Large-scale analysis of macromolecular crowding effects on protein aggregation using a reconstituted cell-free translation system

Proteins must fold into their native structures in the crowded cellular environment, to perform their functions. Although such macromolecular crowding has been considered to affect the folding properties of proteins, large-scale experimental data have so far been lacking. Here, we individually translated 142 <em>Escherichia coli</em> cytoplasmic proteins using a reconstituted cell-free translation system in the presence of macromolecular crowding reagents (MCRs), Ficoll 70 or dextran 70, and evaluated the aggregation propensities of 142 proteins. The results showed that the MCR effects varied depending on the proteins, although the degree of these effects was modest. Statistical analyses suggested that structural parameters were involved in the effects of the MCRs. Our dataset provides a valuable resource to understand protein folding and aggregation inside cells. Table 1 shows the data obtained from this analysis and several properties of tested proteins. Table 2 shows the predicted classification of the Structural Classification of Proteins (SCOP) for the structural analysis. Table 3 shows the templates for constructing the structural models for 41 proteins and several structural features obtained from the calculation with the constructed model.

蛋白质必须在拥挤的细胞环境中折叠为天然构象，方可执行其生物学功能。尽管此前已有研究指出这类大分子拥挤效应会影响蛋白质的折叠特性，但迄今为止仍缺乏大规模的相关实验数据。本研究利用重构型无细胞翻译系统，在大分子拥挤试剂（macromolecular crowding reagents, MCRs）Ficoll 70或葡聚糖70（dextran 70）存在的条件下，分别对142个大肠杆菌（Escherichia coli）胞质蛋白进行了翻译，并评估了这142种蛋白的聚集倾向。研究结果显示，大分子拥挤试剂的效应因蛋白种类而异，尽管这些效应的整体程度较为温和。统计分析表明，结构参数与大分子拥挤试剂的作用效应相关。本数据集为理解细胞内蛋白质折叠与聚集过程提供了宝贵的研究资源。表1展示了本分析所获得的数据以及受试蛋白的多项特性；表2展示了蛋白质结构分类（Structural Classification of Proteins, SCOP）的预测分类结果，用于结构分析；表3展示了用于构建41种蛋白质结构模型的模板，以及通过所构建模型计算得到的多项结构特征。