Macromolecular crowding effects on coupled folding and binding.
Macromolecular crowding effects on coupled folding and binding.
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DOI：
10.1021/jp508046y
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发表时间：
2014-10
期刊：
影响因子：
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通讯作者：
Young C. Kim;Apratim Bhattacharya;J. Mittal
中科院分区：
文献类型：
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作者：
Young C. Kim;Apratim Bhattacharya;J. Mittal
在蛋白质复合物pKID-KIX上进行双交换分子动力学模拟，以了解大分子拥挤对耦合折叠和结合事件的影响。一个基于结构的蛋白质模型在残基水平上被采用的两种蛋白质，包括分子内构象的灵活性，而拥挤的大分子被表示为球形颗粒。拥挤和蛋白质残基之间的相互作用可以是纯粹的排斥或短程排斥和中程吸引的组合。与以往的研究一致的刚性体蛋白结合的存在下，球形拥挤，我们发现，复合物的形成是稳定的排斥蛋白质拥挤的相互作用和不稳定的足够强的吸引力的蛋白质拥挤的相互作用。稳定的排斥和不稳定的吸引力之间的相互作用的竞争定量捕获由以前的理论模型开发用于描述在拥挤的环境中的刚性蛋白质的结合自由能的变化。我们发现，蛋白质的灵活性对热力学的pKID-KIX结合（相对于散装）排斥和弱吸引力的蛋白质-拥挤的相互作用几乎没有影响。对于强蛋白质拥挤吸引力的相互作用，由于拥挤的不稳定的影响是由蛋白质的灵活性减弱。有趣的是，在大量观察到的耦合折叠和结合的机制保持不变，在高度拥挤的条件下，在广泛的蛋白质-拥挤的相互作用强度。此外，强的蛋白质-拥挤吸引相互作用可以显著稳定涉及pKID和KIX结构域之间的部分接触的中间状态。
Replica exchange molecular dynamics simulations are performed on the protein complex pKID-KIX to understand the effects of macromolecular crowding on coupled folding and binding events. A structure-based protein model at the residue level is adopted for the two proteins to include intramolecular conformational flexibility, while crowding macromolecules are represented as spherical particles. The interactions between crowders and protein residues can be either purely repulsive or a combination of short-range repulsion and intermediate-range attraction. Consistent with previous studies on rigid-body protein binding in the presence of spherical crowders, we find that the complex formation is stabilized by repulsive protein-crowder interactions and destabilized by sufficiently strong attractive protein-crowder interactions. Competition between stabilizing repulsive and destabilizing attractive interactions is quantitatively captured by a previous theoretical model developed for describing the change in the binding free energy of rigid proteins in a crowded environment. We find that protein flexibility has little effect on the thermodynamics of the pKID-KIX binding (with respect to bulk) for repulsive and weakly attractive protein-crowder interactions. For strong protein-crowder attractive interactions, the destabilizing effect due to crowding is attenuated by protein flexibility. Interestingly, the mechanism of coupled folding and binding observed in bulk remains unchanged under highly crowded conditions over a broad range of protein-crowder interaction strengths. Also, strong protein-crowder attractive interactions can significantly stabilize intermediate states involving partial contact between pKID and KIX domains.