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Here, we show by solution nuclear magnetic resonance measurements that theurea-unfolded protein apoazurin becomes elongated when the synthetic crowdingagent dextran 20 is present, in contrast to the prediction from themacromolecular crowding effect based on the argument of volume exclusion. Toexplore the complex interactions beyond volume exclusion, we employedcoarse-grained molecular dynamics simulations to explore the conformationalensemble of apoazurin in a box of monodisperse crowders under strong chemicallydenaturing conditions. The elongated conformation of unfolded apoazurin appearsto result from the interplay of the effective attraction between the proteinand crowders and the shape of the crowders. With a volume-conserving crowdermodel, we show that the crowder shape provides an anisotropic direction of thedepletion force, in which a bundle of surrounding rod-like crowders stabilizean elongated conformation of unfolded apoazurin in the presence of effectiveattraction between the protein and crowders.

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