Sapkota Divya, Sanbonmatsu Karissa Y, Girodat Dylan
Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA.
Cellular and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA.
Nat Commun. 2025 Sep 2;16(1):8202. doi: 10.1038/s41467-025-63617-6.
Rigorous studies have characterized the aa-tRNA selection mechanism in bacteria, which is essential for maintaining translational fidelity. Recent investigations have identified critical distinctions in humans, such as the requirement of subunit rolling and a tenfold slower proofreading step. Although these studies captured key intermediates involved in tRNA selection, they did not elucidate the transitions of aa-tRNA between intermediates. Through diverse structure-based simulations, we simulated 1856 aa-tRNA accommodation events into the human ribosomal A site. Here we show the requirement for a distinct ~30° pivoting of aa-tRNA about the anticodon stem within the accommodation corridor. This pivoting is crucial for navigating the crowded accommodation corridor, which becomes more constrained due to subunit rolling. Subunit rolling-dependent4 crowding increases the steric contributions of the accommodation corridor during aa-tRNA accommodation, consistent with the tenfold reduction in the rate of proofreading. Furthermore, we show that eEF1A interacts with the accommodating aa-tRNA through conserved basic residues, limiting premature aa-tRNA dissociation from the A site. These findings provide a structural description of the human aa-tRNA selection process and demonstrate that the aa-tRNA alignment relative to the ribosomal catalytic sites is a critical determinant of translational fidelity.
严谨的研究已对细菌中氨酰 - tRNA选择机制进行了表征，这对于维持翻译保真度至关重要。最近的研究发现了人类中的关键差异，例如亚基滚动的需求以及校对步骤慢十倍。尽管这些研究捕获了参与tRNA选择的关键中间体，但它们并未阐明氨酰 - tRNA在中间体之间的转变。通过各种基于结构的模拟，我们模拟了1856次氨酰 - tRNA进入人核糖体A位点的容纳事件。在这里，我们展示了氨酰 - tRNA在容纳通道内围绕反密码子茎进行约30°独特枢转的需求。这种枢转对于在拥挤的容纳通道中导航至关重要，由于亚基滚动，该通道变得更加受限。亚基滚动依赖性拥挤在氨酰 - tRNA容纳期间增加了容纳通道的空间贡献，这与校对速率降低十倍一致。此外，我们表明eEF1A通过保守的碱性残基与容纳中的氨酰 - tRNA相互作用，限制了氨酰 - tRNA从A位点过早解离。这些发现提供了人类氨酰 - tRNA选择过程的结构描述，并证明氨酰 - tRNA相对于核糖体催化位点的排列是翻译保真度的关键决定因素。
