Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic.
J Phys Chem B. 2012 Oct 25;116(42):12721-34. doi: 10.1021/jp309230v. Epub 2012 Oct 12.
Riboswitches often occur in the 5'-untranslated regions of bacterial mRNA where they regulate gene expression. The preQ(1) riboswitch controls the biosynthesis of a hypermodified nucleoside queuosine in response to binding the queuosine metabolic intermediate. Structures of the ligand-bound and ligand-free states of the preQ(1) riboswitch from Thermoanaerobacter tengcongensis were determined recently by X-ray crystallography. We used multiple, microsecond-long molecular dynamics simulations (29 μs in total) to characterize the structural dynamics of preQ(1) riboswitches in both states. We observed different stabilities of the stem in the bound and free states, resulting in different accessibilities of the ribosome-binding site. These differences are related to different stacking interactions between nucleotides of the stem and the associated loop, which itself adopts different conformations in the bound and free states. We suggest that the loop not only serves to bind preQ(1) but also transmits information about ligand binding from the ligand-binding pocket to the stem, which has implications for mRNA accessibility to the ribosome. We explain functional results obscured by a high salt crystallization medium and help to refine regions of disordered electron density, which demonstrates the predictive power of our approach. Besides investigating the functional dynamics of the riboswitch, we have also utilized this unique small folded RNA system for analysis of performance of the RNA force field on the μs time scale. The latest AMBER parmbsc0χ(OL3) RNA force field is capable of providing stable trajectories of the folded molecule on the μs time scale. On the other hand, force fields that are not properly balanced lead to significant structural perturbations on the sub-μs time scale, which could easily lead to inappropriate interpretation of the simulation data.
Riboswitches 通常出现在细菌 mRNA 的 5'非翻译区，在那里它们调节基因表达。PreQ(1) 核糖开关通过结合 queuosine 代谢中间产物来控制超修饰核苷 queuosine 的生物合成。最近通过 X 射线晶体学确定了 Thermoanaerobacter tengcongensis 中 preQ(1) 核糖开关配体结合和配体自由状态的结构。我们使用多个、微秒长的分子动力学模拟（总共 29 μs）来表征两种状态下 preQ(1) 核糖开关的结构动力学。我们观察到结合态和自由态茎的稳定性不同，导致核糖体结合位点的可及性不同。这些差异与茎和相关环中核苷酸之间不同的堆积相互作用有关，环本身在结合态和自由态中采用不同的构象。我们认为环不仅用于结合 PreQ(1)，还将配体结合的信息从配体结合口袋传递到茎，这对 mRNA 与核糖体的可及性有影响。我们解释了高盐结晶介质掩盖的功能结果，并有助于细化无序电子密度区域，这证明了我们方法的预测能力。除了研究核糖开关的功能动力学外，我们还利用这个独特的小型折叠 RNA 系统分析了 RNA 力场在 μs 时间尺度上的性能。最新的 AMBER parmbsc0χ(OL3) RNA 力场能够在 μs 时间尺度上提供折叠分子的稳定轨迹。另一方面，没有正确平衡的力场会导致亚 μs 时间尺度上的显著结构扰动，这很容易导致对模拟数据的不当解释。
