Crowding-induced Elongated Conformation of Urea-unfolded Apoazurin: Investigating the Role of Crowder Shape In Silico

TL;DR

This study combines NMR experiments and molecular dynamics simulations to reveal that crowder shape influences the elongation of unfolded apoazurin, challenging traditional volume exclusion models in macromolecular crowding.

Contribution

It demonstrates that crowder shape and effective attraction, beyond volume exclusion, induce elongation of unfolded proteins in crowded environments.

Findings

Crowder shape causes anisotropic depletion forces.

Elongation results from interplay of attraction and crowder shape.

Simulations confirm shape-dependent stabilization of elongated conformations.

Abstract

Here, we show by solution nuclear magnetic resonance measurements that the urea-unfolded protein apoazurin becomes elongated when the synthetic crowding agent dextran 20 is present, in contrast to the prediction from the macromolecular crowding effect based on the argument of volume exclusion. To explore the complex interactions beyond volume exclusion, we employed coarse-grained molecular dynamics simulations to explore the conformational ensemble of apoazurin in a box of monodisperse crowders under strong chemically denaturing conditions. The elongated conformation of unfolded apoazurin appears to result from the interplay of the effective attraction between the protein and crowders and the shape of the crowders. With a volume-conserving crowder model, we show that the crowder shape provides an anisotropic direction of the depletion force, in which a bundle of surrounding rod-like crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.