Department of Physics , University of Houston , Houston 77204 , United States.
Department of Physics , Khalifa University of Science and Technology , Abu Dhabi , UAE.
J Phys Chem B. 2019 May 2;123(17):3607-3617. doi: 10.1021/acs.jpcb.9b00782. Epub 2019 Apr 23.
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 rodlike crowders stabilize an elongated conformation of unfolded apoazurin in the presence of effective attraction between the protein and crowders.
在这里，我们通过溶液核磁共振测量表明，与基于体积排阻的大分子拥挤效应的预测相反，当存在合成拥挤剂葡聚糖 20 时，尿素变性的蛋白 apoazurin 会变得伸长。为了探索超出体积排阻的复杂相互作用，我们采用粗粒化分子动力学模拟来探索在强化学变性条件下，apoazurin 在单分散拥挤剂盒中的构象集合。无折叠 apoazurin 的伸长构象似乎是由于蛋白质和拥挤剂之间的有效吸引力以及拥挤剂的形状之间的相互作用产生的。使用具有体积守恒的拥挤剂模型，我们表明，拥挤剂的形状提供了一个各向异性的耗尽力方向，其中一束周围的棒状拥挤剂在蛋白质和拥挤剂之间存在有效吸引力的情况下稳定了无折叠 apoazurin 的伸长构象。
