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Ribosome exit tunnel electrostatics
bioRxiv - Biophysics Pub Date : 2020-10-21 , DOI: 10.1101/2020.10.20.346684
Marc Joiret , Francesca Rapino , Pierre Close , Liesbet Geris

The impact of the ribosome exit tunnel electrostatics on the protein elongation rate or on the forces acting upon the nascent polypeptide chain are currently not fully elucidated. In the past, researchers have measured the electrostatic potential inside the ribosome polypeptide exit tunnel at a limited number of spatial points, at least in prokaryotes. Here, we present a basic electrostatic model of the exit tunnel of the ribosome, providing a quantitative physical description of the tunnel interaction with the nascent proteins at all centro-axial points inside the tunnel. We show how the tunnel geometry causes a positive potential difference between the tunnel exit and entry points which impedes positively charged amino acid residues from progressing through the tunnel, affecting the elongation rate in a range of minus 40% to plus 85% when compared to the average elongation rate. The time spent by the ribosome to decode the genetic encrypted message is constrained accordingly. We quantitatively derived, at single residue resolution, the axial forces acting on the nascent peptide from its particular sequence embedded in the tunnel. The model sheds light on how the experimental data point measurements of the potential are linked to the local structural chemistry of the inner wall and the shape and size of the tunnel. The model consistently connects experimental observations coming from different fields in molecular biology, structural and physical chemistry, biomechanics, synthetic and multi-omics biology. Our model should be a valuable tool to gain insight into protein synthesis dynamics, translational control and into the role of the ribosome's mechanochemistry in the co-translational protein folding.

中文翻译:

核糖体出口隧道静电

目前尚未完全阐明核糖体出口隧道静电对蛋白质伸长率或作用在新生多肽链上的作用力的影响。过去,研究人员至少在原核生物中,在有限数量的空间点上测量了核糖体多肽出口通道内部的静电势。在这里,我们介绍了核糖体出口通道的基本静电模型,提供了在通道内所有中心轴点上通道与新生蛋白质相互作用的定量物理描述。我们展示了隧道的几何形状如何在隧道出口和入口点之间造成正电位差,从而阻止带正电荷的氨基酸残基穿过隧道前进,与平均伸长率相比,影响伸长率的范围是负40%到正85%。因此,核糖体解码遗传加密信息所花费的时间受到限制。我们以单个残基分辨率定量地从新生肽嵌入通道中的特定序列作用于新生肽的轴向力。该模型揭示了电势的实验数据点测量如何与内壁的局部结构化学以及隧道的形状和大小相关联。该模型始终将来自分子生物学,结构和物理化学,生物力学,合成和多组学生物学领域不同领域的实验观察联系起来。我们的模型应该是了解蛋白质合成动力学的有价值的工具,
更新日期:2020-10-26
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