Nguyen Kien, Whitford Paul C
Department of Physics, Northeastern University , Dana Research Center 123, 360 Huntington Avenue, Boston, Massachusetts 02115, United States.
J Phys Chem B. 2016 Sep 1;120(34):8768-75. doi: 10.1021/acs.jpcb.6b04476. Epub 2016 Aug 12.
In order to quantitatively describe the energetics of biomolecular rearrangements, it is necessary to identify reaction coordinates that accurately capture the relevant transition events. Here, we perform simulations of A-site tRNA movement (∼20 Å) during hybrid-state formation in the ribosome and quantify the ability of interatomic distances to capture the transition state ensemble. Numerous coordinates are found to be accurate indicators of the transition state, allowing tRNA rearrangements to be described as diffusion across a one-dimensional free-energy surface. In addition to providing insights into the physical-chemical relationship between biomolecular structure and dynamics, these results can help enable single-molecule techniques to probe the free-energy landscape of the ribosome.
为了定量描述生物分子重排的能量学，有必要确定能够准确捕捉相关转变事件的反应坐标。在此，我们对核糖体杂交态形成过程中A位点tRNA的移动（约20 Å）进行了模拟，并量化了原子间距离捕捉过渡态系综的能力。发现许多坐标都是过渡态的准确指标，这使得tRNA重排可被描述为在一维自由能表面上的扩散。除了深入了解生物分子结构与动力学之间的物理化学关系外，这些结果还有助于使单分子技术能够探测核糖体的自由能景观。
