分子机器的计算研究：核糖体。
Computational studies of molecular machines: the ribosome.
机构信息
Los Alamos National Laboratory, United States.
出版信息
Curr Opin Struct Biol. 2012 Apr;22(2):168-74. doi: 10.1016/j.sbi.2012.01.008. Epub 2012 Feb 13.
Abstract
The past decade has produced an avalanche of experimental data on the structure and dynamics of the ribosome. Groundbreaking studies in structural biology and kinetics have placed important constraints on ribosome structural dynamics. However, a gulf remains between static structures and time dependent data. In particular, X-ray crystallography and cryo-EM studies produce static models of the ribosome in various states, but lack dynamic information. Single molecule studies produce information on the rates of transitions between these states but do not have high-resolution spatial information. Computational studies have aided in bridging this gap by providing atomic resolution simulations of structural fluctuations and transitions between configurations.
摘要
过去十年产生了大量关于核糖体结构和动力学的实验数据。结构生物学和动力学的开创性研究对核糖体结构动力学施加了重要的限制。然而，静态结构和时变数据之间仍然存在差距。特别是，X 射线晶体学和低温电子显微镜研究产生了核糖体在各种状态下的静态模型，但缺乏动态信息。单分子研究提供了这些状态之间跃迁速率的信息，但没有高分辨率的空间信息。计算研究通过提供结构波动和构型之间转换的原子分辨率模拟，有助于弥合这一差距。
相似文献
1
Computational studies of molecular machines: the ribosome.分子机器的计算研究：核糖体。
Curr Opin Struct Biol. 2012 Apr;22(2):168-74. doi: 10.1016/j.sbi.2012.01.008. Epub 2012 Feb 13.
2
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.核糖体动力学：基于原子结构建模对冷冻电子显微镜图谱的见解
Annu Rev Biophys Biomol Struct. 2006;35:299-317. doi: 10.1146/annurev.biophys.35.040405.101950.
3
Ribosomes and cryo-EM: a duet.核糖体与冷冻电镜：一场二重奏。
Curr Opin Struct Biol. 2018 Oct;52:1-7. doi: 10.1016/j.sbi.2018.07.001. Epub 2018 Jul 14.
4
Molecular simulations of the ribosome and associated translation factors.核糖体及相关翻译因子的分子模拟。
Curr Opin Struct Biol. 2018 Apr;49:27-35. doi: 10.1016/j.sbi.2017.11.003. Epub 2017 Dec 1.
5
Structure of the E. coli ribosome-EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM.大肠杆菌核糖体-EF-Tu 复合物的结构通过 Cs 校正的 cryo-EM 解析至 <3Å 分辨率。
Nature. 2015 Apr 23;520(7548):567-70. doi: 10.1038/nature14275. Epub 2015 Feb 23.
6
Ribosomal dynamics explored by cryo-electron microscopy.通过冷冻电子显微镜探索核糖体动力学。
Methods. 2001 Nov;25(3):309-15. doi: 10.1006/meth.2001.1243.
7
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.Cryo-EM 结构和 rRNA 模型：5.5-A 分辨率下的翻译真核 80S 核糖体。
Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):19748-53. doi: 10.1073/pnas.1009999107. Epub 2010 Oct 27.
8
The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly.冷冻电子显微镜技术的近期改进对细菌核糖体组装理解的影响。
Nucleic Acids Res. 2017 Feb 17;45(3):1027-1040. doi: 10.1093/nar/gkw1231.
9
Molding atomic structures into intermediate-resolution cryo-EM density maps of ribosomal complexes using real-space refinement.利用实空间精修将原子结构塑造为核糖体复合物的中等分辨率冷冻电镜密度图。
Structure. 2005 Mar;13(3):401-6. doi: 10.1016/j.str.2005.01.004.
10
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy.通过正常模式分析和冷冻电子显微镜探索功能活跃核糖体的动态重组。
Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9319-23. doi: 10.1073/pnas.1632476100. Epub 2003 Jul 23.
引用本文的文献
1
Discovery of effectors for casein kinase signaling in the African trypanosome.非洲锥虫中酪蛋白激酶信号传导效应物的发现
Sci Rep. 2025 Jul 2;15(1):23284. doi: 10.1038/s41598-025-05668-9.
2
Mechanism for the Unfolding of the TOP7 Protein in Steered Molecular Dynamics Simulations as Revealed by Mutual Information Analysis.通过互信息分析揭示的在定向分子动力学模拟中TOP7蛋白展开的机制
Front Mol Biosci. 2021 Sep 30;8:696609. doi: 10.3389/fmolb.2021.696609. eCollection 2021.
