Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis

Mechanical forces acting on the ribosome can alter the speed of protein synthesis, indicating that mechanochemistry can contribute to translation control of gene expression. The naturally occurring sources of these mechanical forces, the mechanism by which they are transmitted 10 nm to the ribosome’s catalytic core, and how they influence peptide bond formation rates are largely unknown. Here, we identify a new source of mechanical force acting on the ribosome by using in situ experimental measurements of changes in nascent-chain extension in the exit tunnel in conjunction with all-atom and coarse-grained computer simulations. We demonstrate that when the number of residues composing a nascent chain increases, its unstructured segments outside the ribosome exit tunnel generate piconewtons of force that are fully transmitted to the ribosome’s P-site. The route of force transmission is shown to be through the nascent polypetide’s backbone, not through the wall of the ribosome’s exit tunnel. Utilizing quantum mechanical calculations we find that a consequence of such a pulling force is to decrease the transition state free energy barrier to peptide bond formation, indicating that the elongation of a nascent chain can accelerate translation. Since nascent protein segments can start out as largely unfolded structural ensembles, these results suggest a pulling force is present during protein synthesis that can modulate translation speed. The mechanism of force transmission we have identified and its consequences for peptide bond formation should be relevant regardless of the source of the pulling force.

作用于核糖体（ribosome）的机械力可改变蛋白质合成速率，这表明机械化学过程可参与基因表达的翻译调控。目前，这类机械力的天然来源、其传递至核糖体催化核心的10纳米尺度机制，以及它们对肽键形成速率的影响方式，仍未明确。本研究通过结合核糖体出口隧道内新生肽链延伸变化的原位实验测量与全原子、粗粒化计算机模拟，鉴定出一种作用于核糖体的新型机械力来源。我们证实，当新生肽链的残基数目增加时，其位于核糖体出口隧道外的无结构区段会产生皮牛（piconewtons）量级的力，且该力可完全传递至核糖体的P位点（P-site）。力的传递路径被证实为通过新生多肽的主链，而非核糖体出口隧道的管壁。通过量子力学计算，我们发现这类拉力的一个效应是降低肽键形成的过渡态自由能垒，这表明新生肽链的延伸可加速翻译过程。由于新生蛋白质区段初始多为高度解折叠的结构系综，本研究结果暗示蛋白质合成过程中存在可调控翻译速率的拉力。无论拉力来源如何，我们所鉴定的力传递机制及其对肽键形成的影响均具有普适相关性。