Institute for Molecules and Materials, Radboud University , 6525 AJ, Nijmegen, The Netherlands.
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , 9747 AG Groningen, The Netherlands.
J Am Chem Soc. 2015 Oct 14;137(40):13041-8. doi: 10.1021/jacs.5b07898. Epub 2015 Sep 29.
The cytosol of Escherichia coli is an extremely crowded environment, containing high concentrations of biopolymers which occupy 20-30% of the available volume. Such conditions are expected to yield depletion forces, which strongly promote macromolecular complexation. However, crowded macromolecule solutions, like the cytosol, are very prone to nonspecific associative interactions that can potentially counteract depletion. It remains unclear how the cytosol balances these opposing interactions. We used a FRET-based probe to systematically study depletion in vitro in different crowded environments, including a cytosolic mimic, E. coli lysate. We also studied bundle formation of FtsZ protofilaments under identical crowded conditions as a probe for depletion interactions at much larger overlap volumes of the probe molecule. The FRET probe showed a more compact conformation in synthetic crowding agents, suggesting strong depletion interactions. However, depletion was completely negated in cell lysate and other protein crowding agents, where the FRET probe even occupied slightly more volume. In contrast, bundle formation of FtsZ protofilaments proceeded as readily in E. coli lysate and other protein solutions as in synthetic crowding agents. Our experimental results and model suggest that, in crowded biopolymer solutions, associative interactions counterbalance depletion forces for small macromolecules. Furthermore, the net effects of macromolecular crowding will be dependent on both the size of the macromolecule and its associative interactions with the crowded background.
大肠杆菌的细胞质是一种极其拥挤的环境,其中含有高浓度的生物聚合物,占据了可用体积的 20-30%。这种情况预计会产生耗竭力,从而强烈促进大分子复合物的形成。然而,像细胞质这样的拥挤大分子溶液非常容易发生非特异性的缔合相互作用,这可能会抵消耗竭作用。目前尚不清楚细胞质如何平衡这些相互竞争的相互作用。我们使用基于 FRET 的探针在不同的拥挤环境中系统地研究体外耗竭作用,包括细胞质模拟物大肠杆菌裂解物。我们还研究了 FtsZ 原丝在相同拥挤条件下的束形成情况,作为探针研究在探针分子重叠体积较大时的耗竭相互作用。FRET 探针在合成拥挤剂中呈现出更紧凑的构象,表明存在强烈的耗竭相互作用。然而,在细胞裂解物和其他蛋白质拥挤剂中,耗竭作用完全被抵消,FRET 探针甚至占据了稍大的体积。相比之下,FtsZ 原丝的束形成在大肠杆菌裂解物和其他蛋白质溶液中与在合成拥挤剂中一样容易进行。我们的实验结果和模型表明,在拥挤的生物聚合物溶液中,缔合相互作用会平衡小分子的耗竭力。此外,大分子拥挤的净效应将取决于大分子的大小及其与拥挤背景的缔合相互作用。