一种体外进化适配体和人工核糖开关特异性、高亲和力结合四环素的结构基础。
Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.
作者信息
Xiao Hong, Edwards Thomas E, Ferré-D'Amaré Adrian R
机构信息
Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.
出版信息
Chem Biol. 2008 Oct 20;15(10):1125-37. doi: 10.1016/j.chembiol.2008.09.004.
Abstract
The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.
摘要
四环素适配体是一种体外筛选的RNA，它以人工RNA对小分子的已知最高亲和力（解离常数Kd约为0.8 nM）与抗生素结合。它是已知的少数能够在体内调节基因表达的适配体之一。该适配体分辨率为2.2埃的共晶体结构揭示了一种假结样折叠，由一个11个核苷酸的环与不规则螺旋的小沟之间的三级相互作用形成。四环素作为镁离子螯合物结合在这个界面内。该结构与先前的生化和生物物理数据一起表明，适配体在与四环素结合的同时发生局部折叠。这种人工RNA的三螺旋连接、h形结构比大多数适配体的结构更复杂，让人联想到一些天然核糖开关的结构。
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本文引用的文献
1
Processing of X-ray diffraction data collected in oscillation mode.振荡模式下收集的X射线衍射数据的处理。
Methods Enzymol. 1997;276:307-26. doi: 10.1016/S0076-6879(97)76066-X.
2
Ribbons.丝带。
Methods Enzymol. 1997;277:493-505.
3
Methods to crystallize RNA.RNA结晶的方法。
Curr Protoc Nucleic Acid Chem. 2001 May;Chapter 7:Unit 7.6. doi: 10.1002/0471142700.nc0706s00.
4
Engineered riboswitches: overview, problems and trends.工程化核糖开关：概述、问题与趋势
RNA Biol. 2008 Jan-Mar;5(1):24-9. doi: 10.4161/rna.5.1.5955. Epub 2008 Mar 25.
5
Screening for engineered neomycin riboswitches that control translation initiation.筛选控制翻译起始的工程化新霉素核糖开关。
RNA. 2008 Jan;14(1):89-97. doi: 10.1261/rna.772408. Epub 2007 Nov 13.
6
A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.位于赖氨酸适体结构域的环-环相互作用和K-转角基序对核糖开关基因调控控制很重要。
RNA. 2007 Aug;13(8):1256-67. doi: 10.1261/rna.560307. Epub 2007 Jun 21.
7
Riboswitches: small-molecule recognition by gene regulatory RNAs.核糖开关：基因调控RNA对小分子的识别
Curr Opin Struct Biol. 2007 Jun;17(3):273-9. doi: 10.1016/j.sbi.2007.05.004. Epub 2007 Jun 15.
8
Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast.四环素适配体对酵母前体mRNA剪接的调控
Nucleic Acids Res. 2007;35(12):4179-85. doi: 10.1093/nar/gkm425. Epub 2007 Jun 12.
9
A high-throughput screen for synthetic riboswitches reveals mechanistic insights into their function.一项针对合成核糖开关的高通量筛选揭示了其功能的机制性见解。
Chem Biol. 2007 Feb;14(2):173-84. doi: 10.1016/j.chembiol.2006.12.008.
10
Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis.炭疽芽孢杆菌中串联核糖开关的配体结合和基因控制特性
RNA. 2007 Apr;13(4):573-82. doi: 10.1261/rna.407707. Epub 2007 Feb 16.
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