Modeling Crowding and Confinement of Cellular Environments

描述（由申请人提供）：细胞隔间内的拥挤环境与体外和生物分子系统的硅生物物理研究中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热力学和动力学特性的影响来弥合体内外的差距。利用我们的后处理方法为拥挤细胞样环境的建模效果和其他最新进展提供的巨大机会，在这个项目中，我们将(1)推进基于fft的后处理，以实现对拥挤建模的高精度；(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的后处理和开展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深入了解的挑战。本研究提供的使用稀溶液实验和模拟来预测细胞样条件下内在无序蛋白质的构象集合的能力将推动我们在阐明其细胞功能方面取得进展。细胞环境中的大分子拥挤可能是嗜热生物蛋白质稳定性的重要因素，这一概念的进步可能对蛋白质的进化和设计产生广泛的影响。

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.