通过粗糙脉孢菌VS核酶的亲吻相互作用进行的分子内二级结构重排。
Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme.
作者信息
Andersen A A, Collins R A
机构信息
Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8.
出版信息
Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7730-5. doi: 10.1073/pnas.141039198. Epub 2001 Jun 26.
Abstract
Kissing interactions in RNA are formed when bases between two hairpin loops pair. Intra- and intermolecular kissing interactions are important in forming the tertiary or quaternary structure of many RNAs. Self-cleavage of the wild-type Varkud satellite (VS) ribozyme requires a kissing interaction between the hairpin loops of stem-loops I and V. In addition, self-cleavage requires a rearrangement of several base pairs at the base of stem I. We show that the kissing interaction is necessary for the secondary structure rearrangement of wild-type stem-loop I. Surprisingly, isolated stem-loop V in the absence of the rest of the ribozyme is sufficient to rearrange the secondary structure of isolated stem-loop I. In contrast to kissing interactions in other RNAs that are either confined to the loops or culminate in an extended intermolecular duplex, the VS kissing interaction causes changes in intramolecular base pairs within the target stem-loop.
摘要
当两个发夹环之间的碱基配对时，RNA中会形成“亲吻”相互作用。分子内和分子间的“亲吻”相互作用对于许多RNA三级或四级结构的形成很重要。野生型瓦尔库德卫星（VS）核酶的自我切割需要茎环I和V的发夹环之间的“亲吻”相互作用。此外，自我切割需要茎I底部几个碱基对的重排。我们表明，“亲吻”相互作用对于野生型茎环I的二级结构重排是必要的。令人惊讶的是，在没有核酶其余部分的情况下，分离的茎环V足以重排分离的茎环I的二级结构。与其他RNA中的“亲吻”相互作用不同，其他RNA中的“亲吻”相互作用要么局限于环中，要么以延伸的分子间双链体告终，而VS“亲吻”相互作用会导致目标茎环内分子内碱基对的变化。
相似文献
1
Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme.通过粗糙脉孢菌VS核酶的亲吻相互作用进行的分子内二级结构重排。
Proc Natl Acad Sci U S A. 2001 Jul 3;98(14):7730-5. doi: 10.1073/pnas.141039198. Epub 2001 Jun 26.
2
Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme.粗糙脉孢菌Varkud卫星核酶中溶剂不可及核心的快速形成。
EMBO J. 2001 Oct 1;20(19):5461-9. doi: 10.1093/emboj/20.19.5461.
3
NMR structure of varkud satellite ribozyme stem-loop V in the presence of magnesium ions and localization of metal-binding sites.镁离子存在下varKud卫星核酶茎环V的核磁共振结构及金属结合位点的定位
Biochemistry. 2006 Sep 5;45(35):10591-605. doi: 10.1021/bi0607150.
4
A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme.一种极其稳定的吻式环相互作用决定了粗糙脉孢菌瓦尔库德卫星核酶对底物的识别。
RNA. 2014 Sep;20(9):1451-64. doi: 10.1261/rna.046144.114. Epub 2014 Jul 22.
5
Nuclear magnetic resonance structure of the Varkud satellite ribozyme stem-loop V RNA and magnesium-ion binding from chemical-shift mapping.Varkud卫星核酶茎环V RNA的核磁共振结构及基于化学位移图谱的镁离子结合
Biochemistry. 2005 Mar 22;44(11):4157-70. doi: 10.1021/bi047963l.
6
Rearrangement of substrate secondary structure facilitates binding to the Neurospora VS ribozyme.底物二级结构的重排有助于与粗糙脉孢菌VS核酶结合。
J Mol Biol. 2002 Dec 13;324(5):903-15. doi: 10.1016/s0022-2836(02)01151-8.
7
Identification of functional domains in the self-cleaving Neurospora VS ribozyme using damage selection.利用损伤筛选鉴定自我切割的粗糙脉孢菌VS核酶中的功能结构域。
J Mol Biol. 1997 Apr 11;267(4):830-40. doi: 10.1006/jmbi.1997.0921.
8
A long-range pseudoknot is required for activity of the Neurospora VS ribozyme.粗糙脉孢菌VS核酶的活性需要一个远距离假结。
EMBO J. 1996 Jun 3;15(11):2820-5.
9
Effects of cobalt hexammine on folding and self-cleavage of the Neurospora VS ribozyme.六氨合钴对粗糙脉孢菌VS核酶折叠和自我切割的影响。
J Mol Biol. 2001 May 25;309(1):45-56. doi: 10.1006/jmbi.2001.4625.
10
Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme.外周环环相互作用在Neurospora VS 核酶中的其他作用。
Nucleic Acids Res. 2011 Aug;39(14):6223-8. doi: 10.1093/nar/gkr250. Epub 2011 Apr 20.
引用本文的文献
1
Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches.通过钴胺素核糖开关的效应子依赖性构象转换调控基因表达。
J Mol Biol. 2022 Sep 30;434(18):167585. doi: 10.1016/j.jmb.2022.167585. Epub 2022 Apr 12.
2
Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway.RNA 亲吻复合物在盐溶液中的结构折叠：预测 3D 结构、稳定性和折叠途径。
RNA. 2019 Nov;25(11):1532-1548. doi: 10.1261/rna.071662.119. Epub 2019 Aug 7.
