Nummela Jeremiah, Andricioaei Ioan
Biophys J. 2009 Feb 18;96(4):L29-31. doi: 10.1016/j.bpj.2008.12.3761.
Molecular motors involved in the packaging of DNA in tailed viruses are among the strongest known. The mechanism by which the motors operate has long been speculated to involve a coupling between rotation of the portal pore (the gate through which DNA passes upon its packaging or ejection), and translation of DNA. Recent experimental evidence rules out portal rotation with a substantial degree of certainty. We have created an atomistic model for the interaction between DNA and the portal of the bacteriophage SPP1, on the basis of cryo-electron microscopy images and of a recently solved crystal structure. A free energy surface describing the interaction is calculated using molecular dynamics simulations, and found to be inconsistent with a mechanism in which portal rotation drives DNA import. The low-energy pathways on the surface are used to advance a hypothesis on DNA import compatible with all available experiments. Additionally, temperature-dependent kinetic data are used to validate computed barriers to DNA ejection.
参与有尾病毒中DNA包装的分子马达是已知最强的分子马达之一。长期以来，人们一直推测这些马达的运作机制涉及门户孔（DNA在包装或排出时通过的通道）的旋转与DNA的平移之间的耦合。最近的实验证据在很大程度上确定地排除了门户旋转。基于冷冻电子显微镜图像和最近解析的晶体结构，我们创建了一个噬菌体SPP1的DNA与门户之间相互作用的原子模型。使用分子动力学模拟计算了描述这种相互作用的自由能表面，发现其与门户旋转驱动DNA导入的机制不一致。该表面上的低能量路径被用于提出一个与所有现有实验兼容的DNA导入假说。此外，温度依赖性动力学数据被用于验证计算出的DNA排出障碍。
