 70 will occupy 13% of the volume based on its partial specific volume value (Christiansen et al, 2010;Aguilar et al, 2011) and thus the effective concentration of apo-β-PV is not 30 μM but 34 μM in the presence of 200 mg ml À1 Ficoll 70.…”

Liquid–Liquid Phase Separation in the Presence of Macromolecular Crowding and State-dependent Kinetics

“…In particular, macromolecular crowders may bias the reactions either towards products or reactants depending on changes in the free energy of the reaction [54]. Furthermore, the presence of macromolecular crowders has been shown to either speed up, cause no change to, or slow down LLPS when compared to crowder-free solutions [55].…”

Recommendation: Response to crowded conditions reveals compact nucleus for amyloid formation of folded protein — R0/PR3

“…In addition to excluded volume and solvation effects (studied here), also nonspecific chemical interactions may take place between macromolecules and hydrophobic forces within macromolecules, for example, DNA, were shown to be affected by cell-like conditions (Feng et al, 2019). Many more systematic studies of these effects on the molecularmechanistic level are desired, including studies using mixtures of macromolecular crowding agents, protein crowders, as well as assessing combinations of macromolecular crowding agents and osmolytes; all in combination with new theoretical approaches (Schreck et al, 2020). So far, known amyloidogenic proteins involved in human diseases are intrinsically disordered proteins or folded (often oligomeric) proteins that require partial unfolding/ dissociation (i.e.…”