病毒包装马达对 DNA 的压缩作用：对停滞在衣壳-门复合结构上的 Y 型 DNA 底物的压缩。
DNA crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y-DNA substrate.
机构信息
Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, USA.
出版信息
Virology. 2010 Mar 15;398(2):224-32. doi: 10.1016/j.virol.2009.11.047. Epub 2010 Jan 12.
Abstract
Many large double-stranded DNA viruses employ high force-generating ATP-driven molecular motors to package to high density their genomes into empty procapsids. Bacteriophage T4 DNA translocation is driven by a two-component motor consisting of the procapsid portal docked with a packaging terminase-ATPase. Fluorescence resonance energy transfer and fluorescence correlation spectroscopic (FRET-FCS) studies of a branched (Y-junction) DNA substrate with a procapsid-anchoring leader segment and a single dye molecule situated at the junction point reveal that the "Y-DNA" stalls in proximity to the procapsid portal fused to GFP. Comparable structure Y-DNA substrates containing energy transfer dye pairs in the Y-stem separated by 10 or 14 base pairs reveal that B-form DNA is locally compressed 22-24% by the linear force of the packaging motor. Torsional compression of duplex DNA is thus implicated in the mechanism of DNA translocation.
摘要
许多大型双链 DNA 病毒利用高产生力的 ATP 驱动的分子马达，将其基因组高度浓缩到空的原衣壳中。噬菌体 T4 DNA 转位由一个由两个组件组成的马达驱动，该马达由一个与包装终止酶-ATP 酶对接的原衣壳门组成。带有原衣壳附着的引导片段和一个位于连接点的单个染料分子的分支（Y 型接头）DNA 底物的荧光共振能量转移和荧光相关光谱（FRET-FCS）研究表明，“Y-DNA”在靠近融合到 GFP 的原衣壳门的位置停止。类似的结构 Y-DNA 底物在 Y 干中包含能量转移染料对，它们之间相隔 10 或 14 个碱基对，这表明包装马达的线性力使 B 型 DNA 在局部被压缩 22-24%。因此，双链 DNA 的扭转压缩被牵连到 DNA 转位的机制中。
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本文引用的文献
1
Portal control of viral prohead expansion and DNA packaging.病毒原头部扩张和DNA包装的门户控制。
Virology. 2009 Aug 15;391(1):44-50. doi: 10.1016/j.virol.2009.05.029. Epub 2009 Jun 21.
2
Intersubunit coordination in a homomeric ring ATPase.同聚体环状ATP酶中的亚基间协同作用。
Nature. 2009 Jan 22;457(7228):446-50. doi: 10.1038/nature07637. Epub 2009 Jan 7.
3
The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces.噬菌体T4 DNA包装马达的结构提示了一种依赖静电力的机制。
Cell. 2008 Dec 26;135(7):1251-62. doi: 10.1016/j.cell.2008.11.015.
4
Modulation of the packaging reaction of bacteriophage t4 terminase by DNA structure.DNA结构对噬菌体T4端粒酶包装反应的调控
J Mol Biol. 2008 Aug 1;381(1):61-72. doi: 10.1016/j.jmb.2008.05.074. Epub 2008 Jun 5.
5
Single phage T4 DNA packaging motors exhibit large force generation, high velocity, and dynamic variability.单个噬菌体T4 DNA包装马达表现出强大的力产生、高速度和动态变异性。
Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16868-73. doi: 10.1073/pnas.0704008104. Epub 2007 Oct 17.
6
Viral DNA packaging studied by fluorescence correlation spectroscopy.通过荧光相关光谱法研究病毒DNA包装
Biophys J. 2007 Aug 15;93(4):L17-9. doi: 10.1529/biophysj.107.111526. Epub 2007 Jun 8.
7
Structural rearrangements between portal protein subunits are essential for viral DNA translocation.门蛋白亚基之间的结构重排对于病毒DNA转位至关重要。
J Biol Chem. 2007 Jun 29;282(26):18907-13. doi: 10.1074/jbc.M701808200. Epub 2007 Apr 18.
8
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EMBO J. 2007 Apr 4;26(7):1984-94. doi: 10.1038/sj.emboj.7601643. Epub 2007 Mar 15.
9
Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids.在将DNA包装到噬菌体phi29衣壳过程中连接器旋转的实验测试。
PLoS Biol. 2007 Mar;5(3):e59. doi: 10.1371/journal.pbio.0050059.
10
Selective labeling of proteins by using protein farnesyltransferase.利用蛋白质法尼基转移酶对蛋白质进行选择性标记。
Chembiochem. 2007 Jan 2;8(1):98-105. doi: 10.1002/cbic.200600340.
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