蛋白质在核糖体出口通道的逃逸：通道形状的影响
Protein escape at the ribosomal exit tunnel: Effect of the tunnel shape
摘要：
本文基于海绒archeon Haloarcula marismortui核糖体大亚基蛋白质数据库（PDB）的结构，研究了新生蛋白质在核糖体出口隧道中的翻译后逃逸。分子动力学模拟表明，在中等和高温下，包括一个假定的生理温度，蛋白质逃逸过程中的原子隧道是定量相似的长度L = 72毫米，直径d = 16毫米的圆柱隧道。在低温下，原子隧道，然而，产生一个增加的概率蛋白质捕获内的隧道，而圆柱隧道不会导致捕获。全$β$蛋白倾向于比全$α$蛋白更快地逃逸，但这种差异在增加蛋白链长度时变得模糊。一个29残基锌指结构域被严重困在隧道内。然而，大多数考虑的单结构域蛋白质，可以有效地逃逸在生理温度下的逃逸时间分布以下的扩散模型，在我们以前的工作。外推的模拟数据的摩擦系数为氨基酸的现实值表明，逃逸时间的球状蛋白质是在亚毫秒尺度。有人认为，这个时间尺度是足够短的核糖体的顺利运作，不允许新生蛋白质堵塞核糖体隧道。
英文摘要：
We study the post-translational escape of nascent proteins at the ribosomal exit tunnel with the consideration of a real shape atomistic tunnel based on the Protein Data Bank (PDB) structure of the large ribosome subunit of archeon Haloarcula marismortui. Molecular dynamics simulations employing the Go-like model for the proteins show that at intermediate and high temperatures, including a presumable physiological temperature, the protein escape process at the atomistic tunnel is quantitatively similar to that at a cylinder tunnel of length L = 72 Å and diameter d = 16 Å. At low temperatures, the atomistic tunnel, however, yields an increased probability of protein trapping inside the tunnel while the cylinder tunnel does not cause the trapping. All-$β$ proteins tend to escape faster than all-$α$ proteins but this difference is blurred on increasing the protein's chain length. A 29-residue zinc-finger domain is shown to be severely trapped inside the tunnel. Most of the single-domain proteins considered, however, can escape efficiently at the physiological temperature with the escape time distribution following the diffusion model proposed in our previous works. An extrapolation of the simulation data to a realistic value of the friction coefficient for amino acids indicates that the escape times of globular proteins are at the sub-millisecond scale. It is argued that this time scale is short enough for the smooth functioning of the ribosome by not allowing nascent proteins to jam the ribosome tunnel.
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