Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

TL;DR

This study investigates how macromolecular crowding influences the folding mechanisms of apoflavodoxin, revealing that crowding conditions and agent geometry can modulate folding pathways and stability, with implications for cellular protein behavior.

Contribution

It combines in silico simulations and in vitro experiments to demonstrate how crowding agents affect protein folding pathways and stability, highlighting the role of crowding geometry.

Findings

Crowding enhances protein stability under certain conditions.

Folding pathways can be either facilitated or hindered by crowding.

Crowding agent geometry influences folding mechanisms.

Abstract

Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents using in silico and in vitro approaches. By coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fraction of crowding agents (phi_c) as well as of crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have identified in silico crowding conditions that best enhance protein stability and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. The test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. We propose that macromolecular crowding effects may be a tool for manipulation of protein folding and function in living cells.