短暂的离子介导相互作用调节了真核细胞核糖体中的子单元旋转.
George Wanes1,2, Udayan Mohanty3, Paul Whitford1,2
1Center for Theoretical Biological Physics, Northeastern University, Boston.
bioRxiv : the preprint server for biology
|August 20, 2025
概括
这项研究揭示了离子如何调节RNA折叠和核糖体功能. 过渡性离子相互作用,特别是,通过改变能量格局和动力学来控制大规模的核糖体运动.
科学领域:
- 计算生物学 计算生物学
- 生物物理学的生物物理.
- 分子生物物理学 分子生物物理学
背景情况:
- 离子对于RNA折叠至关重要,但它们在动态构造变化中的作用尚不清楚.
- 了解离子介导相互作用是解读RNA的功能机制的关键.
研究的目的:
- 开发一个理论模型,以全原子分辨率模拟离子-RNA相互作用.
- 研究离子对RNA形状重组和生物过程的影响.
主要方法:
- 开发了一个结合明确静电和离子 (K+,Cl-,Mg2+) 的理论模型.
- 使用已建立的RNA系统 (58-mer和Ade riboswitch) 验证了模型.
- 应用该模型模拟酵母核糖体并分析依赖离子的能量景观.
主要成果:
- 该模型准确地捕捉了依赖度的离子环境和离子类型 (化,化).
- 模拟显示,化物 ([MgCl2]) 的毫米级变化会影响核糖体间子单元旋转的能量.
- 离子度的变化改变了旋转状态的分布和动力学超过一个数量级.
结论:
- 短暂的离子介导相互作用,包括内和外,直接调节核糖体子单元的旋转.
- 这为离子如何调节像蛋白质合成这样的大规模生物过程提供了物理基础.
- 这些发现强调了离子环境在RNA动态和功能中的关键作用.
相关概念视频
Cotranslational Protein Translocation
7.5K
Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
7.5K
Ribosomal RNA Synthesis
13.4K
Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
13.4K
Improving Translational Accuracy
11.8K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
11.8K
Ribosomes
8.1K
Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
8.1K
Termination of Translation
25.7K
The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
25.7K
Post-translational Translocation of Proteins to the RER
5.9K
A sizable fraction of proteins destined for ER are first synthesized in the cell cytosol and then transported across the ER membrane–a process called post-translational translocation. Similar to cotranslationally translocated proteins, these proteins also use the Sec translocon complex to enter the ER lumen.
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...
Targeting proteins to the ER
Hsp40 and Hsp70 chaperone molecules bind the translated proteins in the cytosol to prevent their folding. The chaperone binding helps to keep the signal...
5.9K


