Modeling Crowding and Confinement of Cellular Environments

描述（由申请人提供）：细胞室内部的拥挤环境与生物分子系统的体外和计算机生物物理研究的典型稀释条件非常不同。该项目的长期目标是通过定量重建细胞环境对生物分子的热力学和动力学性质的影响来弥合体外-体内差距。利用我们的后处理方法为模拟拥挤的细胞样环境和其他最新进展的影响所开辟的巨大机会，在这个项目中，我们将（1）推进基于FFT的后处理，以实现高精度的拥挤建模;（2）定量描述拥挤效应的温度依赖性;（3）表征拥挤条件下内在无序蛋白质的构象集合和结合。通过利用基于FFT的后处理和进行我们自己的湿实验室研究，我们将紧密结合计算和实验，以克服对体内生化过程的洞察所面临的挑战。这项研究所提供的能力，使用稀溶液实验和模拟预测的构象合奏的内在无序蛋白质在细胞样条件下，将推动我们在阐明其细胞功能。细胞环境中的大分子拥挤可能是嗜热菌中蛋白质稳定性的一个重要因素，这一概念的提出对蛋白质的进化和设计具有广泛的影响。

DESCRIPTION (provided by applicant): The crowded environments inside cellular compartments are very different from the typical dilute conditions of in vitro and in silico biophysical studies of biomolecular systems. The long-term objective of this project is to bridge the in vitro-in vivo gap, by quantitatively reconstructing the influences of cellular environments on the thermodynamic and kinetic properties of biomolecules. Exploiting tremendous opportunities opened by our postprocessing approach for modeling effects of crowded cell-like environments and other recent advances, in this project we will (1) advance FFT-based postprocessing to achieve high accuracy in modeling crowding; (2) quantitatively delineate temperature dependence of crowding effects; and (3) characterize conformational ensembles and binding of intrinsically disordered proteins under crowding. Through capitalizing on FFT-based postprocessing and carrying out our own wet-lab studies, we will closely integrate computation and experiment to overcome challenges toward gaining insights into in vivo biochemical processes. The ability afforded by this research to use dilute-solution experiments and simulations for predicting the conformational ensembles of intrinsically disordered proteins under cell-like conditions will move us forward in elucidating their cellular functions. The conceptual advance that macromolecular crowding in cellular environments may serve as an important factor for protein stability in thermophiles could have broad implications for protein evolution and design.