3
Mg Binding Promotes SLV as a Scaffold in Varkud Satellite Ribozyme SLI-SLV Kissing Loop Junction.镁结合促进瓦库德卫星核酶SLI-SLV接吻环连接处的SLV作为支架。
Biophys J. 2017 Jul 25;113(2):313-320. doi: 10.1016/j.bpj.2017.06.008. Epub 2017 Jun 29.
4
Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme.Varkud 卫星核酶中底物螺旋重塑和切割环激活的结构基础。
J Am Chem Soc. 2017 Jul 19;139(28):9591-9597. doi: 10.1021/jacs.7b03655. Epub 2017 Jul 3.
5
Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme.从近期对粗糙脉孢菌Varkud卫星核酶的核磁共振和X射线研究中洞察RNA的结构与动力学。
Wiley Interdiscip Rev RNA. 2017 Sep;8(5). doi: 10.1002/wrna.1421. Epub 2017 Apr 6.
6
Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions.对粗糙脉孢菌VS核酶进行合理改造，使其能够通过不同的吻式环相互作用实现底物识别。
Nucleic Acids Res. 2016 Aug 19;44(14):6924-34. doi: 10.1093/nar/gkw401. Epub 2016 May 10.
7
Chemistry and Biology of Self-Cleaving Ribozymes.自我切割核酶的化学与生物学
Trends Biochem Sci. 2015 Nov;40(11):648-661. doi: 10.1016/j.tibs.2015.09.001. Epub 2015 Oct 15.
8
Crystal structure of the Varkud satellite ribozyme.瓦库德卫星核酶的晶体结构。
Nat Chem Biol. 2015 Nov;11(11):840-6. doi: 10.1038/nchembio.1929. Epub 2015 Sep 28.
9
MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery.转运RNA及氨酰转运RNA合成酶的分子动力学模拟：动力学、折叠、结合与变构
Int J Mol Sci. 2015 Jul 13;16(7):15872-902. doi: 10.3390/ijms160715872.
10
The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure.来自粗糙脉孢菌VS核酶的II-III-VI三向连接的核磁共振结构揭示了一种关键的三级相互作用，并为整体核酶结构提供了新的见解。
RNA. 2015 Sep;21(9):1621-32. doi: 10.1261/rna.052076.115. Epub 2015 Jun 29.
本文引用的文献
1
Structure of the ribozyme substrate hairpin of Neurospora VS RNA: a close look at the cleavage site.粗糙脉孢菌VS RNA核酶底物发夹结构：对切割位点的仔细观察。
RNA. 2000 Dec;6(12):1821-32. doi: 10.1017/s1355838200001394.
2
Progression of a loop-loop complex to a four-way junction is crucial for the activity of a regulatory antisense RNA.环-环复合物向四链体连接的转变对于一种调控性反义RNA的活性至关重要。
EMBO J. 2000 Nov 1;19(21):5905-15. doi: 10.1093/emboj/19.21.5905.
3
Switching on and off with RNA.通过RNA进行开启和关闭。
Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9824-6. doi: 10.1073/pnas.97.18.9824.
4
A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures.一种作为大肠杆菌控制开关的反式作用RNA：DsrA通过形成可变结构来调节功能。
Proc Natl Acad Sci U S A. 2000 Aug 29;97(18):9919-24. doi: 10.1073/pnas.170281497.
5
A retroviral RNA kissing complex containing only two G.C base pairs.一种仅包含两个G.C碱基对的逆转录病毒RNA接吻复合体。
Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9396-401. doi: 10.1073/pnas.170283697.
6
Rearrangement of a stable RNA secondary structure during VS ribozyme catalysis.VS 核酶催化过程中稳定 RNA 二级结构的重排。
Mol Cell. 2000 Mar;5(3):469-78. doi: 10.1016/s1097-2765(00)80441-4.
7
An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment.由反义靶RNA结合形成的一种异常结构涉及一个具有四向连接和并排螺旋排列的延伸亲吻复合体。
RNA. 2000 Mar;6(3):311-24. doi: 10.1017/s135583820099215x.
8
Fast folding of a ribozyme by stabilizing core interactions: evidence for multiple folding pathways in RNA.通过稳定核心相互作用实现核酶的快速折叠：RNA中多种折叠途径的证据。
J Mol Biol. 2000 Feb 11;296(1):133-44. doi: 10.1006/jmbi.1999.3439.
9
Structural analysis of late intermediate complex formed between plasmid ColIb-P9 Inc RNA and its target RNA. How does a single antisense RNA repress translation of two genes at different rates?质粒ColIb-P9 Inc RNA与其靶RNA形成的晚期中间体复合物的结构分析。单个反义RNA如何以不同速率抑制两个基因的翻译？
J Biol Chem. 2000 Jan 14;275(2):1269-74. doi: 10.1074/jbc.275.2.1269.
10
NMR structure of the mature dimer initiation complex of HIV-1 genomic RNA.HIV-1基因组RNA成熟二聚体起始复合物的核磁共振结构
FEBS Lett. 1999 Sep 24;458(3):387-92. doi: 10.1016/s0014-5793(99)01183-7.
Zotero 插件