Ando Tadashi, Skolnick Jeffrey
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology 250 14th Street NW, Atlanta, GA 30318-5304, USA.
Quantum Bioinform V (2011). 2013 Mar;30:375-387. doi: 10.1142/9789814460026_0032.
The interiors of all living cells are highly crowded with macromolecules, which results in a considerable difference between the thermodynamics and kinetics of biological reactions from that . To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing Brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromolecules from that at infinite dilution. In an cytoplasm modelcomprised of 15 different macromolecule types at physiological concentrations, where macromolecules were represented by spheres with their Stokes radii, BD simulations were performed with and without hydrodynamic interactions (HI). Without HI, the calculated diffusion constant of green fluorescent protein (GFP) is much larger than experiment. On the other hand, when HI were considered, the experimental GFP diffusion constant is almost reproduced without adjustable parameters. In addition, HI give rise to significant, size independent intermolecular dynamic correlations. These results suggest that HI play an important role on macromolecular dynamics .
所有活细胞的内部都充满了大量的大分子，这使得生物反应的热力学和动力学与无限稀释时相比有很大差异。为了开始阐明细胞拥挤环境中分子间动力学的原理，我们采用布朗动力学（BD）模拟，研究了导致大分子扩散常数与无限稀释时相比大幅降低的可能机制。在一个由15种不同类型的大分子以生理浓度组成的细胞质模型中，大分子用具有斯托克斯半径的球体表示，分别在有和没有流体动力学相互作用（HI）的情况下进行BD模拟。没有HI时，计算出的绿色荧光蛋白（GFP）扩散常数比实验值大得多。另一方面，当考虑HI时，几乎无需调整参数就能重现实验中的GFP扩散常数。此外，HI会产生显著的、与大小无关的分子间动态相关性。这些结果表明，HI在大分子动力学中起着重要作用。
