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首页> 外文期刊>Journal of Molecular Biology >Molecular Interactions and Residues Involved in Force Generation in the T4 Viral DNA Packaging Motor
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Molecular Interactions and Residues Involved in Force Generation in the T4 Viral DNA Packaging Motor

机译：T4病毒DNA包装电动机中涉及力产生的分子相互作用和残留物

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摘要

Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. (C) 2014 Elsevier Ltd. All rights reserved.
机译：许多病毒利用分子电机将其基因组封装成预成型的衣壳。这些电机的引人注目是它们能够产生大力以驱动抵抗DNA限制的熵，静电和弯曲力的DNA易位。基于最近解析的噬菌体T4电机蛋白GP17的模型表明该电动机通过从延伸到紧凑状态的构象变化而产生大力。提出这种转变，以通过在GP17的N-和C末端域之间的界面之间的互补的残留物之间的静电相互作用驱动。在这里，我们使用原子分子动力学模拟来详细研究这种压实GP17的分子相互作用和残留物。我们发现，尽管带电残余物之间的静电相互作用对压实的总体自由能量变化有显着贡献，但不带电残留物介导的相互作用如果不是更重要的话。我们在界面中识别五个带电的残基和六个不带电残留物，在压实过渡中发挥着主导作用，并且还揭示由这些残基介导的盐桥，范德华和溶剂氢键相互作用稳定稳定的GP17的紧凑型形式。发现Glu309和Arg494之间的盐桥的形成特别至关重要，与在Glu309lys突变的包装中的完全消除的实验一致。还发现若干其他残基的计算贡献与由地点导向突变引起的DNA易位活动中的单分子测量良好。 （c）2014年elestvier有限公司保留所有权利。

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