Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability
Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability
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DOI：
10.1016/j.bpj.2009.03.066
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发表时间：
2009-07-08
影响因子：
3.4
通讯作者：
Zhou, Huan-Xiang
中科院分区：
文献类型：
--
作者：
Qin, Sanbo;Zhou, Huan-Xiang
理论模型预测大分子拥挤可以提高蛋白质折叠稳定性，但根据模型的细节（例如变性状态的表示方式），预测的稳定水平可能会有很大不同。在这项研究中，我们分别从室温和高温下的显式溶剂分子动力学模拟中采样了构象，以原子方式表示了天然态和变性态。然后，我们设计了一种有效的算法来计算当蛋白质分子被放置在一盒拥挤器中时所允许的分数 f。由于拥挤器的体积排斥，不允许放置一部分蛋白质分子，导致化学势增加，由 Delta mu = -k(B)TInf 给出。天然态和变性态之间的 Delta mu 差异预示着拥挤对折叠自由能的影响。即使当拥挤器占据溶液体积的 35% 时，细胞色素 b(562) 的稳定性也仅达到 1.5 kcal/mol。预测的适度稳定与实验研究一致。有趣的是，发现不同大小的拥挤者的混合物比单个种类的拥挤者的总和发挥更大的效果。基于蛋白质的原子模型，拥挤对 barnase 和 barstar 结合稳定性的稳定同样是适度的。这些发现对细胞内大分子拥挤具有深远的影响。
Theoretical models predict that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how the denatured state is represented), the level of stabilization predicted can be very different. In this study, we represented the native and denatured states atomistically, with conformations sampled from explicit-solvent molecular dynamics simulations at room temperature and high temperature, respectively. We then designed an efficient algorithm to calculate the allowed fraction, f, when the protein molecule is placed inside a box of crowders. That a fraction of placements of the protein molecule is disallowed because of volume exclusion by the crowders leads to an increase in chemical potential, given by Delta mu = -k(B)TInf. The difference in Delta mu between the native and denatured states predicts the effect of crowding on the folding free energy. Even when the crowders occupied 35% of the solution volume, the stabilization reached only 1.5 kcal/mol for cytochrome b(562). The modest stabilization predicted is consistent with experimental studies. Interestingly, a mixture of different sized crowders was found to exert a greater effect than the sum of the individual species of crowders. The stabilization of crowding on the binding stability of barnase and barstar, based on atomistic modeling of the proteins, was similarly modest. These findings have profound implications for macromolecular crowding inside cells.