3
Getting to the bottom of lncRNA mechanism: structure-function relationships.深入探究长链非编码 RNA 的机制：结构-功能关系。
Mamm Genome. 2022 Jun;33(2):343-353. doi: 10.1007/s00335-021-09924-x. Epub 2021 Oct 12.
4
Arginine Methylation Regulates Ribosome CAR Function.精氨酸甲基化调控核糖体 CAR 功能。
Int J Mol Sci. 2021 Jan 29;22(3):1335. doi: 10.3390/ijms22031335.
5
Modeling to Understand Plant Protein Structure-Function Relationships-Implications for Seed Storage Proteins.建模以理解植物蛋白结构-功能关系-对种子贮藏蛋白的影响。
Molecules. 2020 Feb 17;25(4):873. doi: 10.3390/molecules25040873.
6
New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.老方法新应用：通过对非键相互作用进行特定对校正来提高生物分子力场的准确性。
Phys Chem Chem Phys. 2018 Mar 28;20(13):8432-8449. doi: 10.1039/C7CP08185E.
7
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.分子模拟捕捉到的 RNA 结构动力学：全面概述。
Chem Rev. 2018 Apr 25;118(8):4177-4338. doi: 10.1021/acs.chemrev.7b00427. Epub 2018 Jan 3.
8
Solution structure of an ultra-stable single-chain insulin analog connects protein dynamics to a novel mechanism of receptor binding.超稳定单链胰岛素类似物的溶液结构将蛋白质动力学与受体结合的新机制联系起来。
J Biol Chem. 2018 Jan 5;293(1):69-88. doi: 10.1074/jbc.M117.808667. Epub 2017 Nov 7.
9
Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position.核糖体在中间密码子位置对严格核苷酸的识别。
Molecules. 2017 Aug 29;22(9):1427. doi: 10.3390/molecules22091427.
10
The ribosome's energy landscape: Recent insights from computation.核糖体的能量景观：计算领域的最新见解
Biophys Rev. 2015 Sep;7(3):301-310. doi: 10.1007/s12551-014-0155-1. Epub 2015 Jan 18.
本文引用的文献
1
The structure of the eukaryotic ribosome at 3.0 Å resolution.真核生物核糖体的 3.0 Å 分辨率结构。
Science. 2011 Dec 16;334(6062):1524-9. doi: 10.1126/science.1212642. Epub 2011 Nov 17.
2
Excited states of ribosome translocation revealed through integrative molecular modeling.核糖体易位的激发态通过综合分子建模揭示。
Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):18943-8. doi: 10.1073/pnas.1108363108. Epub 2011 Nov 11.
3
Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.灵活拟合方法的共识提高了低温电镜数据的解释。
J Struct Biol. 2012 Feb;177(2):561-70. doi: 10.1016/j.jsb.2011.10.002. Epub 2011 Oct 13.
4
Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.大肠杆菌 70S 核糖体中关键的分子间相互作用通过粗粒化分析揭示。
J Am Chem Soc. 2011 Oct 26;133(42):16828-38. doi: 10.1021/ja2028487. Epub 2011 Oct 3.
5
Stochastic theory of protein synthesis and polysome: ribosome profile on a single mRNA transcript.蛋白质合成和多核糖体的随机理论：单个 mRNA 转录本上的核糖体谱。
J Theor Biol. 2011 Nov 21;289:36-46. doi: 10.1016/j.jtbi.2011.08.023. Epub 2011 Aug 26.
6
The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome.23S rRNA 中 89 号螺旋结构对于大肠杆菌核糖体的肽基转移酶功能很重要。
FEBS Lett. 2011 Oct 3;585(19):3073-8. doi: 10.1016/j.febslet.2011.08.030. Epub 2011 Aug 27.
7
Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.利用冷冻电镜和X射线数据模拟对转运RNA运动范围的检测
J Biophys. 2011;2011:219515. doi: 10.1155/2011/219515. Epub 2011 Mar 28.
8
Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome.将结构信息转化为核糖体对延伸因子 Tu 激活的变构能量图。
Proc Natl Acad Sci U S A. 2011 Jun 14;108(24):9827-32. doi: 10.1073/pnas.1105714108. Epub 2011 May 26.
9
Structures of the bacterial ribosome in classical and hybrid states of tRNA binding.细菌核糖体在 tRNA 结合的经典状态和混合状态下的结构。
Science. 2011 May 20;332(6032):981-4. doi: 10.1126/science.1202692.
10
Mutations of highly conserved bases in the peptidyltransferase center induce compensatory rearrangements in yeast ribosomes.高度保守的肽基转移酶中心碱基的突变诱导酵母核糖体的补偿性重排。
RNA. 2011 May;17(5):855-64. doi: 10.1261/rna.2593211. Epub 2011 Mar 25.
Zotero 插件